Starting phenix.real_space_refine on Wed Aug 5 12:08:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vko_65137/08_2026/9vko_65137.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vko_65137/08_2026/9vko_65137.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vko_65137/08_2026/9vko_65137.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vko_65137/08_2026/9vko_65137.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vko_65137/08_2026/9vko_65137.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vko_65137/08_2026/9vko_65137.map" } resolution = 3.07 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= 0.015 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 32 5.16 5 C 6136 2.51 5 N 1624 2.21 5 O 1776 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9568 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2392 Classifications: {'peptide': 295} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 287} Chain: "B" Number of atoms: 2392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2392 Classifications: {'peptide': 295} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 287} Chain: "C" Number of atoms: 2392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2392 Classifications: {'peptide': 295} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 287} Chain: "D" Number of atoms: 2392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2392 Classifications: {'peptide': 295} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 287} Time building chain proxies: 2.26, per 1000 atoms: 0.24 Number of scatterers: 9568 At special positions: 0 Unit cell: (109.431, 78.813, 132.111, 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 32 16.00 O 1776 8.00 N 1624 7.00 C 6136 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: 0.98 Conformation dependent library (CDL) restraints added in 350.3 milliseconds 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2288 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 0 sheets defined 86.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 89 through 103 Processing helix chain 'A' and resid 107 through 119 Processing helix chain 'A' and resid 121 through 135 removed outlier: 3.771A pdb=" N ARG A 135 " --> pdb=" O GLU A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 156 Processing helix chain 'A' and resid 158 through 168 removed outlier: 3.526A pdb=" N ILE A 166 " --> pdb=" O LEU A 162 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N CYS A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 180 Processing helix chain 'A' and resid 182 through 195 removed outlier: 3.569A pdb=" N LEU A 186 " --> pdb=" O LYS A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 211 Processing helix chain 'A' and resid 215 through 232 removed outlier: 4.028A pdb=" N LEU A 220 " --> pdb=" O ARG A 216 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP A 221 " --> pdb=" O LEU A 217 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 270 removed outlier: 4.171A pdb=" N TYR A 270 " --> pdb=" O THR A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 277 removed outlier: 3.559A pdb=" N ASN A 277 " --> pdb=" O THR A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 293 removed outlier: 3.667A pdb=" N TRP A 283 " --> pdb=" O GLU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 306 removed outlier: 3.559A pdb=" N ASP A 303 " --> pdb=" O SER A 299 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.135A pdb=" N LEU A 310 " --> pdb=" O LEU A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 329 Processing helix chain 'A' and resid 332 through 336 removed outlier: 3.821A pdb=" N PHE A 336 " --> pdb=" O SER A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 354 removed outlier: 3.660A pdb=" N SER A 351 " --> pdb=" O MET A 347 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET A 352 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 372 Processing helix chain 'B' and resid 89 through 103 removed outlier: 3.619A pdb=" N VAL B 103 " --> pdb=" O LYS B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 119 Processing helix chain 'B' and resid 121 through 135 Processing helix chain 'B' and resid 139 through 156 Processing helix chain 'B' and resid 158 through 168 Processing helix chain 'B' and resid 168 through 180 Processing helix chain 'B' and resid 182 through 195 removed outlier: 3.570A pdb=" N LEU B 186 " --> pdb=" O LYS B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 212 Processing helix chain 'B' and resid 215 through 232 removed outlier: 3.974A pdb=" N LEU B 220 " --> pdb=" O ARG B 216 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASP B 221 " --> pdb=" O LEU B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 269 Processing helix chain 'B' and resid 270 through 277 removed outlier: 3.758A pdb=" N LYS B 274 " --> pdb=" O TYR B 270 