Starting phenix.real_space_refine on Tue Feb 13 11:08:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtw_24691/02_2024/7rtw_24691.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtw_24691/02_2024/7rtw_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_24691/02_2024/7rtw_24691.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtw_24691/02_2024/7rtw_24691.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtw_24691/02_2024/7rtw_24691.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtw_24691/02_2024/7rtw_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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 11 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.48, per 1000 atoms: 0.62 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: 2.53 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.46 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: 1.52 Time building geometry restraints manager: 2.72 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 - 22.99: 3224 22.99 - 45.98: 255 45.98 - 68.96: 30 68.96 - 91.95: 39 91.95 - 114.94: 23 Dihedral angle restraints: 3571 sinusoidal: 1545 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 3568 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: 2.830 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: 0.000 Extract box with map and model: 12.160 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 19.550 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.720 ------------------------------------------------------------------------------- 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 : 20.750 114.940 2255 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 88 HIS 0.008 0.001 HIS A 116 PHE 0.015 0.001 PHE A 402 TYR 0.019 0.001 TYR A 296 ARG 0.004 0.000 ARG B 117 *********************** 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 : 0.629 Fit side-chains REVERT: A 405 ILE cc_start: 0.8137 (mp) cc_final: 0.7908 (mp) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.2028 time to fit residues: 20.9865 Evaluate side-chains 60 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.617 ------------------------------------------------------------------------------- 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: 0.6858 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5759 Z= 0.197 Angle : 0.665 8.984 7863 Z= 0.313 Chirality : 0.043 0.305 982 Planarity : 0.004 0.060 963 Dihedral : 15.329 94.369 1064 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.70 % Allowed : 10.37 % Favored : 87.93 % 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 (0.34), residues: 693 helix: 2.17 (0.23), residues: 553 sheet: None (None), residues: 0 loop : -1.50 (0.52), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 11 HIS 0.002 0.001 HIS B 315 PHE 0.023 0.002 PHE A 380 TYR 0.012 0.001 TYR A 373 ARG 0.003 0.000 ARG B 345 *********************** 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 : 0.648 Fit side-chains REVERT: A 171 LEU cc_start: 0.7402 (mt) cc_final: 0.7170 (mt) REVERT: A 405 ILE cc_start: 0.8146 (mp) cc_final: 0.7897 (mt) outliers start: 10 outliers final: 6 residues processed: 72 average time/residue: 0.1710 time to fit residues: 16.5456 Evaluate side-chains 70 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 64 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 226 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 34 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 62 optimal weight: 0.0050 chunk 67 optimal weight: 10.0000 chunk 55 optimal weight: 20.0000 chunk 21 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.9400 ------------------------------------------------------------------------------- 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: 0.7036 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 5759 Z= 0.317 Angle : 0.742 10.169 7863 Z= 0.355 Chirality : 0.046 0.371 982 Planarity : 0.004 0.044 963 Dihedral : 11.974 84.433 1064 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.38 % Allowed : 15.65 % Favored : 81.97 % 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: 1.77 (0.33), residues: 693 helix: 1.90 (0.22), residues: 551 sheet: None (None), residues: 0 loop : -1.78 (0.50), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 210 HIS 0.004 0.001 HIS B 336 PHE 0.014 0.002 PHE A 380 TYR 0.013 0.002 TYR A 373 ARG 0.002 0.000 ARG B 345 *********************** 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 80 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 66 time to evaluate : 0.639 Fit side-chains outliers start: 14 outliers final: 11 residues processed: 74 average time/residue: 0.1870 time to fit residues: 18.1057 Evaluate side-chains 75 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 64 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 325 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 32 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 62 optimal weight: 0.0980 chunk 66 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 55 optimal weight: 20.0000 chunk 37 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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: 0.7008 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5759 Z= 0.234 Angle : 0.665 11.171 7863 Z= 0.314 Chirality : 0.043 0.322 982 Planarity : 0.004 0.037 963 Dihedral : 10.759 74.545 1064 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.89 % Allowed : 18.20 % Favored : 78.91 % 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: 1.95 (0.33), residues: 693 helix: 2.03 (0.22), residues: 554 sheet: None (None), residues: 0 loop : -1.85 (0.51), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 11 HIS 0.003 0.001 HIS B 336 PHE 0.017 0.002 PHE A 60 TYR 0.012 0.001 TYR A 373 ARG 0.002 0.000 ARG A 334 *********************** 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 87 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 70 time to evaluate : 0.628 Fit side-chains REVERT: B 226 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7843 (mp) outliers start: 17 outliers final: 12 residues processed: 80 average time/residue: 0.1888 time to fit residues: 19.7100 Evaluate side-chains 80 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 67 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 325 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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: 0.7063 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5759 Z= 0.289 Angle : 0.707 11.811 7863 Z= 0.337 Chirality : 0.044 0.340 982 Planarity : 0.004 0.038 963 Dihedral : 9.952 61.312 1064 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 4.25 % Allowed : 18.71 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 1.83 (0.33), residues: 693 helix: 1.93 (0.22), residues: 555 sheet: None (None), residues: 0 loop : -1.84 (0.51), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 210 HIS 0.003 0.001 HIS B 336 PHE 0.010 0.002 PHE A 380 TYR 0.014 0.001 TYR A 373 ARG 0.003 0.000 ARG A 156 *********************** 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 92 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 67 time to evaluate : 0.641 Fit side-chains REVERT: A 20 HIS cc_start: 0.4892 (OUTLIER) cc_final: 0.3809 (m90) REVERT: B 226 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7949 (mp) outliers start: 25 outliers final: 19 residues processed: 84 average time/residue: 0.1812 time to fit residues: 19.9659 Evaluate side-chains 87 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 66 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 HIS Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 116 HIS Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 374 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 39 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 30 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 38 optimal weight: 0.0270 overall best weight: 0.7238 ------------------------------------------------------------------------------- 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: 0.6981 moved from start: 0.2285 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= 0.187 Angle : 0.626 10.777 7863 Z= 0.296 Chirality : 0.040 0.290 982 Planarity : 0.003 0.033 963 Dihedral : 8.662 54.837 1064 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.74 % Allowed : 19.90 % 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: 2.15 (0.33), residues: 693 helix: 2.16 (0.22), residues: 559 sheet: None (None), residues: 0 loop : -1.87 (0.51), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 11 HIS 0.002 0.000 HIS B 315 PHE 0.018 0.001 PHE A 60 TYR 0.011 0.001 TYR A 373 ARG 0.002 0.000 ARG B 345 *********************** 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 91 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 69 time to evaluate : 0.631 Fit side-chains outliers start: 22 outliers final: 17 residues processed: 85 average time/residue: 0.1818 time to fit residues: 20.2264 Evaluate side-chains 80 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 63 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 374 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 48 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 26 optimal weight: 0.0270 chunk 39 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 13 optimal weight: 0.0970 overall best weight: 0.5836 ------------------------------------------------------------------------------- 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: 0.6945 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5759 Z= 0.177 Angle : 0.604 7.838 7863 Z= 0.288 Chirality : 0.039 0.291 982 Planarity : 0.003 0.035 963 Dihedral : 7.529 54.649 1064 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.57 % Allowed : 20.41 % Favored : 76.02 % 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: 2.29 (0.33), residues: 693 helix: 2.26 (0.23), residues: 559 sheet: None (None), residues: 0 loop : -1.87 (0.51), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 11 HIS 0.002 0.000 HIS B 315 PHE 0.020 0.001 PHE B 277 TYR 0.012 0.001 TYR A 373 ARG 0.002 0.000 ARG B 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 84 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 63 time to evaluate : 0.578 Fit side-chains REVERT: A 20 HIS cc_start: 0.4657 (OUTLIER) cc_final: 0.3955 (m90) REVERT: A 59 LEU cc_start: 0.7596 (OUTLIER) cc_final: 0.7252 (tt) outliers start: 21 outliers final: 16 residues processed: 79 average time/residue: 0.1685 time to fit residues: 17.5317 Evaluate side-chains 81 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 63 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 HIS Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 374 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 12 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 6 optimal weight: 0.3980 chunk 52 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 61 optimal weight: 0.1980 chunk 37 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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: 0.6929 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5759 Z= 0.174 Angle : 0.598 7.300 7863 Z= 0.284 Chirality : 0.039 0.284 982 Planarity : 0.003 0.036 963 Dihedral : 