Starting phenix.real_space_refine on Wed Feb 4 03:56:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yg4_39235/02_2026/8yg4_39235.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yg4_39235/02_2026/8yg4_39235.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8yg4_39235/02_2026/8yg4_39235.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yg4_39235/02_2026/8yg4_39235.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yg4_39235/02_2026/8yg4_39235.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yg4_39235/02_2026/8yg4_39235.map" } resolution = 2.59 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.062 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: 4 Type Number sf(0) Gaussians S 53 5.16 5 C 5480 2.51 5 N 1514 2.21 5 O 1573 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8620 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1950 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain breaks: 1 Chain: "B" Number of atoms: 2614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2614 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 5, 'TRANS': 335} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 2 Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 983 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "P" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 277 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "R" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2360 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 4, 'TRANS': 282} Chain breaks: 3 Time building chain proxies: 1.80, per 1000 atoms: 0.21 Number of scatterers: 8620 At special positions: 0 Unit cell: (83.22, 99.28, 155.49, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 53 16.00 O 1573 8.00 N 1514 7.00 C 5480 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.86 Conformation dependent library (CDL) restraints added in 322.0 milliseconds 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2036 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 10 sheets defined 44.8% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.641A pdb=" N ALA A 32 " --> pdb=" O GLN A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 57 Processing helix chain 'A' and resid 210 through 216 Processing helix chain 'A' and resid 232 through 245 Processing helix chain 'A' and resid 260 through 271 Processing helix chain 'A' and resid 274 through 279 removed outlier: 4.283A pdb=" N TYR A 278 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 283 Processing helix chain 'A' and resid 298 through 319 removed outlier: 3.638A pdb=" N ILE A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SER A 319 " --> pdb=" O ILE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 358 removed outlier: 4.459A pdb=" N ARG A 340 " --> pdb=" O THR A 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.733A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.643A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.699A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 32 removed outlier: 3.719A pdb=" N GLU P 30 " --> pdb=" O LYS P 26 " (cutoff:3.500A) Processing helix chain 'R' and resid 34 through 46 removed outlier: 4.107A pdb=" N ILE R 38 " --> pdb=" O LYS R 34 " (cutoff:3.500A) Processing helix chain 'R' and resid 179 through 212 removed outlier: 3.573A pdb=" N PHE R 212 " --> pdb=" O ILE R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 245 Processing helix chain 'R' and resid 278 through 312 Processing helix chain 'R' and resid 319 through 329 removed outlier: 3.976A pdb=" N GLY R 323 " --> pdb=" O LYS R 319 " (cutoff:3.500A) Processing helix chain 'R' and resid 329 through 346 removed outlier: 3.929A pdb=" N PHE R 335 " --> pdb=" O LEU R 331 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL R 336 " --> pdb=" O PRO R 332 " (cutoff:3.500A) Processing helix chain 'R' and resid 360 through 391 Proline residue: R 366 - end of helix removed outlier: 3.608A pdb=" N SER R 370 " --> pdb=" O PRO R 366 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN R 374 " --> pdb=" O SER R 370 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE R 375 " --> pdb=" O ILE R 371 " (cutoff:3.500A) Processing helix chain 'R' and resid 400 through 412 removed outlier: 3.552A pdb=" N ARG R 404 " --> pdb=" O ARG R 400 " (cutoff:3.500A) Processing helix chain 'R' and resid 412 through 418 removed outlier: 4.414A pdb=" N LEU R 416 " --> pdb=" O VAL R 412 " (cutoff:3.500A) Processing helix chain 'R' and resid 420 through 425 removed