Starting phenix.real_space_refine on Thu Jul 2 06:52:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e2x_30971/07_2026/7e2x_30971_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e2x_30971/07_2026/7e2x_30971.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7e2x_30971/07_2026/7e2x_30971_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e2x_30971/07_2026/7e2x_30971_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7e2x_30971/07_2026/7e2x_30971.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e2x_30971/07_2026/7e2x_30971.map" } resolution = 3.0 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= 0.008 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 P 2 5.49 5 S 53 5.16 5 C 4708 2.51 5 N 1169 2.21 5 O 1294 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7226 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1766 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 216} Chain breaks: 2 Chain: "B" Number of atoms: 2516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2516 Classifications: {'peptide': 328} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 322} Chain: "G" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 347 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 4, 'TRANS': 40} Chain: "R" Number of atoms: 2197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2197 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 11, 'TRANS': 266} Chain breaks: 2 Chain: "R" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 400 Unusual residues: {'CLR': 10, 'J40': 1, 'PLM': 3} Classifications: {'undetermined': 14, 'water': 9} Link IDs: {None: 22} Time building chain proxies: 1.27, per 1000 atoms: 0.18 Number of scatterers: 7226 At special positions: 0 Unit cell: (79.092, 113.568, 112.554, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 53 16.00 P 2 15.00 O 1294 8.00 N 1169 7.00 C 4708 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.04 Simple disulfide: pdb=" SG CYS R 109 " - pdb=" SG CYS R 187 " distance=2.03 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: 0.58 Conformation dependent library (CDL) restraints added in 356.1 milliseconds 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1642 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 8 sheets defined 47.7% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 4.027A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.658A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TRP A 211 " --> pdb=" O ARG A 208 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.527A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 352 removed outlier: 3.730A pdb=" N VAL A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 25 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.878A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 24 removed outlier: 3.781A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.927A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'R' and resid 36 through 64 removed outlier: 3.665A pdb=" N GLU R 64 " --> pdb=" O ALA R 60 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 68 removed outlier: 3.826A pdb=" N GLN R 68 " --> pdb=" O ARG R 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 65 through 68' Processing helix chain 'R' and resid 69 through 100 removed outlier: 4.232A pdb=" N LEU R 90 " --> pdb=" O SER R 86 " (cutoff:3.500A) Proline residue: R 91 - end of helix Processing helix chain 'R' and resid 105 through 140 Processing helix chain 'R' and resid 140 through 147 Processing helix chain 'R' and resid 149 through 174 removed outlier: 4.379A pdb=" N ALA R 153 " --> pdb=" O THR R 149 " (cutoff:3.500A) Proline residue: R 170 - end of helix Processing helix chain 'R' and resid 192 through 204 Processing helix chain 'R' and resid 204 through 228 Processing helix chain 'R' and resid 325 through 368 removed outlier: 3.809A pdb=" N PHE R 354 " --> pdb=" O ILE R 350 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N CYS R 357 " --> pdb=" O THR R 353 " (cutoff:3.500A) Proline residue: R 360 - end of helix Processing helix chain 'R' and resid 369 through 371 No H-bonds generated for 'chain 'R' and resid 369 through 371' Processing helix chain 'R' and resid 378 through 401 removed outlier: 3.908A pdb=" N GLY R 389 " --> pdb=" O ILE R 385 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N TYR R 390 " --> pdb=" O ASN R 386 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER R 393 " --> pdb=" O GLY R 389 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N LEU R 394 " --> pdb=" O TYR R 390 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU R 395 " --> pdb=" O SER R 391 " (cutoff:3.500A) Proline residue: R 397 - end of helix Processing helix chain 'R' and resid 404 through 415 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.630A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.982A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.906A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 4.167A pdb=" N CYS B 121 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LEU B 139 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.257A 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: 3.594A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.014A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.755A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 277 removed outlier: 6.688A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 371 hydrogen bonds defined for protein. 