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA B 275 " --> pdb=" O SER B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 291 removed outlier: 3.797A pdb=" N TRP B 283 " --> pdb=" O GLU B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 295 No H-bonds generated for 'chain 'B' and resid 293 through 295' Processing helix chain 'B' and resid 296 through 306 removed outlier: 3.579A pdb=" N ILE B 304 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY B 306 " --> pdb=" O ALA B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 331 removed outlier: 3.533A pdb=" N ILE B 331 " --> pdb=" O VAL B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 336 removed outlier: 3.783A pdb=" N LEU B 335 " --> pdb=" O PRO B 332 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHE B 336 " --> pdb=" O SER B 333 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 332 through 336' Processing helix chain 'B' and resid 340 through 372 Processing helix chain 'C' and resid 89 through 103 Processing helix chain 'C' and resid 107 through 119 Processing helix chain 'C' and resid 121 through 135 removed outlier: 3.781A pdb=" N ARG C 135 " --> pdb=" O GLU C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 156 Processing helix chain 'C' and resid 158 through 168 removed outlier: 3.526A pdb=" N ILE C 166 " --> pdb=" O LEU C 162 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N CYS C 168 " --> pdb=" O ALA C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 180 Processing helix chain 'C' and resid 182 through 195 removed outlier: 3.598A pdb=" N LEU C 186 " --> pdb=" O LYS C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 211 Processing helix chain 'C' and resid 215 through 232 removed outlier: 4.029A pdb=" N LEU C 220 " --> pdb=" O ARG C 216 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASP C 221 " --> pdb=" O LEU C 217 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP C 232 " --> pdb=" O LEU C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 270 removed outlier: 4.165A pdb=" N TYR C 270 " --> pdb=" O THR C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 277 removed outlier: 3.553A pdb=" N ASN C 277 " --> pdb=" O THR C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 293 removed outlier: 3.658A pdb=" N TRP C 283 " --> pdb=" O GLU C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 306 removed outlier: 3.583A pdb=" N ASP C 303 " --> pdb=" O SER C 299 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 312 removed outlier: 4.181A pdb=" N LEU C 310 " --> pdb=" O LEU C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 329 Processing helix chain 'C' and resid 332 through 336 removed outlier: 3.794A pdb=" N PHE C 336 " --> pdb=" O SER C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 354 removed outlier: 3.692A pdb=" N SER C 351 " --> pdb=" O MET C 347 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N MET C 352 " --> pdb=" O ALA C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 372 removed outlier: 3.617A pdb=" N SER C 372 " --> pdb=" O ILE C 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 103 removed outlier: 3.572A pdb=" N VAL D 103 " --> pdb=" O LYS D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 119 Processing helix chain 'D' and resid 121 through 135 Processing helix chain 'D' and resid 139 through 156 Processing helix chain 'D' and resid 158 through 168 Processing helix chain 'D' and resid 168 through 180 Processing helix chain 'D' and resid 182 through 195 removed outlier: 3.554A pdb=" N LEU D 186 " --> pdb=" O LYS D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 212 Processing helix chain 'D' and resid 215 through 232 removed outlier: 3.966A pdb=" N LEU D 220 " --> pdb=" O ARG D 216 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASP D 221 " --> pdb=" O LEU D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 269 Processing helix chain 'D' and resid 270 through 277 removed outlier: 3.769A pdb=" N LYS D 274 " --> pdb=" O TYR D 270 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA D 275 " --> pdb=" O SER D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 291 removed outlier: 3.799A pdb=" N TRP D 283 " --> pdb=" O GLU D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 295 No H-bonds generated for 'chain 'D' and resid 293 through 295' Processing helix chain 'D' and resid 296 through 306 removed outlier: 3.551A pdb=" N ILE D 304 " --> pdb=" O LEU D 300 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY D 306 " --> pdb=" O ALA D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 331 removed outlier: 3.525A pdb=" N ILE D 331 " --> pdb=" O VAL D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 336 removed outlier: 3.781A pdb=" N LEU D 335 " --> pdb=" O PRO D 332 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE D 336 " --> pdb=" O SER D 333 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 332 through 336' Processing helix chain 'D' and resid 340 through 372 691 hydrogen bonds defined for protein. 