outlier: 3.861A pdb=" N PHE R 424 " --> pdb=" O HIS R 420 " (cutoff:3.500A) Processing helix chain 'R' and resid 434 through 460 removed outlier: 3.885A pdb=" N LEU R 446 " --> pdb=" O HIS R 442 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLY R 452 " --> pdb=" O ASN R 448 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N PHE R 453 " --> pdb=" O SER R 449 " (cutoff:3.500A) Processing helix chain 'R' and resid 463 through 481 Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191 removed outlier: 4.317A pdb=" N VAL A 201 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N GLY A 40 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA A 220 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 51 removed outlier: 6.941A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.969A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.526A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.860A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.624A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.552A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.482A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.567A pdb=" N GLN N 3 " --> pdb=" O SER N 25 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.611A pdb=" N SER N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) 468 hydrogen bonds defined for protein. 1347 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: 1.60 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2814 1.34 - 1.46: 2080 1.46 - 1.58: 3831 1.58 - 1.69: 0 1.69 - 1.81: 78 Bond restraints: 8803 Sorted by residual: bond pdb=" CA TYR R 191 " pdb=" CB TYR R 191 " ideal model delta sigma weight residual 1.528 1.541 -0.013 1.66e-02 3.63e+03 5.70e-01 bond pdb=" C VAL R 365 " pdb=" N PRO R 366 " ideal model delta sigma weight residual 1.335 1.343 -0.009 1.28e-02 6.10e+03 4.52e-01 bond pdb=" CA VAL R 382 " pdb=" C VAL R 382 " ideal model delta sigma weight residual 1.524 1.516 0.008 1.22e-02 6.72e+03 4.11e-01 bond pdb=" CB TYR R 191 " pdb=" CG TYR R 191 " ideal model delta sigma weight residual 1.512 1.525 -0.013 2.20e-02 2.07e+03 3.62e-01 bond pdb=" CA THR B 87 " pdb=" CB THR B 87 " ideal model delta sigma weight residual 1.533 1.543 -0.010 1.66e-02 3.63e+03 3.51e-01 ... (remaining 8798 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.07: 11593 1.07 - 2.14: 258 2.14 - 3.22: 47 3.22 - 4.29: 3 4.29 - 5.36: 7 Bond angle restraints: 11908 Sorted by residual: angle pdb=" CA TYR R 191 " pdb=" CB TYR R 191 " pdb=" CG TYR R 191 " ideal model delta sigma weight residual 113.90 119.26 -5.36 1.80e+00 3.09e-01 8.87e+00 angle pdb=" C ASP B 195 " pdb=" N THR B 196 " pdb=" CA THR B 196 " ideal model delta sigma weight residual 121.54 126.59 -5.05 1.91e+00 2.74e-01 7.00e+00 angle pdb=" C TYR A 56 " pdb=" N HIS A 57 " pdb=" CA HIS A 57 " ideal model delta sigma weight residual 121.54 126.07 -4.53 1.91e+00 2.74e-01 5.63e+00 angle pdb=" C GLN R 364 " pdb=" N VAL R 365 " pdb=" CA VAL R 365 " ideal model delta sigma weight residual 120.33 122.22 -1.89 8.00e-01 1.56e+00 5.56e+00 angle pdb=" N ILE B 93 " pdb=" CA ILE B 93 " pdb=" C ILE B 93 " ideal model delta sigma weight residual 107.76 109.86 -2.10 1.01e+00 9.80e-01 4.32e+00 ... (remaining 11903 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.86: 4984 16.86 - 33.72: 181 33.72 - 50.58: 38 50.58 - 67.44: 3 67.44 - 84.30: 1 Dihedral angle restraints: 5207 sinusoidal: 2059 harmonic: 3148 Sorted by residual: dihedral pdb=" N GLN R 45 " pdb=" CA GLN R 45 " pdb=" CB GLN R 45 " pdb=" CG GLN R 45 " ideal model delta sinusoidal sigma weight residual -180.00 -120.72 -59.28 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N LYS A 210 " pdb=" CA LYS A 210 " pdb=" CB LYS A 210 " pdb=" CG LYS A 210 " ideal model delta sinusoidal sigma weight residual -60.00 -113.61 53.61 3 1.50e+01 4.44e-03 9.22e+00 dihedral pdb=" N PHE B 234 " pdb=" CA PHE B 234 " pdb=" CB PHE B 234 " pdb=" CG PHE B 234 " ideal model delta sinusoidal sigma weight residual -60.00 -112.51 52.51 3 1.50e+01 4.44e-03 9.12e+00 ... (remaining 5204 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 853 0.027 - 0.054: 300 0.054 - 0.081: 99 0.081 - 0.108: 51 0.108 - 0.135: 22 Chirality restraints: 1325 Sorted by residual: chirality pdb=" CA ILE N 58 " pdb=" N ILE N 58 " pdb=" C ILE N 58 " pdb=" CB ILE N 58 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.57e-01 chirality pdb=" CA THR B 87 " pdb=" N THR B 87 " pdb=" C THR B 87 " pdb=" CB THR B 87 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.13 