7.089 54.504 1064 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.57 % Allowed : 20.58 % Favored : 75.85 % 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: 2.45 (0.33), residues: 693 helix: 2.38 (0.23), residues: 559 sheet: None (None), residues: 0 loop : -1.82 (0.51), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 11 HIS 0.002 0.000 HIS B 315 PHE 0.017 0.001 PHE A 60 TYR 0.012 0.001 TYR A 373 ARG 0.002 0.000 ARG A 156 *********************** 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 83 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 62 time to evaluate : 0.589 Fit side-chains REVERT: A 34 PRO cc_start: 0.7477 (Cg_exo) cc_final: 0.7240 (Cg_endo) REVERT: A 59 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7225 (tt) outliers start: 21 outliers final: 19 residues processed: 79 average time/residue: 0.1733 time to fit residues: 18.1690 Evaluate side-chains 82 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 62 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 366 CYS Chi-restraints excluded: chain B residue 374 VAL 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: 1.9990 chunk 19 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 65 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 31 optimal weight: 0.3980 chunk 45 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.6941 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5759 Z= 0.187 Angle : 0.608 7.204 7863 Z= 0.288 Chirality : 0.039 0.284 982 Planarity : 0.003 0.032 963 Dihedral : 6.946 54.635 1064 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 4.25 % Allowed : 20.92 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.33), residues: 693 helix: 2.40 (0.23), residues: 559 sheet: None (None), residues: 0 loop : -1.83 (0.51), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 11 HIS 0.002 0.000 HIS B 315 PHE 0.021 0.001 PHE B 277 TYR 0.012 0.001 TYR A 373 ARG 0.004 0.000 ARG A 156 *********************** 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 88 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 63 time to evaluate : 0.639 Fit side-chains REVERT: A 34 PRO cc_start: 0.7556 (Cg_exo) cc_final: 0.7312 (Cg_endo) REVERT: A 59 LEU cc_start: 0.7484 (OUTLIER) cc_final: 0.7232 (tt) outliers start: 25 outliers final: 22 residues processed: 83 average time/residue: 0.1840 time to fit residues: 20.2869 Evaluate side-chains 86 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 63 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 366 CYS Chi-restraints excluded: chain B residue 374 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 68 optimal weight: 5.9990 chunk 63 optimal weight: 0.6980 chunk 54 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 42 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 16 optimal weight: 0.0470 chunk 50 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- 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: 0.6933 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5759 Z= 0.187 Angle : 0.608 7.192 7863 Z= 0.290 Chirality : 0.039 0.266 982 Planarity : 0.004 0.031 963 Dihedral : 6.839 54.591 1064 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.08 % Allowed : 21.43 % Favored : 74.49 % 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: 2.55 (0.33), residues: 693 helix: 2.45 (0.23), residues: 558 sheet: None (None), residues: 0 loop : -1.77 (0.50), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 11 HIS 0.002 0.000 HIS B 315 PHE 0.016 0.001 PHE A 60 TYR 0.012 0.001 TYR A 373 ARG 0.004 0.000 ARG A 156 ********************** 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 90 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 66 time to evaluate : 0.650 Fit side-chains REVERT: A 20 HIS cc_start: 0.5013 (OUTLIER) cc_final: 0.4476 (m90) REVERT: A 34 PRO cc_start: 0.7508 (Cg_exo) cc_final: 0.7277 (Cg_endo) REVERT: A 59 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.7178 (tt) outliers start: 24 outliers final: 22 residues processed: 85 average time/residue: 0.1827 time to fit residues: 20.3709 Evaluate side-chains 88 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 64 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 HIS Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 366 CYS Chi-restraints excluded: chain B residue 374 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 15 optimal weight: 0.0970 chunk 54 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 3 optimal weight: 0.0000 chunk 39 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 overall best weight: 0.5982 ------------------------------------------------------------------------------- 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 = 0.4302 r_free = 0.4302 target = 0.158682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.141065 restraints weight = 10923.076| |-----------------------------------------------------------------------------| r_work (start): 0.4110 rms_B_bonded: 2.48 r_work: 0.4011 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5759 Z= 0.185 Angle : 0.611 7.088 7863 Z= 0.292 Chirality : 0.039 0.265 982 Planarity : 0.004 0.031 963 Dihedral : 6.681 54.484 1064 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.91 % Allowed : 21.94 % Favored : 74.15 % 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 : -1.76 (0.50), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 11 HIS 0.002 0.000 HIS B 315 PHE 0.023 0.001 PHE B 277 TYR 0.012 0.001 TYR A 373 ARG 0.008 0.000 ARG B 117 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1429.00 seconds wall clock time: 26 minutes 39.76 seconds (1599.76 seconds total)