Starting phenix.real_space_refine on Fri Oct 23 15:55:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ka2_22756/10_2026/7ka2_22756.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ka2_22756/10_2026/7ka2_22756.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ka2_22756/10_2026/7ka2_22756.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ka2_22756/10_2026/7ka2_22756.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ka2_22756/10_2026/7ka2_22756.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ka2_22756/10_2026/7ka2_22756.map" } resolution = 3.6 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= 0.002 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 44 5.16 5 C 6588 2.51 5 N 1860 2.21 5 O 1980 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10472 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2618 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324} Restraints were copied for chains: A, C, D Time building chain proxies: 2.40, per 1000 atoms: 0.23 Number of scatterers: 10472 At special positions: 0 Unit cell: (97.37, 79.17, 106.47, 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 44 16.00 O 1980 8.00 N 1860 7.00 C 6588 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: 0.81 Conformation dependent library (CDL) restraints added in 400.6 milliseconds 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2520 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 8 sheets defined 55.7% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'B' and resid 8 through 24 Processing helix chain 'B' and resid 35 through 47 Processing helix chain 'B' and resid 51 through 64 Processing helix chain 'B' and resid 66 through 70 Processing helix chain 'B' and resid 80 through 85 Processing helix chain 'B' and resid 92 through 100 removed outlier: 3.729A pdb=" N LYS B 100 " --> pdb=" O VAL B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 140 Processing helix chain 'B' and resid 159 through 180 removed outlier: 3.558A pdb=" N ASN B 180 " --> pdb=" O ILE B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 219 removed outlier: 3.539A pdb=" N CYS B 201 " --> pdb=" O ASP B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 225 Processing helix chain 'B' and resid 244 through 258 Processing helix chain 'B' and resid 275 through 287 removed outlier: 3.637A pdb=" N ALA B 279 " --> pdb=" O SER B 275 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N SER B 280 " --> pdb=" O GLU B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 314 removed outlier: 3.706A pdb=" N GLN B 306 " --> pdb=" O GLY B 302 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N SER B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ALA B 309 " --> pdb=" O LEU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 318 No H-bonds generated for 'chain 'B' and resid 316 through 318' Processing helix chain 'B' and resid 319 through 340 Processing helix chain 'A' and resid 8 through 24 Processing helix chain 'A' and resid 35 through 47 Processing helix chain 'A' and resid 51 through 64 Processing helix chain 'A' and resid 66 through 70 Processing helix chain 'A' and resid 80 through 85 Processing helix chain 'A' and resid 92 through 100 removed outlier: 3.730A pdb=" N LYS A 100 " --> pdb=" O VAL A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 140 Processing helix chain 'A' and resid 159 through 180 removed outlier: 3.558A pdb=" N ASN A 180 " --> pdb=" O ILE A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 219 removed outlier: 3.539A pdb=" N CYS A 201 " --> pdb=" O ASP A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 225 Processing helix chain 'A' and resid 244 through 258 Processing helix chain 'A' and resid 275 through 287 removed outlier: 3.636A pdb=" N ALA A 279 " --> pdb=" O SER A 275 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N SER A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 314 removed outlier: 3.705A pdb=" N GLN A 306 " --> pdb=" O GLY A 302 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N SER A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ALA A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 318 No H-bonds generated for 'chain 'A' and resid 316 through 318' Processing helix chain 'A' and resid 319 through 340 Processing helix chain 'C' and resid 8 through 