1086 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: 0.90 Time building geometry restraints manager: 0.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1129 1.31 - 1.43: 1876 1.43 - 1.56: 4237 1.56 - 1.69: 61 1.69 - 1.81: 74 Bond restraints: 7377 Sorted by residual: bond pdb=" C15 J40 R 601 " pdb=" C16 J40 R 601 " ideal model delta sigma weight residual 1.329 1.527 -0.198 2.00e-02 2.50e+03 9.78e+01 bond pdb=" C18 J40 R 601 " pdb=" C19 J40 R 601 " ideal model delta sigma weight residual 1.330 1.526 -0.196 2.00e-02 2.50e+03 9.64e+01 bond pdb=" C24 J40 R 601 " pdb=" C25 J40 R 601 " ideal model delta sigma weight residual 1.332 1.528 -0.196 2.00e-02 2.50e+03 9.61e+01 bond pdb=" C21 J40 R 601 " pdb=" C22 J40 R 601 " ideal model delta sigma weight residual 1.332 1.528 -0.196 2.00e-02 2.50e+03 9.60e+01 bond pdb=" C5 CLR R 605 " pdb=" C6 CLR R 605 " ideal model delta sigma weight residual 1.332 1.469 -0.137 2.00e-02 2.50e+03 4.68e+01 ... (remaining 7372 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.54: 9880 3.54 - 7.07: 126 7.07 - 10.61: 6 10.61 - 14.14: 8 14.14 - 17.68: 4 Bond angle restraints: 10024 Sorted by residual: angle pdb=" O11 J40 R 601 " pdb=" P1 J40 R 601 " pdb=" O12 J40 R 601 " ideal model delta sigma weight residual 119.00 101.32 17.68 3.00e+00 1.11e-01 3.47e+01 angle pdb=" O1 J40 R 601 " pdb=" P1 J40 R 601 " pdb=" O13 J40 R 601 " ideal model delta sigma weight residual 92.86 109.79 -16.93 3.00e+00 1.11e-01 3.19e+01 angle pdb=" C24 J40 R 601 " pdb=" C25 J40 R 601 " pdb=" C26 J40 R 601 " ideal model delta sigma weight residual 127.60 113.09 14.51 3.00e+00 1.11e-01 2.34e+01 angle pdb=" C23 J40 R 601 " pdb=" C24 J40 R 601 " pdb=" C25 J40 R 601 " ideal model delta sigma weight residual 127.40 113.04 14.36 3.00e+00 1.11e-01 2.29e+01 angle pdb=" C21 J40 R 601 " pdb=" C22 J40 R 601 " pdb=" C23 J40 R 601 " ideal model delta sigma weight residual 126.99 113.67 13.32 3.00e+00 1.11e-01 1.97e+01 ... (remaining 10019 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 4638 17.77 - 35.54: 222 35.54 - 53.31: 41 53.31 - 71.08: 16 71.08 - 88.85: 3 Dihedral angle restraints: 4920 sinusoidal: 2389 harmonic: 2531 Sorted by residual: dihedral pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 130.24 -37.24 1 1.00e+01 1.00e-02 1.96e+01 dihedral pdb=" CA ASP A 337 " pdb=" CB ASP A 337 " pdb=" CG ASP A 337 " pdb=" OD1 ASP A 337 " ideal model delta sinusoidal sigma weight residual -30.00 -88.07 58.07 1 2.00e+01 2.50e-03 1.13e+01 dihedral pdb=" CB GLU R 330 " pdb=" CG GLU R 330 " pdb=" CD GLU R 330 " pdb=" OE1 GLU R 330 " ideal model delta sinusoidal sigma weight residual 0.00 84.35 -84.35 1 3.00e+01 1.11e-03 9.62e+00 ... (remaining 4917 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 944 0.048 - 0.096: 149 0.096 - 0.144: 58 0.144 - 0.192: 10 0.192 - 0.240: 11 Chirality restraints: 1172 Sorted by residual: chirality pdb=" C14 CLR R 605 " pdb=" C13 CLR R 605 " pdb=" C15 CLR R 605 " pdb=" C8 CLR R 605 " both_signs ideal model delta sigma weight residual False -2.32 -2.56 0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" C14 CLR R 602 " pdb=" C13 CLR R 602 " pdb=" C15 CLR R 602 " pdb=" C8 CLR R 602 " both_signs ideal model delta sigma weight residual False -2.32 -2.56 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" C14 CLR R 607 " pdb=" C13 CLR R 607 " pdb=" C15 CLR R 607 " pdb=" C8 CLR R 607 " both_signs ideal model delta sigma weight residual False -2.32 -2.55 0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 1169 not shown) Planarity restraints: 1192 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C20 J40 R 601 " 0.137 2.00e-02 2.50e+03 2.35e-01 5.53e+02 pdb=" C21 J40 R 601 " -0.304 2.00e-02 2.50e+03 pdb=" C22 J40 R 601 " 0.303 2.00e-02 2.50e+03 pdb=" C23 J40 R 601 " -0.135 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C23 J40 R 601 " -0.136 2.00e-02 2.50e+03 2.30e-01 5.28e+02 pdb=" C24 J40 R 601 " 0.295 2.00e-02 2.50e+03 pdb=" C25 J40 R 601 " -0.295 2.00e-02 2.50e+03 pdb=" C26 J40 R 601 " 0.136 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 J40 R 601 " -0.133 2.00e-02 2.50e+03 1.33e-01 1.78e+02 pdb=" C18 J40 R 601 " 0.134 2.00e-02 2.50e+03 pdb=" C19 