2055 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: 1.24 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3110 1.34 - 1.46: 1080 1.46 - 1.57: 5490 1.57 - 1.69: 0 1.69 - 1.81: 52 Bond restraints: 9732 Sorted by residual: bond pdb=" N TYR C 211 " pdb=" CA TYR C 211 " ideal model delta sigma weight residual 1.460 1.490 -0.030 1.22e-02 6.72e+03 6.08e+00 bond pdb=" N TYR A 211 " pdb=" CA TYR A 211 " ideal model delta sigma weight residual 1.460 1.489 -0.029 1.22e-02 6.72e+03 5.70e+00 bond pdb=" N SER A 189 " pdb=" CA SER A 189 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.60e+00 bond pdb=" N SER C 189 " pdb=" CA SER C 189 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.21e-02 6.83e+03 5.39e+00 bond pdb=" N ARG A 187 " pdb=" CA ARG A 187 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.21e-02 6.83e+03 5.33e+00 ... (remaining 9727 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 12860 1.62 - 3.25: 216 3.25 - 4.87: 32 4.87 - 6.50: 7 6.50 - 8.12: 5 Bond angle restraints: 13120 Sorted by residual: angle pdb=" CB LYS C 99 " pdb=" CG LYS C 99 " pdb=" CD LYS C 99 " ideal model delta sigma weight residual 111.30 118.29 -6.99 2.30e+00 1.89e-01 9.25e+00 angle pdb=" N TYR A 190 " pdb=" CA TYR A 190 " pdb=" CB TYR A 190 " ideal model delta sigma weight residual 110.01 114.40 -4.39 1.45e+00 4.76e-01 9.15e+00 angle pdb=" CB LYS A 99 " pdb=" CG LYS A 99 " pdb=" CD LYS A 99 " ideal model delta sigma weight residual 111.30 118.19 -6.89 2.30e+00 1.89e-01 8.98e+00 angle pdb=" N TYR C 190 " pdb=" CA TYR C 190 " pdb=" CB TYR C 190 " ideal model delta sigma weight residual 110.01 114.34 -4.33 1.45e+00 4.76e-01 8.93e+00 angle pdb=" N TYR C 190 " pdb=" CA TYR C 190 " pdb=" C TYR C 190 " ideal model delta sigma weight residual 111.07 108.00 3.07 1.07e+00 8.73e-01 8.23e+00 ... (remaining 13115 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.52: 5271 16.52 - 33.03: 516 33.03 - 49.55: 127 49.55 - 66.07: 65 66.07 - 82.59: 13 Dihedral angle restraints: 5992 sinusoidal: 2492 harmonic: 3500 Sorted by residual: dihedral pdb=" N ASP D 260 " pdb=" CA ASP D 260 " pdb=" CB ASP D 260 " pdb=" CG ASP D 260 " ideal model delta sinusoidal sigma weight residual 60.00 119.66 -59.66 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CB MET D 255 " pdb=" CG MET D 255 " pdb=" SD MET D 255 " pdb=" CE MET D 255 " ideal model delta sinusoidal sigma weight residual -60.00 -0.61 -59.39 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N ASP B 260 " pdb=" CA ASP B 260 " pdb=" CB ASP B 260 " pdb=" CG ASP B 260 " ideal model delta sinusoidal sigma weight residual 60.00 119.37 -59.37 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 5989 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1054 0.032 - 0.065: 358 0.065 - 0.097: 71 0.097 - 0.130: 25 0.130 - 0.162: 4 Chirality restraints: 1512 Sorted by residual: chirality pdb=" CA ASP C 232 " pdb=" N ASP C 232 " pdb=" C ASP C 232 " pdb=" CB ASP C 232 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.59e-01 chirality pdb=" CA ASP A 232 " pdb=" N ASP A 232 " pdb=" C ASP A 232 " pdb=" CB ASP A 232 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.52e-01 chirality pdb=" CG LEU B 86 " pdb=" CB LEU B 86 " pdb=" CD1 LEU B 86 " pdb=" CD2 LEU B 86 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.95e-01 ... (remaining 1509 not shown) Planarity restraints: 1652 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 232 " -0.013 2.00e-02 2.50e+03 2.55e-02 6.50e+00 pdb=" C ASP C 232 " 0.044 2.00e-02 2.50e+03 pdb=" O ASP C 232 " -0.017 2.00e-02 2.50e+03 pdb=" N ALA C 233 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 232 " 0.013 2.00e-02 2.50e+03 2.52e-02 6.36e+00 pdb=" C ASP A 232 " -0.044 2.00e-02 2.50e+03 pdb=" O ASP A 232 " 0.016 2.00e-02 2.50e+03 pdb=" N ALA A 233 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 191 " 0.226 9.50e-02 1.11e+02 1.02e-01 6.33e+00 pdb=" NE ARG C 191 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG C 191 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG C 191 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG C 191 " 0.008 2.00e-02 2.50e+03 ... (remaining 1649 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1801 2.77 - 3.30: 9177 3.30 - 3.83: 15521 3.83 - 4.37: 17914 4.37 - 4.90: 31098 Nonbonded interactions: 75511 Sorted by model distance: nonbonded pdb=" O VAL B 153 " pdb=" OG1 THR B 157 " model vdw 2.234 3.040 nonbonded pdb=" O VAL D 153 " pdb=" OG1 THR D 157 " model vdw 2.234 3.040 nonbonded pdb=" OE1 GLU A 131 " pdb=" NH2 ARG A 134 " model vdw 2.250 3.120 nonbonded pdb=" OD1 ASP C 260 " pdb=" N LEU C 261 " model vdw 2.265 3.120 nonbonded pdb=" OD1 ASP A 260 " pdb=" N LEU A 261 " model vdw 2.265 3.120 ... (remaining 75506 