24 Processing helix chain 'C' and resid 35 through 47 Processing helix chain 'C' and resid 51 through 64 Processing helix chain 'C' and resid 66 through 70 Processing helix chain 'C' and resid 80 through 85 Processing helix chain 'C' and resid 92 through 100 removed outlier: 3.729A pdb=" N LYS C 100 " --> pdb=" O VAL C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 140 Processing helix chain 'C' and resid 159 through 180 removed outlier: 3.558A pdb=" N ASN C 180 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 219 removed outlier: 3.538A pdb=" N CYS C 201 " --> pdb=" O ASP C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 225 Processing helix chain 'C' and resid 244 through 258 Processing helix chain 'C' and resid 275 through 287 removed outlier: 3.637A pdb=" N ALA C 279 " --> pdb=" O SER C 275 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N SER C 280 " --> pdb=" O GLU C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 314 removed outlier: 3.705A pdb=" N GLN C 306 " --> pdb=" O GLY C 302 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N SER C 308 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ALA C 309 " --> pdb=" O LEU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 318 No H-bonds generated for 'chain 'C' and resid 316 through 318' Processing helix chain 'C' and resid 319 through 340 Processing helix chain 'D' and resid 8 through 24 Processing helix chain 'D' and resid 35 through 47 Processing helix chain 'D' and resid 51 through 64 Processing helix chain 'D' and resid 66 through 70 Processing helix chain 'D' and resid 80 through 85 Processing helix chain 'D' and resid 92 through 100 removed outlier: 3.729A pdb=" N LYS D 100 " --> pdb=" O VAL D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 140 Processing helix chain 'D' and resid 159 through 180 removed outlier: 3.558A pdb=" N ASN D 180 " --> pdb=" O ILE D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 219 removed outlier: 3.539A pdb=" N CYS D 201 " --> pdb=" O ASP D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 225 Processing helix chain 'D' and resid 244 through 258 Processing helix chain 'D' and resid 275 through 287 removed outlier: 3.637A pdb=" N ALA D 279 " --> pdb=" O SER D 275 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N SER D 280 " --> pdb=" O GLU D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 314 removed outlier: 3.706A pdb=" N GLN D 306 " --> pdb=" O GLY D 302 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N SER D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ALA D 309 " --> pdb=" O LEU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 318 No H-bonds generated for 'chain 'D' and resid 316 through 318' Processing helix chain 'D' and resid 319 through 340 Processing sheet with id=AA1, first strand: chain 'B' and resid 28 through 32 removed outlier: 7.121A pdb=" N GLY B 28 " --> pdb=" O GLY B 74 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N VAL B 76 " --> pdb=" O GLY B 28 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU B 30 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N LEU B 78 " --> pdb=" O LEU B 30 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ALA B 32 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N VAL B 104 " --> pdb=" O ASP B 143 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ALA B 145 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N ILE B 106 " --> pdb=" O ALA B 145 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N TRP B 147 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ILE B 185 " --> pdb=" O ASP B 143 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ALA B 145 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N GLU B 187 " --> pdb=" O ALA B 145 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N TRP B 147 " --> pdb=" O GLU B 187 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLU B 189 " --> pdb=" O TRP B 147 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N CYS B 149 " --> pdb=" O GLU B 189 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N LEU B 191 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N LEU B 151 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU B 228 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA B 31 " --> pdb=" O TYR B 301 