J40 R 601 " 0.133 2.00e-02 2.50e+03 pdb=" C20 J40 R 601 " -0.133 2.00e-02 2.50e+03 ... (remaining 1189 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 51 2.59 - 3.16: 5909 3.16 - 3.74: 10334 3.74 - 4.32: 14153 4.32 - 4.90: 23964 Nonbonded interactions: 54411 Sorted by model distance: nonbonded pdb=" O ARG B 314 " pdb=" OG SER B 331 " model vdw 2.008 3.040 nonbonded pdb=" OG SER B 147 " pdb=" O MET B 188 " model vdw 2.023 3.040 nonbonded pdb=" O ASP B 333 " pdb=" OG SER B 334 " model vdw 2.094 3.040 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.183 3.040 nonbonded pdb=" NZ LYS A 271 " pdb=" O THR A 324 " model vdw 2.202 3.120 ... (remaining 54406 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: 0.430 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.260 Find NCS groups from input model: 0.030 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:7.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5960 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 : 0.010 0.198 7379 Z= 0.485 Angle : 0.902 17.677 10028 Z= 0.365 Chirality : 0.048 0.240 1172 Planarity : 0.010 0.235 1192 Dihedral : 11.405 88.854 3272 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 2.48 (0.31), residues: 854 helix: 3.90 (0.27), residues: 378 sheet: 1.14 (0.42), residues: 151 loop : -1.02 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 220 TYR 0.011 0.001 TYR B 59 PHE 0.019 0.001 PHE R 411 TRP 0.008 0.001 TRP B 297 HIS 0.004 0.000 HIS R 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00966 / 0.49 ( 7377) covalent geometry : angle 0.90249 / 0.37 (10024) SS BOND : bond 0.00491 / 0.26 ( 2) SS BOND : angle 0.53799 / 0.28 ( 4) hydrogen bonds : bond 0.11037 / 7.53 ( 371) hydrogen bonds : angle 4.39525 / 2.98 ( 1086) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.194 Fit side-chains REVERT: A 29 LYS cc_start: 0.6209 (tmtt) cc_final: 0.5588 (ttmt) REVERT: A 188 HIS cc_start: 0.8327 (m-70) cc_final: 0.8086 (m90) REVERT: A 257 LYS cc_start: 0.7780 (ptmm) cc_final: 0.7301 (tppt) REVERT: A 269 ASN cc_start: 0.8706 (m-40) cc_final: 0.8468 (m-40) REVERT: A 282 PRO cc_start: 0.7589 (Cg_endo) cc_final: 0.7340 (Cg_exo) REVERT: A 324 THR cc_start: 0.7294 (m) cc_final: 0.6858 (m) REVERT: A 331 ASN cc_start: 0.8076 (m110) cc_final: 0.7801 (m110) REVERT: B 58 ILE cc_start: 0.7645 (pt) cc_final: 0.7365 (pp) REVERT: B 153 ASP cc_start: 0.7541 (m-30) cc_final: 0.6963 (p0) REVERT: B 214 ARG cc_start: 0.7935 (ttt-90) cc_final: 0.7540 (tmt170) REVERT: B 237 ASN cc_start: 0.8312 (t0) cc_final: 0.8037 (t0) REVERT: B 316 SER cc_start: 0.7517 (p) cc_final: 0.7261 (p) REVERT: B 322 ASP cc_start: 0.8370 (t70) cc_final: 0.8164 (t70) REVERT: G 38 MET cc_start: 0.7476 (ttm) cc_final: 0.7275 (tpt) outliers start: 0 outliers final: 1 residues processed: 145 average time/residue: 0.3753 time to fit residues: 57.8872 Evaluate side-chains 108 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 107 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 198 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.1980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.0870 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS A 256 ASN A 331 ASN B 175 GLN R 100 ASN R 126 HIS R 409 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.178835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.131306 restraints weight = 8451.390| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 3.59 r_work: 0.3417 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6120 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7379 Z= 0.108 Angle : 0.522 8.842 10028 Z= 0.262 Chirality : 0.039 0.148 1172 Planarity : 0.003 0.029 1192 Dihedral : 7.836 58.063 1703 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.35 % Allowed : 10.80 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.17 (0.30), residues: 854 helix: 3.57 (0.26), residues: 380 sheet: 1.03 (0.41), residues: 153 loop : -1.13 (0.34), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 15 TYR 0.016 0.001 TYR A 296 PHE 0.009 0.001 PHE B 222 TRP 0.005 0.001 TRP B 297 HIS 0.003 0.001 HIS R 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 ( 7377) covalent geometry : angle 0.52189 / 0.26 (10024) SS BOND : bond 0.00756 / 0.40 ( 2) SS BOND : angle 0.31525 / 0.15 ( 4) hydrogen bonds : bond 0.03459 / 2.33 ( 371) hydrogen bonds : angle 3.75627 / 2.61 ( 1086) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 0.165 Fit side-chains REVERT: A 29 LYS cc_start: 0.5898 (tmtt) cc_final: 0.5353 (ttmt) REVERT: A 242 ARG cc_start: 0.7503 (ptm160) cc_final: 0.7303 (ptp-110) REVERT: A 257 LYS cc_start: 0.7951 (ptmm) cc_final: 0.7416 (tppt) REVERT: A 308 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7758 (mt-10) REVERT: A 324 THR cc_start: 0.7264 (m) cc_final: 0.7036 (m) REVERT: A 331 ASN cc_start: 0.7935 (m-40) cc_final: 