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 5.890 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: 0.330 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.400 Find NCS groups from input model: 0.140 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9732 Z= 0.201 Angle : 0.545 8.122 13120 Z= 0.304 Chirality : 0.035 0.162 1512 Planarity : 0.006 0.102 1652 Dihedral : 15.559 82.585 3704 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.42 % Allowed : 14.34 % Favored : 84.25 % 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: 1.88 (0.25), residues: 1172 helix: 1.61 (0.17), residues: 946 sheet: None (None), residues: 0 loop : -0.12 (0.39), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 116 TYR 0.013 0.002 TYR C 204 PHE 0.023 0.002 PHE D 263 TRP 0.006 0.001 TRP C 207 HIS 0.002 0.001 HIS B 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.20 ( 9732) covalent geometry : angle 0.54481 / 0.30 (13120) hydrogen bonds : bond 0.18417 / 12.09 ( 691) hydrogen bonds : angle 5.89575 / 4.29 ( 2055) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 0.325 Fit side-chains REVERT: B 235 ASP cc_start: 0.8232 (m-30) cc_final: 0.7998 (m-30) REVERT: D 321 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7806 (mm) outliers start: 15 outliers final: 11 residues processed: 119 average time/residue: 0.0781 time to fit residues: 13.6044 Evaluate side-chains 109 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain B residue 82 PHE Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain D residue 321 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 152 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.206022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.149586 restraints weight = 10912.379| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 2.81 r_work: 0.3408 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9732 Z= 0.130 Angle : 0.453 6.448 13120 Z= 0.239 Chirality : 0.033 0.128 1512 Planarity : 0.003 0.028 1652 Dihedral : 5.670 59.657 1316 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 3.21 % Allowed : 12.08 % Favored : 84.72 % 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: 2.71 (0.25), residues: 1172 helix: 2.17 (0.17), residues: 980 sheet: None (None), residues: 0 loop : -0.10 (0.44), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 116 TYR 0.011 0.001 TYR A 204 PHE 0.019 0.001 PHE D 263 TRP 0.008 0.001 TRP D 341 HIS 0.002 0.001 HIS A 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 ( 9732) covalent geometry : angle 0.45310 / 0.24 (13120) hydrogen bonds : bond 0.05378 / 3.62 ( 691) hydrogen bonds : angle 4.01428 / 2.92 ( 2055) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 103 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 317 HIS cc_start: 0.7647 (OUTLIER) cc_final: 0.7107 (m90) REVERT: B 321 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7804 (mm) REVERT: D 321 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7758 (mm) outliers start: 34 outliers final: 20 residues processed: 132 average time/residue: 0.0735 time to fit residues: 14.5897 Evaluate side-chains 121 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 98 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain B residue 82 PHE Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 82 PHE Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 321 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 67 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 chunk 62 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 92 optimal weight: 10.0000 chunk 111 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.206618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.151968 restraints weight = 10964.552| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 2.88 r_work: 0.3398 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9732 Z= 0.113 Angle : 0.418 6.156 13120 Z= 0.217 Chirality : 0.032 0.128 1512 Planarity : 0.003 0.033 1652 Dihedral : 5.375 59.994 1310 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 3.02 % Allowed : 12.08 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.95 (0.25), residues: 1172 helix: 2.34 (0.17), residues: 978 sheet: None (None), residues: 0 loop : -0.03 (0.43), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 116 TYR 0.010 0.001 TYR A 204 PHE 0.019 0.001 PHE D 263 TRP 0.006 0.001 TRP D 341 HIS 0.002 0.000 HIS A 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 ( 9732) covalent geometry : angle 0.41844 / 0.22 (13120) hydrogen bonds : bond 0.04410 / 2.99 ( 691) hydrogen bonds : angle 3.74543 / 2.73 ( 2055) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 108 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 260 ASP cc_start: 0.8394 (OUTLIER) cc_final: 0.7884 (p0) REVERT: B 317 HIS cc_start: 0.7664 (OUTLIER) cc_final: 0.7121 (m90) REVERT: B 321 