2.00e-01 2.50e+01 4.45e-01 chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.90e-01 ... (remaining 1322 not shown) Planarity restraints: 1510 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL R 382 " 0.008 2.00e-02 2.50e+03 1.65e-02 2.72e+00 pdb=" C VAL R 382 " -0.029 2.00e-02 2.50e+03 pdb=" O VAL R 382 " 0.011 2.00e-02 2.50e+03 pdb=" N ARG R 383 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL G 54 " 0.027 5.00e-02 4.00e+02 4.12e-02 2.71e+00 pdb=" N PRO G 55 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO G 55 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO G 55 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 381 " -0.008 2.00e-02 2.50e+03 1.64e-02 2.67e+00 pdb=" C ILE R 381 " 0.028 2.00e-02 2.50e+03 pdb=" O ILE R 381 " -0.011 2.00e-02 2.50e+03 pdb=" N VAL R 382 " -0.009 2.00e-02 2.50e+03 ... (remaining 1507 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 960 2.75 - 3.29: 8646 3.29 - 3.83: 14823 3.83 - 4.36: 17189 4.36 - 4.90: 30098 Nonbonded interactions: 71716 Sorted by model distance: nonbonded pdb=" OD2 ASP N 50 " pdb=" OG SER N 59 " model vdw 2.216 3.040 nonbonded pdb=" OG SER R 198 " pdb=" O SER R 449 " model vdw 2.248 3.040 nonbonded pdb=" O ILE R 367 " pdb=" OG SER R 370 " model vdw 2.250 3.040 nonbonded pdb=" OG SER N 52 " pdb=" OG SER N 57 " model vdw 2.251 3.040 nonbonded pdb=" O VAL R 338 " pdb=" OG SER R 341 " model vdw 2.271 3.040 ... (remaining 71711 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 4.660 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: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 9.520 Find NCS groups from input model: 0.040 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:9.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 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 : 0.001 0.016 8803 Z= 0.092 Angle : 0.420 5.362 11908 Z= 0.251 Chirality : 0.037 0.135 1325 Planarity : 0.003 0.041 1510 Dihedral : 9.027 84.305 3171 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.11 % Allowed : 6.49 % Favored : 93.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.26), residues: 1061 helix: 2.27 (0.25), residues: 429 sheet: 1.26 (0.33), residues: 228 loop : 0.11 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 347 TYR 0.026 0.001 TYR R 191 PHE 0.010 0.001 PHE R 453 TRP 0.013 0.001 TRP B 82 HIS 0.003 0.000 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00147 ( 8803) covalent geometry : angle 0.41967 (11908) hydrogen bonds : bond 0.13700 ( 468) hydrogen bonds : angle 5.84225 ( 1347) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 180 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: A 13 VAL cc_start: 0.7827 (t) cc_final: 0.7548 (m) REVERT: A 193 LYS cc_start: 0.7042 (mmtt) cc_final: 0.6606 (mttt) REVERT: A 250 ARG cc_start: 0.6595 (mmt180) cc_final: 0.6377 (mtp-110) REVERT: B 155 ASN cc_start: 0.6821 (t0) cc_final: 0.6480 (t0) REVERT: B 175 GLN cc_start: 0.7881 (mt0) cc_final: 0.7652 (mm-40) REVERT: B 197 ARG cc_start: 0.6999 (mmm-85) cc_final: 0.6533 (ptt-90) REVERT: R 228 LEU cc_start: 0.7551 (tp) cc_final: 0.7097 (mp) REVERT: R 287 PHE cc_start: 0.7687 (m-10) cc_final: 0.7447 (m-80) REVERT: R 408 LYS cc_start: 0.7833 (tmtp) cc_final: 0.7481 (tppt) outliers start: 1 outliers final: 1 residues processed: 181 average time/residue: 0.5880 time to fit residues: 112.7002 Evaluate side-chains 112 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 111 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.0570 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 0.0570 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN A 238 ASN A 357 GLN P 16 GLN R 463 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.206167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.172182 restraints weight = 10103.637| |-----------------------------------------------------------------------------| r_work (start): 0.4025 rms_B_bonded: 1.93 r_work: 0.3926 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3819 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8803 Z= 0.115 Angle : 0.474 5.947 11908 Z= 0.263 Chirality : 0.040 0.158 1325 Planarity : 0.004 0.036 1510 Dihedral : 3.838 46.822 1188 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.62 % Allowed : 13.62 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.12 (0.26), residues: 1061 helix: 2.80 (0.24), residues: 445 sheet: 1.06 (0.33), residues: 226 loop : -0.02 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 214 