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 112 through 114 Processing sheet with id=AA3, first strand: chain 'A' and resid 28 through 32 removed outlier: 7.121A pdb=" N GLY A 28 " --> pdb=" O GLY A 74 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N VAL A 76 " --> pdb=" O GLY A 28 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU A 30 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N LEU A 78 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ALA A 32 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N VAL A 104 " --> pdb=" O ASP A 143 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ALA A 145 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ILE A 106 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N TRP A 147 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ILE A 185 " --> pdb=" O ASP A 143 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ALA A 145 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N GLU A 187 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N TRP A 147 " --> pdb=" O GLU A 187 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N GLU A 189 " --> pdb=" O TRP A 147 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N CYS A 149 " --> pdb=" O GLU A 189 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N LEU A 191 " --> pdb=" O CYS A 149 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N LEU A 151 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU A 228 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA A 31 " --> pdb=" O TYR A 301 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 112 through 114 Processing sheet with id=AA5, first strand: chain 'C' and resid 28 through 32 removed outlier: 7.120A pdb=" N GLY C 28 " --> pdb=" O GLY C 74 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N VAL C 76 " --> pdb=" O GLY C 28 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU C 30 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N LEU C 78 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ALA C 32 " --> pdb=" O LEU C 78 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N VAL C 104 " --> pdb=" O ASP C 143 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ALA C 145 " --> pdb=" O VAL C 104 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N ILE C 106 " --> pdb=" O ALA C 145 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N TRP C 147 " --> pdb=" O ILE C 106 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ILE C 185 " --> pdb=" O ASP C 143 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ALA C 145 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N GLU C 187 " --> pdb=" O ALA C 145 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N TRP C 147 " --> pdb=" O GLU C 187 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLU C 189 " --> pdb=" O TRP C 147 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N CYS C 149 " --> pdb=" O GLU C 189 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N LEU C 191 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N LEU C 151 " --> pdb=" O LEU C 191 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU C 228 " --> pdb=" O THR C 268 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA C 31 " --> pdb=" O TYR C 301 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 112 through 114 Processing sheet with id=AA7, first strand: chain 'D' and resid 28 through 32 removed outlier: 7.120A pdb=" N GLY D 28 " --> pdb=" O GLY D 74 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N VAL D 76 " --> pdb=" O GLY D 28 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU D 30 " --> pdb=" O VAL D 76 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N LEU D 78 " --> pdb=" O LEU D 30 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ALA D 32 " --> pdb=" O LEU D 78 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N VAL D 104 " --> pdb=" O ASP D 143 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ALA D 145 " --> pdb=" O VAL D 104 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ILE D 106 " --> pdb=" O ALA D 145 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N TRP D 147 " --> pdb=" O ILE D 106 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ILE D 185 " --> pdb=" O ASP D 143 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ALA D 145 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N