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7773 (mm) REVERT: C 260 ASP cc_start: 0.8359 (OUTLIER) cc_final: 0.7803 (p0) outliers start: 32 outliers final: 18 residues processed: 135 average time/residue: 0.0708 time to fit residues: 14.6115 Evaluate side-chains 121 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain B residue 82 PHE Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain C residue 298 ASP Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 82 PHE Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain D residue 305 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 10 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 chunk 109 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 102 optimal weight: 0.0270 chunk 30 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 overall best weight: 1.5844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.203510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.149831 restraints weight = 11085.852| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 3.10 r_work: 0.3330 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9732 Z= 0.158 Angle : 0.474 7.101 13120 Z= 0.243 Chirality : 0.034 0.126 1512 Planarity : 0.003 0.029 1652 Dihedral : 4.846 57.752 1302 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.58 % Allowed : 12.17 % Favored : 84.25 % 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: 2.75 (0.25), residues: 1172 helix: 2.19 (0.17), residues: 978 sheet: None (None), residues: 0 loop : -0.06 (0.44), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 116 TYR 0.013 0.001 TYR C 204 PHE 0.022 0.002 PHE D 263 TRP 0.005 0.001 TRP A 207 HIS 0.003 0.001 HIS A 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 ( 9732) covalent geometry : angle 0.47408 / 0.24 (13120) hydrogen bonds : bond 0.04905 / 3.33 ( 691) hydrogen bonds : angle 3.87268 / 2.82 ( 2055) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 104 time to evaluate : 0.233 Fit side-chains REVERT: A 139 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6518 (pp20) REVERT: A 260 ASP cc_start: 0.8442 (OUTLIER) cc_final: 0.8136 (p0) REVERT: B 317 HIS cc_start: 0.7664 (OUTLIER) cc_final: 0.7097 (m90) REVERT: B 321 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7802 (mm) REVERT: C 139 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6441 (pp20) REVERT: C 260 ASP cc_start: 0.8431 (OUTLIER) cc_final: 0.8100 (p0) REVERT: D 321 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7764 (mm) outliers start: 38 outliers final: 27 residues processed: 136 average time/residue: 0.0640 time to fit residues: 13.4277 Evaluate side-chains 130 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 96 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain B residue 82 PHE Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 298 ASP Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 82 PHE Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 361 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 3.9990 chunk 93 optimal weight: 20.0000 chunk 75 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 65 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 81 optimal weight: 0.0030 chunk 54 optimal weight: 0.9980 overall best weight: 0.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.206202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.151527 restraints weight = 11068.186| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 3.08 r_work: 0.3379 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9732 Z= 0.113 Angle : 0.411 5.819 13120 Z= 0.214 Chirality : 0.032 0.127 1512 Planarity : 0.003 0.031 1652 Dihedral : 4.722 58.370 1302 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 3.49 % Allowed : 12.74 % Favored : 83.77 % 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: 3.04 (0.25), residues: 1172 helix: 2.41 (0.17), residues: 978 sheet: None (None), residues: 0 loop : -0.07 (0.43), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 116 TYR 0.008 0.001 TYR C 204 PHE 0.018 0.001 PHE D 263 TRP 0.003 0.001 TRP A 283 HIS 0.002 0.000 HIS A 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 ( 9732) covalent geometry : angle 0.41082 / 0.21 (13120) hydrogen bonds : bond 0.04045 / 2.75 ( 691) hydrogen bonds : angle 3.62162 / 2.63 ( 2055) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 107 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: A 260 ASP cc_start: 0.8338 (OUTLIER) cc_final: 0.8063 (p0) REVERT: B 317 HIS cc_start: 0.7703 (OUTLIER) cc_final: 0.7109 (m90) REVERT: B 321 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7765 (mm) REVERT: C 139 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6432 (pp20) REVERT: C 260 ASP cc_start: 0.8363 (OUTLIER) cc_final: 0.7841 (p0) REVERT: D 116 ARG cc_start: 0.6617 (mtt90) cc_final: 0.6356 (mtt90) REVERT: D 321 