0.7644 (m110) REVERT: B 58 ILE cc_start: 0.7735 (pt) cc_final: 0.7479 (pp) REVERT: B 153 ASP cc_start: 0.7305 (m-30) cc_final: 0.6824 (p0) REVERT: B 214 ARG cc_start: 0.8075 (ttt-90) cc_final: 0.7588 (tmt170) REVERT: B 221 THR cc_start: 0.8256 (t) cc_final: 0.8033 (m) REVERT: B 237 ASN cc_start: 0.8395 (t0) cc_final: 0.8086 (t0) REVERT: B 322 ASP cc_start: 0.8650 (t70) cc_final: 0.8296 (t0) REVERT: B 325 MET cc_start: 0.7986 (tpp) cc_final: 0.7685 (tpp) REVERT: G 32 LYS cc_start: 0.8384 (tppt) cc_final: 0.8142 (tppt) REVERT: G 42 GLU cc_start: 0.8543 (tm-30) cc_final: 0.8340 (tt0) outliers start: 10 outliers final: 5 residues processed: 110 average time/residue: 0.3637 time to fit residues: 42.5672 Evaluate side-chains 105 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 100 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain R residue 189 ILE Chi-restraints excluded: chain R residue 353 THR Chi-restraints excluded: chain R residue 407 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 62 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 5 optimal weight: 0.0670 chunk 4 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 30 optimal weight: 0.0270 chunk 77 optimal weight: 4.9990 overall best weight: 0.5376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 256 ASN B 75 GLN B 175 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.179156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.132448 restraints weight = 8344.253| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 3.60 r_work: 0.3458 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6030 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7379 Z= 0.095 Angle : 0.486 10.910 10028 Z= 0.246 Chirality : 0.038 0.144 1172 Planarity : 0.003 0.042 1192 Dihedral : 7.278 59.884 1701 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.89 % Allowed : 12.69 % Favored : 85.43 % 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: 1.98 (0.30), residues: 854 helix: 3.43 (0.26), residues: 382 sheet: 0.63 (0.42), residues: 146 loop : -1.08 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 24 TYR 0.011 0.001 TYR A 296 PHE 0.010 0.001 PHE B 222 TRP 0.010 0.001 TRP B 297 HIS 0.004 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.09 ( 7377) covalent geometry : angle 0.48643 / 0.25 (10024) SS BOND : bond 0.00686 / 0.36 ( 2) SS BOND : angle 0.36644 / 0.19 ( 4) hydrogen bonds : bond 0.03196 / 2.16 ( 371) hydrogen bonds : angle 3.58739 / 2.50 ( 1086) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 0.206 Fit side-chains REVERT: A 29 LYS cc_start: 0.5968 (tmtt) cc_final: 0.5446 (ttmt) REVERT: A 257 LYS cc_start: 0.7917 (ptmm) cc_final: 0.7433 (tppt) REVERT: A 308 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7748 (mt-10) REVERT: B 37 ILE cc_start: 0.7689 (mm) cc_final: 0.7202 (tt) REVERT: B 153 ASP cc_start: 0.7189 (m-30) cc_final: 0.6629 (p0) REVERT: B 214 ARG cc_start: 0.8068 (ttt-90) cc_final: 0.7646 (tmt170) REVERT: B 220 GLN cc_start: 0.5430 (mt0) cc_final: 0.5197 (mt0) REVERT: B 221 THR cc_start: 0.8177 (t) cc_final: 0.7949 (m) REVERT: B 237 ASN cc_start: 0.8402 (t0) cc_final: 0.8120 (t0) REVERT: B 322 ASP cc_start: 0.8860 (t70) cc_final: 0.8518 (t70) outliers start: 14 outliers final: 7 residues processed: 114 average time/residue: 0.3366 time to fit residues: 41.1312 Evaluate side-chains 106 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 99 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain R residue 189 ILE Chi-restraints excluded: chain R residue 349 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 54 optimal weight: 10.0000 chunk 34 optimal weight: 0.2980 chunk 46 optimal weight: 5.9990 chunk 76 optimal weight: 7.9990 chunk 55 optimal weight: 7.9990 chunk 12 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 53 optimal weight: 0.0050 chunk 14 optimal weight: 6.9990 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 256 ASN A 306 GLN B 75 GLN B 175 GLN R 100 ASN R 409 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.178533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.131427 restraints weight = 8463.974| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 3.63 r_work: 0.3446 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6004 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7379 Z= 0.095 Angle : 0.488 8.489 10028 Z= 0.248 Chirality : 0.038 0.157 1172 Planarity : 0.003 0.036 1192 Dihedral : 6.977 56.925 1701 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.56 % Allowed : 13.77 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.91 (0.30), residues: 854 helix: 3.34 (0.26), residues: 382 sheet: 0.61 (0.41), residues: 152 loop : -1.10 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 24 TYR 0.009 0.001 TYR A 296 PHE 0.012 0.001 PHE B 222 TRP 0.011 0.001 TRP B 169 HIS 0.003 