GLU D 187 " --> pdb=" O ALA D 145 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N TRP D 147 " --> pdb=" O GLU D 187 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLU D 189 " --> pdb=" O TRP D 147 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N CYS D 149 " --> pdb=" O GLU D 189 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N LEU D 191 " --> pdb=" O CYS D 149 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N LEU D 151 " --> pdb=" O LEU D 191 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU D 228 " --> pdb=" O THR D 268 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA D 31 " --> pdb=" O TYR D 301 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 112 through 114 564 hydrogen bonds defined for protein. 1608 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: 1.57 Time building geometry restraints manager: 1.11 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: 3443 1.34 - 1.46: 1851 1.46 - 1.57: 5322 1.57 - 1.69: 0 1.69 - 1.81: 56 Bond restraints: 10672 Sorted by residual: bond pdb=" C ASN D 70 " pdb=" N PRO D 71 " ideal model delta sigma weight residual 1.334 1.386 -0.052 2.34e-02 1.83e+03 4.92e+00 bond pdb=" C ASN C 70 " pdb=" N PRO C 71 " ideal model delta sigma weight residual 1.334 1.386 -0.052 2.34e-02 1.83e+03 4.87e+00 bond pdb=" C ASN B 70 " pdb=" N PRO B 71 " ideal model delta sigma weight residual 1.334 1.385 -0.051 2.34e-02 1.83e+03 4.77e+00 bond pdb=" C ASN A 70 " pdb=" N PRO A 71 " ideal model delta sigma weight residual 1.334 1.385 -0.051 2.34e-02 1.83e+03 4.74e+00 bond pdb=" CB GLU B 14 " pdb=" CG GLU B 14 " ideal model delta sigma weight residual 1.520 1.473 0.047 3.00e-02 1.11e+03 2.42e+00 ... (remaining 10667 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 13401 1.63 - 3.25: 883 3.25 - 4.88: 115 4.88 - 6.50: 53 6.50 - 8.13: 12 Bond angle restraints: 14464 Sorted by residual: angle pdb=" C ASN D 319 " pdb=" N LEU D 320 " pdb=" CA LEU D 320 " ideal model delta sigma weight residual 121.19 129.32 -8.13 1.59e+00 3.96e-01 2.61e+01 angle pdb=" C ASN A 319 " pdb=" N LEU A 320 " pdb=" CA LEU A 320 " ideal model delta sigma weight residual 121.19 129.31 -8.12 1.59e+00 3.96e-01 2.61e+01 angle pdb=" C ASN B 319 " pdb=" N LEU B 320 " pdb=" CA LEU B 320 " ideal model delta sigma weight residual 121.19 129.27 -8.08 1.59e+00 3.96e-01 2.58e+01 angle pdb=" C ASN C 319 " pdb=" N LEU C 320 " pdb=" CA LEU C 320 " ideal model delta sigma weight residual 121.19 129.26 -8.07 1.59e+00 3.96e-01 2.58e+01 angle pdb=" CA GLU C 49 " pdb=" CB GLU C 49 " pdb=" CG GLU C 49 " ideal model delta sigma weight residual 114.10 121.78 -7.68 2.00e+00 2.50e-01 1.47e+01 ... (remaining 14459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.52: 5733 16.52 - 33.03: 591 33.03 - 49.55: 112 49.55 - 66.07: 56 66.07 - 82.58: 12 Dihedral angle restraints: 6504 sinusoidal: 2572 harmonic: 3932 Sorted by residual: dihedral pdb=" CA VAL C 264 " pdb=" C VAL C 264 " pdb=" N THR C 265 " pdb=" CA THR C 265 " ideal model delta harmonic sigma weight residual -180.00 -154.69 -25.31 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA VAL A 264 " pdb=" C VAL A 264 " pdb=" N THR A 265 " pdb=" CA THR A 265 " ideal model delta harmonic sigma weight residual -180.00 -154.70 -25.30 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA VAL B 264 " pdb=" C VAL B 264 " pdb=" N THR B 265 " pdb=" CA THR B 265 " ideal model delta harmonic sigma weight residual 180.00 -154.72 -25.28 0 5.00e+00 4.00e-02 2.56e+01 ... (remaining 6501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1094 0.044 - 0.088: 390 0.088 - 0.133: 116 0.133 - 0.177: 32 0.177 - 0.221: 12 Chirality restraints: 1644 Sorted by residual: chirality pdb=" CB ILE B 46 " pdb=" CA ILE B 46 " pdb=" CG1 ILE B 46 " pdb=" CG2 ILE B 46 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CB ILE C 46 " pdb=" CA ILE C 46 " pdb=" CG1 ILE C 46 " pdb=" CG2 ILE C 46 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CB ILE A 46 " pdb=" CA ILE A 46 " pdb=" CG1 ILE A 46 " pdb=" CG2 ILE A 46 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 1641 not shown) Planarity restraints: 1880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS D 329 " -0.014 2.00e-02 2.50e+03 2.91e-02 8.45e+00 pdb=" C LYS D 329 " 0.050 2.00e-02 2.50e+03 pdb=" O LYS D 329 " -0.019 2.00e-02 2.50e+03 pdb=" N ARG D 330 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 329 " 0.014 2.00e-02 2.50e+03 2.91e-02 8.45e+00 pdb=" C LYS C 329 " -0.050 2.00e-02 2.50e+03 pdb=" O LYS C 329 " 0.019 2.00e-02 2.50e+03 pdb=" N ARG C 330 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 329 " -0.014 2.00e-02 2.50e+03 2.90e-02 8.39e+00 pdb=" C LYS A 329 " 0.050 2.00e-02 2.50e+03 pdb=" O LYS A 329 " -0.019 2.00e-02 2.50e+03 pdb=" N ARG A 330 " -0.017 2.00e-02 2.50e+03 ... (remaining 1877 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2592 2.78 - 3.31: 9896 3.31 - 3.84: 18124 3.84 - 4.37: 21109 4.37 - 4.90: 35941 Nonbonded interactions: 87662 Sorted by model distance: nonbonded pdb=" O MET D 250 " pdb=" OG1 THR D 254 " model vdw 2.254 3.040 nonbonded pdb=" O MET A 250 " pdb=" OG1 THR A 254 " model vdw 2.254 3.040 nonbonded pdb=" O MET B 250 " pdb=" OG1 THR B 254 " model vdw 2.254 3.040 nonbonded pdb=" O MET C 250 " pdb=" OG1 THR C 254 " model vdw 2.254 3.040 nonbonded pdb=" O THR B 64 " pdb=" OG1 THR B 64 " model vdw 2.259 3.040 ... (remaining 87657 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: 0.04 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' 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 group one per residue 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: 1.820 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.240 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 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:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 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 : 0.008 0.054 10672 Z= 0.353 Angle : 0.961 8.127 14464 Z= 0.549 Chirality : 0.053 0.221 1644 Planarity : 0.008 0.049 1880 Dihedral : 15.204 82.581 3984 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 6.12 % Allowed : 6.47 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.99 (0.20), residues: 1364 helix: -1.10 (0.16), residues: 672 sheet: -2.01 (0.33), residues: 200 loop : -0.99 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 172 TYR 0.017 0.003 TYR A 213 PHE 0.017 0.003 PHE A 144 TRP 0.022 0.004 TRP B 295 HIS 0.005 0.001 HIS C 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00797 / 0.35 (10672) covalent geometry : angle 0.96122 / 0.55 (14464) hydrogen bonds : bond 0.16327 / 11.13 ( 564) hydrogen bonds : angle 6.81305 / 4.76 ( 1608) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 334 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 250 MET cc_start: 0.8742 (tpp) cc_final: 0.8428 (tpt) REVERT: A 233 VAL cc_start: 0.8331 (OUTLIER) cc_final: 0.6805 (p) REVERT: A 250 MET cc_start: 0.8667 (tpp) cc_final: 0.8419 (tpt) REVERT: A 271 SER cc_start: 0.8415 (OUTLIER) cc_final: 0.7989 (p) REVERT: A 301 TYR cc_start: 0.7412 (m-10) cc_final: 0.7003 (m-10) REVERT: C 39 ILE cc_start: 0.9263 (tp) cc_final: 0.8931 (tp) REVERT: C 60 GLN cc_start: 0.8489 (mt0) cc_final: 0.7667 (mt0) REVERT: C 250 MET cc_start: 0.8731 (tpp) cc_final: 0.8468 (tpt) REVERT: C 271 SER cc_start: 0.8465 (OUTLIER) cc_final: 0.8102 (p) REVERT: C 301 TYR cc_start: 0.7570 (m-10) cc_final: 0.7022 (m-10) outliers start: 68 outliers final: 6 residues processed: 373 average time/residue: 0.1101 time to fit residues: 55.9502 Evaluate side-chains 195 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 186 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain D residue 64 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 55] chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 44 GLN B 60 GLN B 80 HIS B 125 GLN B 168 ASN A 60 GLN A 80 HIS A 125 GLN A 168 ASN C 60 GLN C 80 HIS C 125 GLN D 80 HIS D 168 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.095180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.072447 restraints weight = 29113.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.074807 restraints weight = 16953.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.076352 restraints weight = 12059.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.077260 restraints weight = 9658.