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7718 (mm) outliers start: 37 outliers final: 23 residues processed: 138 average time/residue: 0.0682 time to fit residues: 14.1647 Evaluate side-chains 125 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 96 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain B residue 82 PHE Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 298 ASP Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 82 PHE Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 361 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 102 optimal weight: 3.9990 chunk 105 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 chunk 106 optimal weight: 0.8980 chunk 113 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 7 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.205545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.151224 restraints weight = 11029.336| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 3.06 r_work: 0.3368 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9732 Z= 0.122 Angle : 0.428 5.834 13120 Z= 0.222 Chirality : 0.033 0.130 1512 Planarity : 0.003 0.027 1652 Dihedral : 4.722 57.556 1302 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.96 % Allowed : 13.21 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.09 (0.25), residues: 1172 helix: 2.45 (0.17), residues: 978 sheet: None (None), residues: 0 loop : -0.10 (0.43), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 116 TYR 0.010 0.001 TYR C 204 PHE 0.019 0.001 PHE D 263 TRP 0.003 0.001 TRP A 283 HIS 0.002 0.000 HIS A 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 ( 9732) covalent geometry : angle 0.42848 / 0.22 (13120) hydrogen bonds : bond 0.04155 / 2.82 ( 691) hydrogen bonds : angle 3.61054 / 2.62 ( 2055) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 106 time to evaluate : 0.339 Fit side-chains REVERT: A 139 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6531 (pp20) REVERT: A 260 ASP cc_start: 0.8374 (OUTLIER) cc_final: 0.8088 (p0) REVERT: B 317 HIS cc_start: 0.7726 (OUTLIER) cc_final: 0.7129 (m90) REVERT: B 321 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7764 (mm) REVERT: C 139 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6441 (pp20) REVERT: C 260 ASP cc_start: 0.8381 (OUTLIER) cc_final: 0.7857 (p0) REVERT: D 321 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7731 (mm) outliers start: 42 outliers final: 25 residues processed: 140 average time/residue: 0.0632 time to fit residues: 13.4791 Evaluate side-chains 130 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 98 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain B residue 82 PHE Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 298 ASP Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain D residue 82 PHE Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 361 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 91 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 chunk 54 optimal weight: 0.4980 chunk 90 optimal weight: 0.9990 chunk 63 optimal weight: 9.9990 chunk 66 optimal weight: 0.9990 chunk 59 optimal weight: 0.2980 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.207008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.151202 restraints weight = 11037.505| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 3.04 r_work: 0.3420 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 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 0.032 9732 Z= 0.103 Angle : 0.401 5.928 13120 Z= 0.209 Chirality : 0.032 0.127 1512 Planarity : 0.003 0.027 1652 Dihedral : 4.554 58.092 1300 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 3.30 % Allowed : 13.77 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.27 (0.25), residues: 1172 helix: 2.57 (0.17), residues: 982 sheet: None (None), residues: 0 loop : -0.07 (0.43), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 116 TYR 0.007 0.001 TYR C 204 PHE 0.017 0.001 PHE D 263 TRP 0.003 0.001 TRP A 283 HIS 0.002 0.000 HIS A 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 ( 9732) covalent geometry : angle 0.40092 / 0.21 (13120) hydrogen bonds : bond 0.03725 / 2.53 ( 691) hydrogen bonds : angle 3.47617 / 2.52 ( 2055) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 102 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: A 139 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.6549 (pp20) REVERT: A 260 ASP cc_start: 0.8271 (OUTLIER) cc_final: 0.7780 (p0) REVERT: B 317 HIS cc_start: 0.7760 (OUTLIER) cc_final: 0.7174 (m90) REVERT: B 321 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7737 (mm) REVERT: C 139 GLU cc_start: 0.7141 (OUTLIER) cc_final: 0.6438 (pp20) REVERT: C 260 ASP cc_start: 0.8301 (OUTLIER) cc_final: 0.7780 (p0) REVERT: D 321 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7695 (mm) outliers start: 35 outliers final: 22 residues processed: 