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.09 ( 7377) covalent geometry : angle 0.48725 / 0.25 (10024) SS BOND : bond 0.00975 / 0.51 ( 2) SS BOND : angle 1.32236 / 0.62 ( 4) hydrogen bonds : bond 0.03113 / 2.12 ( 371) hydrogen bonds : angle 3.59432 / 2.51 ( 1086) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.229 Fit side-chains REVERT: A 29 LYS cc_start: 0.5991 (tmtt) cc_final: 0.5486 (ttmt) REVERT: A 242 ARG cc_start: 0.7540 (ptm160) cc_final: 0.7270 (ptp-110) REVERT: A 257 LYS cc_start: 0.7872 (ptmm) cc_final: 0.7361 (tppt) REVERT: A 308 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7734 (mt-10) REVERT: B 37 ILE cc_start: 0.7557 (mm) cc_final: 0.7204 (tt) REVERT: B 153 ASP cc_start: 0.7205 (m-30) cc_final: 0.6628 (p0) REVERT: B 220 GLN cc_start: 0.5382 (mt0) cc_final: 0.5127 (mt0) REVERT: B 221 THR cc_start: 0.8195 (t) cc_final: 0.7915 (m) REVERT: B 237 ASN cc_start: 0.8401 (t0) cc_final: 0.8117 (t0) REVERT: B 322 ASP cc_start: 0.8812 (t70) cc_final: 0.8463 (t70) REVERT: B 325 MET cc_start: 0.7878 (tpp) cc_final: 0.7349 (tpp) REVERT: G 32 LYS cc_start: 0.8386 (tppt) cc_final: 0.8148 (tppt) outliers start: 19 outliers final: 7 residues processed: 116 average time/residue: 0.3547 time to fit residues: 43.9409 Evaluate side-chains 107 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 100 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain R residue 189 ILE Chi-restraints excluded: chain R residue 349 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 73 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 chunk 29 optimal weight: 0.3980 chunk 42 optimal weight: 5.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 256 ASN A 306 GLN B 62 HIS B 175 GLN R 100 ASN R 392 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.169004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.120488 restraints weight = 8575.831| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 3.63 r_work: 0.3312 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6105 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7379 Z= 0.148 Angle : 0.562 13.428 10028 Z= 0.282 Chirality : 0.041 0.168 1172 Planarity : 0.003 0.038 1192 Dihedral : 7.108 54.114 1701 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.37 % Allowed : 13.63 % Favored : 83.00 % 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: 1.75 (0.30), residues: 854 helix: 3.09 (0.26), residues: 388 sheet: 0.56 (0.39), residues: 169 loop : -1.21 (0.35), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 24 TYR 0.016 0.001 TYR R 195 PHE 0.013 0.001 PHE R 354 TRP 0.023 0.002 TRP B 297 HIS 0.004 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 ( 7377) covalent geometry : angle 0.56135 / 0.28 (10024) SS BOND : bond 0.01433 / 0.75 ( 2) SS BOND : angle 1.13517 / 0.54 ( 4) hydrogen bonds : bond 0.04008 / 2.71 ( 371) hydrogen bonds : angle 3.74668 / 2.62 ( 1086) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 0.183 Fit side-chains REVERT: A 29 LYS cc_start: 0.5940 (tmtt) cc_final: 0.5433 (ttmt) REVERT: A 230 TYR cc_start: 0.5384 (m-80) cc_final: 0.5170 (m-10) REVERT: A 242 ARG cc_start: 0.7519 (ptm160) cc_final: 0.7294 (ptp-110) REVERT: A 257 LYS cc_start: 0.8052 (ptmm) cc_final: 0.7553 (tppt) REVERT: B 37 ILE cc_start: 0.7624 (mm) cc_final: 0.7230 (tt) REVERT: B 153 ASP cc_start: 0.7310 (m-30) cc_final: 0.6783 (p0) REVERT: B 220 GLN cc_start: 0.5492 (mt0) cc_final: 0.5183 (mt0) REVERT: B 221 THR cc_start: 0.8155 (t) cc_final: 0.7849 (m) REVERT: B 262 MET cc_start: 0.7662 (pmm) cc_final: 0.7336 (ppp) REVERT: B 322 ASP cc_start: 0.8887 (t70) cc_final: 0.8546 (t70) REVERT: G 32 LYS cc_start: 0.8436 (tppt) cc_final: 0.8191 (tppt) REVERT: R 356 LEU cc_start: 0.7828 (tp) cc_final: 0.7624 (tm) REVERT: R 407 PHE cc_start: 0.5307 (OUTLIER) cc_final: 0.5049 (t80) outliers start: 25 outliers final: 14 residues processed: 121 average time/residue: 0.3410 time to fit residues: 44.1735 Evaluate side-chains 119 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain R residue 84 MET Chi-restraints excluded: chain R residue 188 THR Chi-restraints excluded: chain R residue 189 ILE Chi-restraints excluded: chain R residue 349 ILE Chi-restraints excluded: chain R residue 353 THR Chi-restraints excluded: chain R residue 407 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 61 optimal weight: 0.9990 chunk 44 optimal weight: 7.9990 chunk 81 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 45 optimal weight: 0.9990 chunk 36 optimal weight: 6.9990 chunk 48 optimal weight: 0.6980 chunk 67 optimal weight: 0.0010 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 256 ASN A 306 GLN B 175 GLN R 100 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.171818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.123168 restraints weight = 