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.077915 restraints weight = 8466.205| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10672 Z= 0.138 Angle : 0.651 8.932 14464 Z= 0.337 Chirality : 0.043 0.170 1644 Planarity : 0.004 0.031 1880 Dihedral : 4.904 28.865 1481 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.33 % Allowed : 14.48 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.03 (0.22), residues: 1364 helix: 0.79 (0.18), residues: 684 sheet: -1.26 (0.35), residues: 188 loop : -0.49 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 59 TYR 0.019 0.002 TYR C 203 PHE 0.013 0.002 PHE B 93 TRP 0.005 0.001 TRP A 147 HIS 0.003 0.001 HIS D 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (10672) covalent geometry : angle 0.65111 / 0.34 (14464) hydrogen bonds : bond 0.04446 / 3.02 ( 564) hydrogen bonds : angle 4.54653 / 3.24 ( 1608) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 242 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 165 GLU cc_start: 0.7807 (tp30) cc_final: 0.7306 (tp30) REVERT: B 229 LYS cc_start: 0.9236 (tttt) cc_final: 0.8939 (tptp) REVERT: B 311 LYS cc_start: 0.9463 (ttpp) cc_final: 0.9227 (ptmm) REVERT: B 316 LYS cc_start: 0.8981 (mmmt) cc_final: 0.8740 (mmtm) REVERT: A 60 GLN cc_start: 0.8845 (mt0) cc_final: 0.8503 (mt0) REVERT: A 82 THR cc_start: 0.9056 (m) cc_final: 0.8795 (m) REVERT: A 250 MET cc_start: 0.8762 (tpp) cc_final: 0.8558 (tpt) REVERT: C 60 GLN cc_start: 0.8754 (mt0) cc_final: 0.8478 (mt0) REVERT: C 82 THR cc_start: 0.9077 (m) cc_final: 0.8850 (m) REVERT: C 250 MET cc_start: 0.8850 (tpp) cc_final: 0.8618 (tpt) REVERT: C 301 TYR cc_start: 0.7500 (m-10) cc_final: 0.7284 (m-10) outliers start: 37 outliers final: 18 residues processed: 259 average time/residue: 0.0959 time to fit residues: 35.7407 Evaluate side-chains 185 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 167 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 80 HIS Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 343 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: [122, 2, 118, 133, 102, 69, 5, 112, 44, 124, 50] chunk 122 optimal weight: 0.8980 chunk 2 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 58.2868 > 50:) chunk 118 optimal weight: 0.7980 chunk 133 optimal weight: 10.0000 chunk 102 optimal weight: 8.9990 chunk 69 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 80 HIS B 168 ASN A 80 HIS A 168 ASN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 HIS C 168 ASN D 125 GLN D 168 ASN D 339 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.093440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.071157 restraints weight = 29739.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.073535 restraints weight = 17202.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.075037 restraints weight = 12078.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.075938 restraints weight = 9649.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.076589 restraints weight = 8430.917| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10672 Z= 0.140 Angle : 0.616 8.216 14464 Z= 0.318 Chirality : 0.042 0.159 1644 Planarity : 0.004 0.063 1880 Dihedral : 4.508 20.037 1472 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.06 % Allowed : 15.74 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.56 (0.22), residues: 1364 helix: 1.40 (0.19), residues: 676 sheet: -0.99 (0.36), residues: 188 loop : -0.39 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 59 TYR 0.016 0.002 TYR B 203 PHE 0.020 0.002 PHE B 93 TRP 0.004 0.001 TRP A 147 HIS 0.006 0.001 HIS A 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (10672) covalent geometry : angle 0.61603 / 0.32 (14464) hydrogen bonds : bond 0.04003 / 2.75 ( 564) hydrogen bonds : angle 4.31177 / 3.08 ( 1608) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 187 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 134 CYS cc_start: 0.8304 (p) cc_final: 0.7994 (p) REVERT: B 229 LYS cc_start: 0.9218 (tttt) cc_final: 0.8779 (tptp) REVERT: A 60 GLN cc_start: 0.8804 (mt0) cc_final: 0.8495 (mt0) REVERT: A 66 ASP cc_start: 0.9015 (t70) cc_final: 0.8788 (p0) REVERT: A 250 MET cc_start: 0.8747 (tpp) cc_final: 0.8512 (tpt) REVERT: A 252 THR cc_start: 0.8503 (OUTLIER) cc_final: 0.8269 (p) REVERT: A 301 TYR cc_start: 0.7379 (m-10) cc_final: 0.7156 (m-10) REVERT: C 60 GLN cc_start: 0.8697 (mt0) cc_final: 0.8426 (mt0) REVERT: C 67 ASP cc_start: 0.8917 (t0) cc_final: 0.8701 (p0) REVERT: D 250 MET cc_start: 0.8779 (mmm) cc_final: 0.8409 (tpp) outliers start: 34 outliers final: 20 residues