TYR 0.024 0.002 TYR R 191 PHE 0.019 0.001 PHE R 335 TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS A 354 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 8803) covalent geometry : angle 0.47418 (11908) hydrogen bonds : bond 0.04132 ( 468) hydrogen bonds : angle 4.27571 ( 1347) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: A 13 VAL cc_start: 0.7883 (t) cc_final: 0.7580 (m) REVERT: A 193 LYS cc_start: 0.7272 (mmtt) cc_final: 0.6904 (mttt) REVERT: A 238 ASN cc_start: 0.8367 (m110) cc_final: 0.8163 (m-40) REVERT: B 45 MET cc_start: 0.7463 (mtt) cc_final: 0.7176 (mtt) REVERT: B 155 ASN cc_start: 0.7201 (t0) cc_final: 0.6784 (t0) REVERT: B 175 GLN cc_start: 0.8484 (mt0) cc_final: 0.7886 (mm-40) REVERT: G 21 MET cc_start: 0.7564 (tpp) cc_final: 0.7289 (mmt) REVERT: R 228 LEU cc_start: 0.7577 (tp) cc_final: 0.7314 (mp) REVERT: R 312 MET cc_start: 0.6536 (OUTLIER) cc_final: 0.6288 (tpp) REVERT: R 408 LYS cc_start: 0.7716 (tmtp) cc_final: 0.7133 (tppt) REVERT: R 443 TYR cc_start: 0.8240 (t80) cc_final: 0.8012 (t80) outliers start: 15 outliers final: 4 residues processed: 140 average time/residue: 0.5154 time to fit residues: 76.7543 Evaluate side-chains 111 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 106 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 312 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 6 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 chunk 92 optimal weight: 0.6980 chunk 16 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN A 357 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.200854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.165695 restraints weight = 9912.607| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 1.89 r_work: 0.3850 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3743 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8803 Z= 0.131 Angle : 0.478 5.918 11908 Z= 0.264 Chirality : 0.041 0.157 1325 Planarity : 0.003 0.038 1510 Dihedral : 4.072 44.512 1188 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.24 % Allowed : 14.16 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.26), residues: 1061 helix: 2.61 (0.24), residues: 444 sheet: 0.84 (0.33), residues: 219 loop : -0.14 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 214 TYR 0.024 0.002 TYR R 191 PHE 0.020 0.002 PHE R 335 TRP 0.018 0.002 TRP A 248 HIS 0.004 0.001 HIS A 354 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 8803) covalent geometry : angle 0.47806 (11908) hydrogen bonds : bond 0.04280 ( 468) hydrogen bonds : angle 4.32042 ( 1347) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 109 time to evaluate : 0.239 Fit side-chains REVERT: A 13 VAL cc_start: 0.7874 (t) cc_final: 0.7583 (m) REVERT: A 20 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7559 (mm-30) REVERT: A 193 LYS cc_start: 0.7198 (mmtt) cc_final: 0.6779 (mttt) REVERT: A 238 ASN cc_start: 0.8431 (m110) cc_final: 0.8148 (m-40) REVERT: A 266 GLU cc_start: 0.6860 (OUTLIER) cc_final: 0.6365 (pt0) REVERT: A 353 MET cc_start: 0.9028 (OUTLIER) cc_final: 0.8671 (tmm) REVERT: B 175 GLN cc_start: 0.8514 (mt0) cc_final: 0.7897 (mm-40) outliers start: 30 outliers final: 10 residues processed: 127 average time/residue: 0.4658 time to fit residues: 63.1201 Evaluate side-chains 114 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain R residue 241 ASP Chi-restraints excluded: chain R residue 312 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 99 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 63 optimal weight: 0.0870 chunk 61 optimal weight: 0.7980 chunk 2 optimal weight: 0.0170 chunk 10 optimal weight: 5.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.201996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.167775 restraints weight = 10115.602| |-----------------------------------------------------------------------------| r_work (start): 0.3969 rms_B_bonded: 1.79 r_work: 0.3870 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3763 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8803 Z= 0.104 Angle : 0.445 5.926 11908 Z= 0.247 Chirality : 0.040 0.165 1325 Planarity : 0.003 0.037 1510 Dihedral : 3.636 18.801 1186 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.03 % Allowed : 15.24 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.26), residues: 1061 helix: 2.81 (0.24), residues: 435 sheet: 0.70 (0.33), residues: 231 loop : -0.06 (0.31), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 250 TYR 0.024 0.001 TYR R 191 PHE 0.017 0.001 PHE R 335 