8519.118| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 3.62 r_work: 0.3349 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6062 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7379 Z= 0.106 Angle : 0.532 10.911 10028 Z= 0.265 Chirality : 0.039 0.159 1172 Planarity : 0.003 0.037 1192 Dihedral : 6.788 57.152 1701 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.56 % Allowed : 16.19 % Favored : 81.24 % 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: 1.78 (0.30), residues: 854 helix: 3.11 (0.26), residues: 387 sheet: 0.47 (0.41), residues: 158 loop : -1.05 (0.34), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 24 TYR 0.010 0.001 TYR R 195 PHE 0.017 0.001 PHE B 292 TRP 0.011 0.001 TRP B 169 HIS 0.002 0.000 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 ( 7377) covalent geometry : angle 0.53156 / 0.27 (10024) SS BOND : bond 0.00953 / 0.50 ( 2) SS BOND : angle 0.92090 / 0.43 ( 4) hydrogen bonds : bond 0.03442 / 2.34 ( 371) hydrogen bonds : angle 3.60952 / 2.53 ( 1086) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.197 Fit side-chains REVERT: A 29 LYS cc_start: 0.5804 (tmtt) cc_final: 0.5308 (ttmt) REVERT: A 242 ARG cc_start: 0.7532 (ptm160) cc_final: 0.7292 (ptp-110) REVERT: A 257 LYS cc_start: 0.8054 (ptmm) cc_final: 0.7509 (tppt) REVERT: A 308 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7747 (mt-10) REVERT: B 37 ILE cc_start: 0.7616 (mm) cc_final: 0.7216 (tt) REVERT: B 153 ASP cc_start: 0.7226 (m-30) cc_final: 0.6703 (p0) REVERT: B 221 THR cc_start: 0.8134 (t) cc_final: 0.7819 (m) REVERT: B 322 ASP cc_start: 0.8838 (t70) cc_final: 0.8473 (t70) REVERT: B 325 MET cc_start: 0.7904 (tpp) cc_final: 0.7523 (tpp) REVERT: G 32 LYS cc_start: 0.8447 (tppt) cc_final: 0.8225 (tppt) outliers start: 19 outliers final: 14 residues processed: 109 average time/residue: 0.3670 time to fit residues: 42.7640 Evaluate side-chains 113 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 188 THR Chi-restraints excluded: chain R residue 189 ILE Chi-restraints excluded: chain R residue 349 ILE Chi-restraints excluded: chain R residue 353 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 82 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 52 optimal weight: 9.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 256 ASN A 306 GLN B 175 GLN R 100 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.170132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.121516 restraints weight = 8528.732| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 3.58 r_work: 0.3325 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6096 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7379 Z= 0.124 Angle : 0.539 10.761 10028 Z= 0.270 Chirality : 0.039 0.163 1172 Planarity : 0.003 0.036 1192 Dihedral : 6.801 59.351 1701 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.64 % Allowed : 14.98 % Favored : 81.38 % 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: 1.69 (0.30), residues: 854 helix: 3.05 (0.26), residues: 392 sheet: 0.43 (0.41), residues: 158 loop : -1.19 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 24 TYR 0.016 0.001 TYR A 230 PHE 0.016 0.001 PHE B 292 TRP 0.011 0.001 TRP B 297 HIS 0.002 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.12 ( 7377) covalent geometry : angle 0.53924 / 0.27 (10024) SS BOND : bond 0.01138 / 0.60 ( 2) SS BOND : angle 0.90060 / 0.42 ( 4) hydrogen bonds : bond 0.03639 / 2.45 ( 371) hydrogen bonds : angle 3.62559 / 2.52 ( 1086) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 106 time to evaluate : 0.270 Fit side-chains REVERT: A 29 LYS cc_start: 0.5650 (tmtt) cc_final: 0.5190 (ttmt) REVERT: A 242 ARG cc_start: 0.7548 (ptm160) cc_final: 0.7294 (ptp-110) REVERT: A 257 LYS cc_start: 0.8077 (ptmm) cc_final: 0.7571 (tppt) REVERT: A 308 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7732 (mt-10) REVERT: A 318 GLU cc_start: 0.5828 (OUTLIER) cc_final: 0.5463 (mm-30) REVERT: B 153 ASP cc_start: 0.7355 (m-30) cc_final: 0.6807 (p0) REVERT: B 219 ARG cc_start: 0.6433 (OUTLIER) cc_final: 0.6176 (mmp80) REVERT: B 221 THR cc_start: 0.8136 (t) cc_final: 0.7811 (m) REVERT: B 274 THR cc_start: 0.8355 (m) cc_final: 0.8052 (p) REVERT: B 322 ASP cc_start: 0.8910 (t70) cc_final: 0.8551 (t70) REVERT: R 356 LEU cc_start: 0.7764 (tp) cc_final: 0.7529 (tm) outliers start: 27 outliers final: 16 residues processed: 121 average time/residue: 0.3801 time to fit residues: 49.1702 Evaluate side-chains 120 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 84 MET Chi-restraints excluded: chain R residue 188 THR Chi-restraints excluded: chain R residue 189 ILE Chi-restraints excluded: chain R residue 349 ILE Chi-restraints excluded: chain R residue 353 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 4 optimal weight: 5.9990 chunk 83 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 