processed: 209 average time/residue: 0.0908 time to fit residues: 27.9130 Evaluate side-chains 176 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 HIS Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 80 HIS Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 339 GLN Chi-restraints excluded: chain D residue 343 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: [95, 59, 78, 41, 127, 36, 3, 48, 54, 107, 34] chunk 95 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 78 optimal weight: 7.9990 chunk 41 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 3 optimal weight: 8.9990 chunk 48 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 80 HIS ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 168 ASN ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 HIS C 168 ASN D 80 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.093885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.071584 restraints weight = 29550.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.073959 restraints weight = 17134.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.075471 restraints weight = 12060.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.076415 restraints weight = 9618.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.076956 restraints weight = 8365.545| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10672 Z= 0.126 Angle : 0.613 11.978 14464 Z= 0.311 Chirality : 0.042 0.165 1644 Planarity : 0.004 0.066 1880 Dihedral : 4.350 19.505 1472 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.16 % Allowed : 18.44 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.72 (0.22), residues: 1364 helix: 1.55 (0.19), residues: 680 sheet: -0.81 (0.36), residues: 188 loop : -0.42 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 59 TYR 0.020 0.002 TYR B 203 PHE 0.014 0.002 PHE C 93 TRP 0.011 0.001 TRP D 313 HIS 0.007 0.001 HIS C 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (10672) covalent geometry : angle 0.61279 / 0.31 (14464) hydrogen bonds : bond 0.03753 / 2.59 ( 564) hydrogen bonds : angle 4.20704 / 3.01 ( 1608) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 189 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 134 CYS cc_start: 0.8319 (p) cc_final: 0.7986 (p) REVERT: B 250 MET cc_start: 0.8666 (tpt) cc_final: 0.8322 (tpp) REVERT: A 60 GLN cc_start: 0.8799 (mt0) cc_final: 0.8515 (mt0) REVERT: A 250 MET cc_start: 0.8741 (tpp) cc_final: 0.8510 (tpt) REVERT: A 252 THR cc_start: 0.8437 (OUTLIER) cc_final: 0.8201 (p) REVERT: C 60 GLN cc_start: 0.8717 (mt0) cc_final: 0.8421 (mt0) REVERT: D 164 MET cc_start: 0.8581 (tmm) cc_final: 0.8378 (tmm) REVERT: D 229 LYS cc_start: 0.9299 (tttt) cc_final: 0.9034 (tptp) REVERT: D 250 MET cc_start: 0.8766 (mmm) cc_final: 0.8444 (tpp) outliers start: 24 outliers final: 16 residues processed: 202 average time/residue: 0.0882 time to fit residues: 26.1055 Evaluate side-chains 178 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 161 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 80 HIS Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 343 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: [74, 45, 26, 91, 30, 128, 28, 47, 39, 87, 127] chunk 74 optimal weight: 4.9990 chunk 45 optimal weight: 0.0980 chunk 26 optimal weight: 0.7980 chunk 91 optimal weight: 0.0050 chunk 30 optimal weight: 0.9990 chunk 128 optimal weight: 2.9990 chunk 28 optimal weight: 0.0030 chunk 47 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 87 optimal weight: 0.7980 chunk 127 optimal weight: 2.9990 overall best weight: 0.3404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 80 HIS ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 HIS A 168 ASN ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 HIS C 168 ASN D 60 GLN D 80 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.095465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.073371 restraints weight = 29164.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.075810 restraints weight = 16816.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.077355 restraints weight = 11798.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.078356 restraints weight = 9389.