TRP 0.018 0.001 TRP A 248 HIS 0.003 0.001 HIS A 354 Details of bonding type rmsd covalent geometry : bond 0.00218 ( 8803) covalent geometry : angle 0.44470 (11908) hydrogen bonds : bond 0.03944 ( 468) hydrogen bonds : angle 4.17380 ( 1347) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 116 time to evaluate : 0.208 Fit side-chains REVERT: A 13 VAL cc_start: 0.7880 (t) cc_final: 0.7607 (m) REVERT: A 20 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7529 (mm-30) REVERT: A 33 THR cc_start: 0.8497 (t) cc_final: 0.8160 (m) REVERT: A 193 LYS cc_start: 0.7256 (mmtt) cc_final: 0.6806 (mttt) REVERT: A 238 ASN cc_start: 0.8428 (m110) cc_final: 0.8141 (m-40) REVERT: B 155 ASN cc_start: 0.7435 (t0) cc_final: 0.7115 (t0) REVERT: B 175 GLN cc_start: 0.8533 (mt0) cc_final: 0.7948 (mm-40) REVERT: G 21 MET cc_start: 0.7480 (tpp) cc_final: 0.7206 (mmt) REVERT: R 312 MET cc_start: 0.6353 (OUTLIER) cc_final: 0.6101 (tpp) REVERT: R 445 MET cc_start: 0.7616 (mmp) cc_final: 0.7316 (mmp) outliers start: 28 outliers final: 8 residues processed: 132 average time/residue: 0.4817 time to fit residues: 67.5707 Evaluate side-chains 113 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain R residue 312 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 69 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 99 optimal weight: 0.0670 chunk 73 optimal weight: 7.9990 chunk 4 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 45 optimal weight: 0.4980 chunk 52 optimal weight: 5.9990 overall best weight: 0.9122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN A 357 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.197800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.160353 restraints weight = 9814.168| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 1.98 r_work: 0.3766 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3649 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8803 Z= 0.135 Angle : 0.495 6.142 11908 Z= 0.273 Chirality : 0.041 0.159 1325 Planarity : 0.004 0.040 1510 Dihedral : 3.898 20.134 1186 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.46 % Allowed : 15.14 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.26), residues: 1061 helix: 2.68 (0.24), residues: 432 sheet: 0.43 (0.33), residues: 224 loop : -0.20 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 250 TYR 0.025 0.002 TYR R 191 PHE 0.020 0.002 PHE R 335 TRP 0.024 0.002 TRP A 248 HIS 0.005 0.001 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 8803) covalent geometry : angle 0.49546 (11908) hydrogen bonds : bond 0.04277 ( 468) hydrogen bonds : angle 4.32857 ( 1347) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 116 time to evaluate : 0.223 Fit side-chains REVERT: A 13 VAL cc_start: 0.7898 (t) cc_final: 0.7577 (m) REVERT: A 42 ASP cc_start: 0.7034 (OUTLIER) cc_final: 0.6751 (p0) REVERT: A 193 LYS cc_start: 0.7239 (mmtt) cc_final: 0.6732 (mttt) REVERT: A 238 ASN cc_start: 0.8420 (m110) cc_final: 0.8097 (m-40) REVERT: A 266 GLU cc_start: 0.6831 (OUTLIER) cc_final: 0.6281 (pt0) REVERT: B 175 GLN cc_start: 0.8535 (mt0) cc_final: 0.7860 (mm-40) REVERT: B 197 ARG cc_start: 0.7094 (mmp-170) cc_final: 0.6803 (ppt90) REVERT: G 21 MET cc_start: 0.7482 (tpp) cc_final: 0.7105 (mmt) REVERT: R 224 MET cc_start: 0.7911 (ttp) cc_final: 0.7704 (ttp) REVERT: R 312 MET cc_start: 0.6318 (OUTLIER) cc_final: 0.6035 (tpp) REVERT: R 414 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.7870 (mmt) REVERT: R 445 MET cc_start: 0.7771 (mmp) cc_final: 0.7463 (mmp) outliers start: 32 outliers final: 14 residues processed: 133 average time/residue: 0.4774 time to fit residues: 67.6008 Evaluate side-chains 124 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LYS Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain R residue 241 ASP Chi-restraints excluded: chain R residue 307 HIS Chi-restraints excluded: chain R residue 312 MET Chi-restraints excluded: chain R residue 408 LYS Chi-restraints excluded: chain R residue 414 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 100 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.197201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.159800 restraints weight = 9757.016| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 1.94 r_work: 0.3759 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3642 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8803 Z= 0.138 Angle : 0.492 6.323 11908 Z= 0.273 Chirality : 0.041 0.203 1325 Planarity : 0.004 0.046 1510 Dihedral : 3.999 