24 optimal weight: 8.9990 chunk 36 optimal weight: 0.9980 chunk 67 optimal weight: 0.3980 chunk 18 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 41 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 256 ASN A 306 GLN B 175 GLN R 97 GLN R 100 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.167957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.119150 restraints weight = 8623.286| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 3.58 r_work: 0.3293 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6151 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7379 Z= 0.150 Angle : 0.575 10.609 10028 Z= 0.289 Chirality : 0.041 0.168 1172 Planarity : 0.003 0.037 1192 Dihedral : 6.846 55.129 1701 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 4.05 % Allowed : 16.06 % Favored : 79.89 % 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: 1.52 (0.30), residues: 854 helix: 2.91 (0.26), residues: 392 sheet: 0.53 (0.42), residues: 150 loop : -1.34 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 24 TYR 0.014 0.001 TYR R 195 PHE 0.017 0.001 PHE B 292 TRP 0.009 0.001 TRP B 169 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.15 ( 7377) covalent geometry : angle 0.57482 / 0.29 (10024) SS BOND : bond 0.01278 / 0.67 ( 2) SS BOND : angle 0.84778 / 0.40 ( 4) hydrogen bonds : bond 0.03928 / 2.65 ( 371) hydrogen bonds : angle 3.69866 / 2.58 ( 1086) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 98 time to evaluate : 0.196 Fit side-chains revert: symmetry clash REVERT: A 29 LYS cc_start: 0.5771 (tmtt) cc_final: 0.5317 (ttmt) REVERT: A 242 ARG cc_start: 0.7571 (ptm160) cc_final: 0.7335 (ptp-110) REVERT: A 257 LYS cc_start: 0.8148 (ptmm) cc_final: 0.7636 (tppt) REVERT: A 308 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7767 (mt-10) REVERT: A 318 GLU cc_start: 0.5808 (OUTLIER) cc_final: 0.5483 (mm-30) REVERT: B 153 ASP cc_start: 0.7415 (m-30) cc_final: 0.6854 (p0) REVERT: B 219 ARG cc_start: 0.6521 (OUTLIER) cc_final: 0.6251 (mmp80) REVERT: B 221 THR cc_start: 0.8157 (t) cc_final: 0.7824 (m) REVERT: B 262 MET cc_start: 0.7578 (pmm) cc_final: 0.7347 (ppp) REVERT: B 274 THR cc_start: 0.8351 (m) cc_final: 0.8046 (p) REVERT: B 322 ASP cc_start: 0.8876 (t70) cc_final: 0.8537 (t70) REVERT: R 356 LEU cc_start: 0.7781 (tp) cc_final: 0.7539 (tm) outliers start: 30 outliers final: 19 residues processed: 117 average time/residue: 0.4277 time to fit residues: 53.3074 Evaluate side-chains 117 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 188 THR Chi-restraints excluded: chain R residue 189 ILE Chi-restraints excluded: chain R residue 347 LEU Chi-restraints excluded: chain R residue 349 ILE Chi-restraints excluded: chain R residue 353 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 56 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 22 optimal weight: 0.4980 chunk 6 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 256 ASN A 306 GLN B 75 GLN B 175 GLN R 100 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.170449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.121800 restraints weight = 8454.303| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 3.60 r_work: 0.3333 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6104 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7379 Z= 0.111 Angle : 0.542 10.043 10028 Z= 0.273 Chirality : 0.039 0.159 1172 Planarity : 0.003 0.035 1192 Dihedral : 6.616 51.633 1701 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.78 % Allowed : 16.06 % Favored : 80.16 % 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: 1.57 (0.30), residues: 854 helix: 3.00 (0.26), residues: 392 sheet: 0.36 (0.41), residues: 156 loop : -1.31 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 15 TYR 0.010 0.001 TYR A 302 PHE 0.017 0.001 PHE B 292 TRP 0.013 0.001 TRP A 211 HIS 0.002 0.000 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 ( 7377) covalent geometry : angle 0.54192 / 0.27 (10024) SS BOND : bond 0.01010 / 0.53 ( 2) SS BOND : angle 0.75999 / 0.35 ( 4) hydrogen bonds : bond 0.03507 / 2.36 ( 371) hydrogen bonds : angle 3.58214 / 2.49 ( 1086) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 94 time to evaluate : 0.244 Fit side-chains REVERT: A 29 LYS cc_start: 0.5689 (tmtt) cc_final: 0.5223 (ttmt) REVERT: A 242 ARG cc_start: 0.7578 (ptm160) cc_final: 0.7340 (ptp-110) REVERT: A 254 CYS cc_start: 0.6641 (t) cc_final: 0.5949 (m) REVERT: A 257 LYS cc_start: 0.8137 (ptmm) cc_final: 0.7614 (tppt) REVERT: A 308 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7672 (mt-10) REVERT: B 153 ASP cc_start: 0.7404 (m-30) cc_final: 0.6938 (p0) REVERT: B 219 ARG cc_start: 0.6535 (OUTLIER) cc_final: 0.6284 (mmp80) REVERT: B 221 THR cc_start: 0.8141 (t) cc_final: 0.7805 (m) REVERT: B 262 MET cc_start: 0.7494 (pmm) cc_final: 0.7268 (ppp) REVERT: B 274 