132 average time/residue: 0.0616 time to fit residues: 12.3027 Evaluate side-chains 126 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 97 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain B residue 82 PHE Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 298 ASP Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 354 ASP Chi-restraints excluded: chain D residue 82 PHE Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain D residue 321 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 102 optimal weight: 0.6980 chunk 48 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 110 optimal weight: 9.9990 chunk 114 optimal weight: 8.9990 chunk 100 optimal weight: 0.9980 chunk 84 optimal weight: 0.4980 chunk 11 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 57 optimal weight: 9.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.207090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.152466 restraints weight = 11050.969| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 2.96 r_work: 0.3409 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9732 Z= 0.102 Angle : 0.402 6.259 13120 Z= 0.209 Chirality : 0.032 0.151 1512 Planarity : 0.003 0.032 1652 Dihedral : 4.549 57.923 1300 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 3.40 % Allowed : 13.87 % Favored : 82.74 % 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: 3.38 (0.25), residues: 1172 helix: 2.64 (0.17), residues: 982 sheet: None (None), residues: 0 loop : -0.04 (0.44), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 116 TYR 0.008 0.001 TYR C 204 PHE 0.017 0.001 PHE B 263 TRP 0.003 0.001 TRP A 283 HIS 0.002 0.000 HIS A 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 ( 9732) covalent geometry : angle 0.40212 / 0.21 (13120) hydrogen bonds : bond 0.03677 / 2.50 ( 691) hydrogen bonds : angle 3.43402 / 2.49 ( 2055) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 103 time to evaluate : 0.258 Fit side-chains REVERT: A 139 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.6536 (pp20) REVERT: B 82 PHE cc_start: 0.4522 (OUTLIER) cc_final: 0.3123 (t80) REVERT: B 317 HIS cc_start: 0.7743 (OUTLIER) cc_final: 0.7162 (m90) REVERT: B 321 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7724 (mm) REVERT: C 139 GLU cc_start: 0.7168 (OUTLIER) cc_final: 0.6446 (pp20) REVERT: C 260 ASP cc_start: 0.8306 (OUTLIER) cc_final: 0.7791 (p0) REVERT: D 321 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7711 (mm) outliers start: 36 outliers final: 24 residues processed: 133 average time/residue: 0.0610 time to fit residues: 12.4063 Evaluate side-chains 125 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 94 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain B residue 82 PHE Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 298 ASP Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain D residue 82 PHE Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain D residue 321 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 75 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 chunk 54 optimal weight: 0.0010 chunk 2 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 chunk 60 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 81 optimal weight: 9.9990 chunk 110 optimal weight: 20.0000 chunk 33 optimal weight: 7.9990 overall best weight: 1.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.204213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.147203 restraints weight = 10988.191| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 3.25 r_work: 0.3372 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9732 Z= 0.154 Angle : 0.471 6.658 13120 Z= 0.244 Chirality : 0.034 0.168 1512 Planarity : 0.003 0.034 1652 Dihedral : 4.699 56.921 1300 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 3.40 % Allowed : 14.34 % Favored : 82.26 % 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: 3.14 (0.25), residues: 1172 helix: 2.48 (0.17), residues: 978 sheet: None (None), residues: 0 loop : -0.07 (0.43), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 116 TYR 0.010 0.001 TYR A 337 PHE 0.021 0.001 PHE D 263 TRP 0.004 0.001 TRP A 207 HIS 0.002 0.001 HIS A 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.15 ( 9732) covalent geometry : angle 0.47144 / 0.24 (13120) hydrogen bonds : bond 0.04468 / 3.04 ( 691) hydrogen bonds : angle 3.65146 / 2.65 ( 2055) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 96 time to evaluate : 0.225 Fit side-chains REVERT: A 139 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.6508 (pp20) REVERT: A 260 ASP cc_start: 0.8410 (OUTLIER) cc_final: 0.8111 (p0) REVERT: B 82 PHE cc_start: 0.4591 (OUTLIER) cc_final: 0.3173 (t80) REVERT: B 317 HIS cc_start: 0.7759 (OUTLIER) cc_final: 0.7154 (m90) REVERT: B 321 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7769 (mm) REVERT: C 139 GLU