20.760 1186 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.46 % Allowed : 15.35 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.26), residues: 1061 helix: 2.63 (0.24), residues: 430 sheet: 0.38 (0.33), residues: 218 loop : -0.35 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 250 TYR 0.025 0.002 TYR R 191 PHE 0.020 0.002 PHE R 335 TRP 0.025 0.002 TRP A 248 HIS 0.004 0.001 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 8803) covalent geometry : angle 0.49241 (11908) hydrogen bonds : bond 0.04295 ( 468) hydrogen bonds : angle 4.36699 ( 1347) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 111 time to evaluate : 0.277 Fit side-chains REVERT: A 13 VAL cc_start: 0.7956 (t) cc_final: 0.7626 (m) REVERT: A 42 ASP cc_start: 0.7038 (OUTLIER) cc_final: 0.6740 (p0) REVERT: A 193 LYS cc_start: 0.7221 (mmtt) cc_final: 0.6724 (mttt) REVERT: A 238 ASN cc_start: 0.8434 (m110) cc_final: 0.8204 (m110) REVERT: A 266 GLU cc_start: 0.6928 (OUTLIER) cc_final: 0.6361 (pt0) REVERT: B 175 GLN cc_start: 0.8526 (mt0) cc_final: 0.7867 (mm-40) REVERT: G 21 MET cc_start: 0.7544 (OUTLIER) cc_final: 0.7208 (mmt) REVERT: R 414 MET cc_start: 0.8314 (OUTLIER) cc_final: 0.7892 (mmt) REVERT: R 445 MET cc_start: 0.7793 (mmp) cc_final: 0.7540 (mmp) outliers start: 32 outliers final: 16 residues processed: 127 average time/residue: 0.5014 time to fit residues: 67.7130 Evaluate side-chains 123 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LYS Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain R residue 241 ASP Chi-restraints excluded: chain R residue 307 HIS Chi-restraints excluded: chain R residue 312 MET Chi-restraints excluded: chain R residue 408 LYS Chi-restraints excluded: chain R residue 414 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 7 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 40 optimal weight: 0.0270 chunk 15 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 93 optimal weight: 8.9990 chunk 25 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 94 optimal weight: 0.0370 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN R 348 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.197487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.158766 restraints weight = 9466.116| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 2.14 r_work: 0.3716 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3589 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8803 Z= 0.107 Angle : 0.456 6.097 11908 Z= 0.253 Chirality : 0.040 0.190 1325 Planarity : 0.003 0.040 1510 Dihedral : 3.826 20.123 1186 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.70 % Allowed : 16.86 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.26), residues: 1061 helix: 2.81 (0.24), residues: 426 sheet: 0.40 (0.34), residues: 212 loop : -0.37 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 250 TYR 0.025 0.001 TYR R 191 PHE 0.018 0.001 PHE R 335 TRP 0.021 0.002 TRP A 248 HIS 0.003 0.001 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 8803) covalent geometry : angle 0.45594 (11908) hydrogen bonds : bond 0.03936 ( 468) hydrogen bonds : angle 4.21311 ( 1347) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 0.305 Fit side-chains REVERT: A 13 VAL cc_start: 0.7848 (t) cc_final: 0.7516 (m) REVERT: A 193 LYS cc_start: 0.7153 (mmtt) cc_final: 0.6650 (mttt) REVERT: A 238 ASN cc_start: 0.8412 (m110) cc_final: 0.8079 (m-40) REVERT: B 175 GLN cc_start: 0.8539 (mt0) cc_final: 0.7831 (mm-40) REVERT: B 260 GLU cc_start: 0.7108 (pt0) cc_final: 0.6754 (tt0) REVERT: G 21 MET cc_start: 0.7478 (OUTLIER) cc_final: 0.7138 (mmt) REVERT: R 312 MET cc_start: 0.6219 (OUTLIER) cc_final: 0.5932 (tpp) REVERT: R 414 MET cc_start: 0.8263 (OUTLIER) cc_final: 0.7881 (mmt) REVERT: R 445 MET cc_start: 0.7797 (mmp) cc_final: 0.7578 (mmp) outliers start: 25 outliers final: 15 residues processed: 121 average time/residue: 0.5079 time to fit residues: 65.2678 Evaluate side-chains 118 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LYS Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain R residue 189 MET Chi-restraints excluded: chain R residue 307 HIS Chi-restraints excluded: chain R residue 312 MET Chi-restraints excluded: chain R residue 354 LEU Chi-restraints excluded: chain R residue 408 LYS Chi-restraints excluded: chain R residue 414 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 68 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 39 optimal weight: 0.2980 chunk 97 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 