THR cc_start: 0.8348 (m) cc_final: 0.8057 (p) REVERT: B 322 ASP cc_start: 0.8894 (t70) cc_final: 0.8552 (t70) outliers start: 28 outliers final: 16 residues processed: 112 average time/residue: 0.4116 time to fit residues: 48.9872 Evaluate side-chains 106 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 189 ILE Chi-restraints excluded: chain R residue 347 LEU Chi-restraints excluded: chain R residue 349 ILE Chi-restraints excluded: chain R residue 353 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 2.9990 chunk 83 optimal weight: 0.3980 chunk 80 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 10 optimal weight: 0.0770 chunk 63 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 28 optimal weight: 0.0070 chunk 9 optimal weight: 4.9990 overall best weight: 1.4960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 256 ASN A 306 GLN B 75 GLN B 175 GLN R 100 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.166242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.117304 restraints weight = 8523.908| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 3.58 r_work: 0.3280 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6153 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7379 Z= 0.155 Angle : 0.625 12.730 10028 Z= 0.308 Chirality : 0.041 0.163 1172 Planarity : 0.003 0.034 1192 Dihedral : 6.809 48.185 1701 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.51 % Allowed : 16.73 % Favored : 79.76 % 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: 1.48 (0.30), residues: 854 helix: 2.86 (0.26), residues: 392 sheet: 0.37 (0.39), residues: 176 loop : -1.40 (0.35), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 15 TYR 0.014 0.001 TYR R 195 PHE 0.017 0.001 PHE B 292 TRP 0.010 0.001 TRP A 211 HIS 0.002 0.001 HIS B 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.15 ( 7377) covalent geometry : angle 0.62475 / 0.31 (10024) SS BOND : bond 0.01298 / 0.68 ( 2) SS BOND : angle 0.84090 / 0.40 ( 4) hydrogen bonds : bond 0.04014 / 2.72 ( 371) hydrogen bonds : angle 3.73619 / 2.61 ( 1086) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 98 time to evaluate : 0.239 Fit side-chains REVERT: A 29 LYS cc_start: 0.5805 (tmtt) cc_final: 0.5340 (ttmt) REVERT: A 242 ARG cc_start: 0.7596 (ptm160) cc_final: 0.7313 (ptp-110) REVERT: A 257 LYS cc_start: 0.8163 (ptmm) cc_final: 0.7629 (tppt) REVERT: A 308 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7499 (mp0) REVERT: B 96 ARG cc_start: 0.8012 (ptm160) cc_final: 0.7453 (ptp-170) REVERT: B 153 ASP cc_start: 0.7488 (m-30) cc_final: 0.6945 (p0) REVERT: B 262 MET cc_start: 0.7510 (pmm) cc_final: 0.7147 (pmm) REVERT: B 274 THR cc_start: 0.8341 (m) cc_final: 0.8050 (p) REVERT: B 322 ASP cc_start: 0.8881 (t70) cc_final: 0.8555 (t70) REVERT: R 356 LEU cc_start: 0.7779 (tp) cc_final: 0.7512 (tm) outliers start: 26 outliers final: 19 residues processed: 114 average time/residue: 0.3976 time to fit residues: 48.2715 Evaluate side-chains 114 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 100 ASN Chi-restraints excluded: chain R residue 188 THR Chi-restraints excluded: chain R residue 189 ILE Chi-restraints excluded: chain R residue 347 LEU Chi-restraints excluded: chain R residue 349 ILE Chi-restraints excluded: chain R residue 353 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 73 optimal weight: 0.0370 chunk 68 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 overall best weight: 1.1862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 256 ASN A 306 GLN B 75 GLN B 175 GLN R 100 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.166982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.118387 restraints weight = 8544.243| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 3.57 r_work: 0.3293 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6136 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7379 Z= 0.135 Angle : 0.592 11.703 10028 Z= 0.294 Chirality : 0.040 0.166 1172 Planarity : 0.003 0.032 1192 Dihedral : 6.756 47.821 1701 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.10 % Allowed : 17.27 % Favored : 79.62 % 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: 1.47 (0.30), residues: 854 helix: 2.87 (0.26), residues: 388 sheet: 0.29 (0.40), residues: 161 loop : -1.24 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 15 TYR 0.014 0.001 TYR A 302 PHE 0.017 0.001 PHE B 292 TRP 0.010 0.001 TRP A 211 HIS 0.002 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.13 ( 7377) covalent geometry : angle 0.59231 / 0.29 (10024) SS BOND : bond 0.01186 / 0.62 ( 2) SS BOND : angle 0.79651 / 0.38 ( 4) hydrogen bonds : bond 0.03819 / 2.57 ( 371) hydrogen bonds : angle 3.68228 / 2.57 ( 1086) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1954.64 seconds wall clock time: 34 minutes 9.13 seconds (2049.13 seconds total)