cc_start: 0.7158 (OUTLIER) cc_final: 0.6410 (pp20) REVERT: C 161 THR cc_start: 0.7592 (OUTLIER) cc_final: 0.7328 (p) REVERT: C 260 ASP cc_start: 0.8418 (OUTLIER) cc_final: 0.8086 (p0) REVERT: D 321 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7779 (mm) outliers start: 36 outliers final: 25 residues processed: 129 average time/residue: 0.0616 time to fit residues: 12.3228 Evaluate side-chains 127 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 93 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain B residue 82 PHE Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 298 ASP Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain D residue 82 PHE Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 361 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 15 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 89 optimal weight: 20.0000 chunk 115 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 110 optimal weight: 20.0000 chunk 43 optimal weight: 0.7980 chunk 31 optimal weight: 6.9990 chunk 81 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.205126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.148919 restraints weight = 10993.162| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 3.03 r_work: 0.3388 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9732 Z= 0.136 Angle : 0.464 7.655 13120 Z= 0.242 Chirality : 0.034 0.207 1512 Planarity : 0.003 0.033 1652 Dihedral : 4.723 57.488 1300 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 3.02 % Allowed : 14.62 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.11 (0.25), residues: 1172 helix: 2.46 (0.17), residues: 978 sheet: None (None), residues: 0 loop : -0.07 (0.43), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 116 TYR 0.009 0.001 TYR A 337 PHE 0.020 0.001 PHE D 263 TRP 0.003 0.001 TRP C 207 HIS 0.002 0.001 HIS A 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 9732) covalent geometry : angle 0.46400 / 0.24 (13120) hydrogen bonds : bond 0.04227 / 2.88 ( 691) hydrogen bonds : angle 3.66715 / 2.65 ( 2055) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 96 time to evaluate : 0.287 Fit side-chains REVERT: A 139 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6499 (pp20) REVERT: A 260 ASP cc_start: 0.8384 (OUTLIER) cc_final: 0.8090 (p0) REVERT: B 82 PHE cc_start: 0.4547 (OUTLIER) cc_final: 0.3134 (t80) REVERT: B 96 GLN cc_start: 0.7030 (mp10) cc_final: 0.6816 (mp10) REVERT: B 317 HIS cc_start: 0.7769 (OUTLIER) cc_final: 0.7159 (m90) REVERT: B 321 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7754 (mm) REVERT: B 347 MET cc_start: 0.7729 (mtp) cc_final: 0.7470 (mtt) REVERT: C 139 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.6419 (pp20) REVERT: C 161 THR cc_start: 0.7539 (OUTLIER) cc_final: 0.7329 (p) REVERT: C 260 ASP cc_start: 0.8407 (OUTLIER) cc_final: 0.7862 (p0) REVERT: D 321 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7773 (mm) outliers start: 32 outliers final: 23 residues processed: 125 average time/residue: 0.0636 time to fit residues: 12.1741 Evaluate side-chains 126 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 94 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain B residue 82 PHE Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 298 ASP Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain D residue 82 PHE Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 361 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 91 optimal weight: 0.0770 chunk 22 optimal weight: 0.6980 chunk 29 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 98 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 12 optimal weight: 0.0570 chunk 14 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.209118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.154074 restraints weight = 10956.105| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 3.05 r_work: 0.3445 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9732 Z= 0.093 Angle : 0.412 7.170 13120 Z= 0.216 Chirality : 0.032 0.200 1512 Planarity : 0.003 0.028 1652 Dihedral : 4.572 58.824 1300 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 2.26 % Allowed : 15.09 % Favored : 82.64 % 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: 3.45 (0.25), residues: 1172 helix: 2.69 (0.17), residues: 982 sheet: None (None), residues: 0 loop : 0.00 (0.43), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 116 TYR 0.007 0.001 TYR A 204 PHE 0.016 0.001 PHE D 263 TRP 0.006 0.001 TRP A 283 HIS 0.002 0.000 HIS A 314 Details of bonding type rmsd/Z covalent geometry : bond 0.00195 / 0.09 ( 9732) covalent geometry : angle 0.41250 / 0.22 (13120) hydrogen bonds : bond 0.03310 / 2.24 ( 691) hydrogen bonds : angle 3.42020 / 2.46 ( 2055) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2405.37 seconds wall clock time: 41 minutes 41.62 seconds (2501.62 seconds total)