61 optimal weight: 0.2980 chunk 43 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN A 357 GLN R 348 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.194456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.155306 restraints weight = 9337.769| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 2.10 r_work: 0.3677 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3551 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8803 Z= 0.150 Angle : 0.516 6.445 11908 Z= 0.284 Chirality : 0.042 0.214 1325 Planarity : 0.004 0.039 1510 Dihedral : 4.060 20.975 1186 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.92 % Allowed : 16.54 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.26), residues: 1061 helix: 2.55 (0.24), residues: 432 sheet: 0.32 (0.33), residues: 217 loop : -0.40 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 250 TYR 0.025 0.002 TYR R 191 PHE 0.019 0.002 PHE R 335 TRP 0.029 0.002 TRP A 248 HIS 0.005 0.001 HIS R 307 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 8803) covalent geometry : angle 0.51586 (11908) hydrogen bonds : bond 0.04359 ( 468) hydrogen bonds : angle 4.40521 ( 1347) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 99 time to evaluate : 0.244 Fit side-chains REVERT: A 13 VAL cc_start: 0.7870 (t) cc_final: 0.7531 (m) REVERT: A 42 ASP cc_start: 0.7035 (OUTLIER) cc_final: 0.6722 (p0) REVERT: A 193 LYS cc_start: 0.7244 (mmtt) cc_final: 0.6716 (mttt) REVERT: A 238 ASN cc_start: 0.8445 (m110) cc_final: 0.8196 (m110) REVERT: A 266 GLU cc_start: 0.6957 (OUTLIER) cc_final: 0.6346 (pt0) REVERT: B 76 ASP cc_start: 0.8341 (p0) cc_final: 0.7870 (p0) REVERT: B 175 GLN cc_start: 0.8523 (mt0) cc_final: 0.7820 (mm-40) REVERT: G 21 MET cc_start: 0.7569 (OUTLIER) cc_final: 0.7187 (mmt) REVERT: R 312 MET cc_start: 0.6316 (OUTLIER) cc_final: 0.5913 (tpp) REVERT: R 414 MET cc_start: 0.8314 (OUTLIER) cc_final: 0.7915 (mmt) outliers start: 27 outliers final: 18 residues processed: 115 average time/residue: 0.4735 time to fit residues: 57.9701 Evaluate side-chains 116 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LYS Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain R residue 241 ASP Chi-restraints excluded: chain R residue 307 HIS Chi-restraints excluded: chain R residue 312 MET Chi-restraints excluded: chain R residue 408 LYS Chi-restraints excluded: chain R residue 414 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 9 optimal weight: 0.0000 chunk 4 optimal weight: 0.0370 chunk 64 optimal weight: 8.9990 chunk 35 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 overall best weight: 0.5062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN R 348 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.196238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.159344 restraints weight = 9386.118| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 1.89 r_work: 0.3717 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3591 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 8803 Z= 0.106 Angle : 0.463 6.789 11908 Z= 0.256 Chirality : 0.040 0.186 1325 Planarity : 0.003 0.040 1510 Dihedral : 3.849 20.197 1186 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.81 % Allowed : 16.97 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.26), residues: 1061 helix: 2.83 (0.24), residues: 428 sheet: 0.40 (0.33), residues: 212 loop : -0.44 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 250 TYR 0.026 0.001 TYR R 191 PHE 0.023 0.002 PHE N 108 TRP 0.024 0.002 TRP A 248 HIS 0.002 0.001 HIS R 307 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 8803) covalent geometry : angle 0.46278 (11908) hydrogen bonds : bond 0.03913 ( 468) hydrogen bonds : angle 4.21093 ( 1347) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 102 time to evaluate : 0.237 Fit side-chains REVERT: A 13 VAL cc_start: 0.7815 (t) cc_final: 0.7486 (m) REVERT: A 193 LYS cc_start: 0.7193 (mmtt) cc_final: 0.6664 (mttt) REVERT: A 238 ASN cc_start: 0.8398 (m110) cc_final: 0.8061 (m-40) REVERT: A 266 GLU cc_start: 0.6846 (OUTLIER) cc_final: 0.6306 (pt0) REVERT: B 76 ASP cc_start: 0.8202 (p0) cc_final: 0.7728 (p0) REVERT: B 175 GLN cc_start: 0.8536 (mt0) cc_final: 0.7832 (mm-40) REVERT: B 260 GLU cc_start: 0.7070 (pt0) cc_final: 0.6709 (tt0) REVERT: G 21 MET cc_start: 0.7498 (OUTLIER) cc_final: 0.7112 (mmt) REVERT: R 312 MET cc_start: 0.6168 (OUTLIER) cc_final: 0.5893 (tpp) REVERT: R 414 MET cc_start: 0.8212 (OUTLIER) cc_final: 0.7813 (mmt) outliers start: 26 outliers final: 15 residues processed: 118 average time/residue: 0.4474 time to fit residues: 56.1287 Evaluate side-chains 115 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LYS Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain R residue 307 HIS Chi-restraints excluded: chain R residue 312 MET Chi-restraints excluded: chain R residue 414 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 41 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 50 optimal weight: 0.0670 chunk 99 optimal weight: 2.9990 chunk 53 optimal weight: 0.0030 chunk 82 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 57 optimal weight: 8.9990 chunk 92 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 overall best weight: 0.5728 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN R 348 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.197110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.158088 restraints weight = 9297.749| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 2.22 r_work: 0.3704 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3577 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8803 Z= 0.110 Angle : 0.469 6.629 11908 Z= 0.258 Chirality : 0.040 0.211 1325 Planarity : 0.003 0.039 1510 Dihedral : 3.827 19.929 1186 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.16 % Allowed : 17.41 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.26), residues: 1061 helix: 2.83 (0.24), residues: 430 sheet: 0.38 (0.33), residues: 212 loop : -0.40 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 250 TYR 0.026 0.001 TYR R 191 PHE 0.023 0.002 PHE N 108 TRP 0.029 0.002 TRP A 248 HIS 0.003 0.001 HIS R 307 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 8803) covalent geometry : angle 0.46914 (11908) hydrogen bonds : bond 0.03920 ( 468) hydrogen bonds : angle 4.19078 ( 1347) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.319 Fit side-chains REVERT: A 193 LYS cc_start: 0.7260 (mmtt) cc_final: 0.6730 (mttt) REVERT: A 238 ASN cc_start: 0.8434 (m110) cc_final: 0.8083 (m-40) REVERT: A 266 GLU cc_start: 0.6833 (OUTLIER) cc_final: 0.6281 (pt0) REVERT: B 76 ASP cc_start: 0.8259 (p0) cc_final: 0.7761 (p0) REVERT: B 175 GLN cc_start: 0.8564 (mt0) cc_final: 0.7827 (mm-40) REVERT: B 260 GLU cc_start: 0.7094 (pt0) cc_final: 0.6729 (tt0) REVERT: G 21 MET cc_start: 0.7468 (OUTLIER) cc_final: 0.7074 (mmt) REVERT: R 312 MET cc_start: 0.6147 (OUTLIER) cc_final: 0.5879 (tpp) REVERT: R 414 MET cc_start: 0.8252 (OUTLIER) cc_final: 0.7864 (mmt) outliers start: 20 outliers final: 14 residues processed: 115 average time/residue: 0.4617 time to fit residues: 56.6930 Evaluate side-chains 113 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LYS Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain R residue 307 HIS Chi-restraints excluded: chain R residue 312 MET Chi-restraints excluded: chain R residue 414 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 101 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 23 optimal weight: 5.9990 chunk 88 optimal weight: 0.8980 chunk 53 optimal weight: 0.0370 chunk 3 optimal weight: 3.9990 chunk 39 optimal weight: 0.0670 chunk 26 optimal weight: 0.1980 chunk 74 optimal weight: 0.7980 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN R 348 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.200253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.163828 restraints weight = 9666.065| |-----------------------------------------------------------------------------| r_work (start): 0.3904 rms_B_bonded: 1.98 r_work: 0.3788 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3673 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8803 Z= 0.098 Angle : 0.449 6.639 11908 Z= 0.248 Chirality : 0.039 0.218 1325 Planarity : 0.003 0.040 1510 Dihedral : 3.696 19.042 1186 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.84 % Allowed : 18.16 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.26), residues: 1061 helix: 2.92 (0.24), residues: 430 sheet: 0.42 (0.33), residues: 212 loop : -0.36 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 250 TYR 0.026 0.001 TYR R 191 PHE 0.025 0.001 PHE R 184 TRP 0.025 0.002 TRP A 248 HIS 0.002 0.001 HIS R 307 Details of bonding type rmsd covalent geometry : bond 0.00204 ( 8803) covalent geometry : angle 0.44879 (11908) hydrogen bonds : bond 0.03698 ( 468) hydrogen bonds : angle 4.08647 ( 1347) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3095.13 seconds wall clock time: 53 minutes 19.49 seconds (3199.49 seconds total)