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.078959 restraints weight = 8121.479| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.4222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10672 Z= 0.113 Angle : 0.599 11.852 14464 Z= 0.303 Chirality : 0.042 0.164 1644 Planarity : 0.004 0.054 1880 Dihedral : 4.147 16.998 1472 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.25 % Allowed : 18.35 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.71 (0.22), residues: 1364 helix: 1.64 (0.19), residues: 684 sheet: -1.19 (0.33), residues: 220 loop : -0.32 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 303 TYR 0.021 0.001 TYR B 203 PHE 0.018 0.002 PHE B 79 TRP 0.007 0.001 TRP B 313 HIS 0.011 0.001 HIS C 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (10672) covalent geometry : angle 0.59923 / 0.30 (14464) hydrogen bonds : bond 0.03351 / 2.32 ( 564) hydrogen bonds : angle 4.02794 / 2.89 ( 1608) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 190 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 134 CYS cc_start: 0.8336 (p) cc_final: 0.7927 (p) REVERT: B 250 MET cc_start: 0.8705 (tpt) cc_final: 0.8324 (tpp) REVERT: A 60 GLN cc_start: 0.8758 (mt0) cc_final: 0.8493 (mt0) REVERT: A 250 MET cc_start: 0.8722 (tpp) cc_final: 0.8494 (tpt) REVERT: A 325 GLU cc_start: 0.9029 (tm-30) cc_final: 0.8280 (pp20) REVERT: C 60 GLN cc_start: 0.8704 (mt0) cc_final: 0.8478 (mt0) REVERT: C 67 ASP cc_start: 0.8979 (p0) cc_final: 0.8744 (t0) REVERT: C 330 ARG cc_start: 0.9111 (mmm160) cc_final: 0.8847 (ttp-170) REVERT: D 250 MET cc_start: 0.8773 (mmm) cc_final: 0.8453 (tpp) REVERT: D 306 GLN cc_start: 0.7751 (pp30) cc_final: 0.7511 (pp30) outliers start: 25 outliers final: 17 residues processed: 203 average time/residue: 0.0894 time to fit residues: 26.6350 Evaluate side-chains 179 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 162 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain A residue 80 HIS Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 343 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: [110, 79, 0, 129, 90, 97, 83, 23, 85, 9, 22] chunk 110 optimal weight: 6.9990 chunk 79 optimal weight: 0.0670 chunk 0 optimal weight: 10.0000 chunk 129 optimal weight: 0.0370 chunk 90 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 chunk 22 optimal weight: 0.9990 overall best weight: 0.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 60 GLN B 80 HIS ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 54 ASN A 168 ASN ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 ASN D 80 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.094815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.073300 restraints weight = 29872.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.075777 restraints weight = 16597.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.077297 restraints weight = 11390.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.078252 restraints weight = 8993.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.078869 restraints weight = 7779.429| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.4380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10672 Z= 0.117 Angle : 0.612 12.083 14464 Z= 0.310 Chirality : 0.042 0.176 1644 Planarity : 0.004 0.054 1880 Dihedral : 4.073 17.870 1472 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.06 % Allowed : 18.79 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.84 (0.22), residues: 1364 helix: 1.75 (0.19), residues: 680 sheet: -0.97 (0.33), residues: 208 loop : -0.37 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 303 TYR 0.020 0.001 TYR B 203 PHE 0.019 0.002 PHE B 79 TRP 0.007 0.001 TRP B 313 HIS 0.004 0.000 HIS D 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (10672) covalent geometry : angle 0.61211 / 0.31 (14464) hydrogen bonds : bond 0.03373 / 2.33 ( 564) hydrogen bonds : angle 3.98391 / 2.86 ( 1608) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 172 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 134 CYS cc_start: 0.8342 (p) cc_final: 0.7926 (p) REVERT: B 250 MET cc_start: 0.8726 (tpt) cc_final: 0.8334 (tpp) REVERT: A 60 GLN cc_start: 0.8727 (mt0) cc_final: 0.8468 (mt0) REVERT: A 250 MET cc_start: 0.8726 (tpp) cc_final: 0.8502 (tpt) REVERT: A 311 LYS cc_start: 0.9623 (ttpp) cc_final: 0.9394 (ptmm) REVERT: C 57 PHE cc_start: 0.8994 (t80) cc_final: 0.8773 (t80) REVERT: C 60 GLN cc_start: 0.8674 (mt0) cc_final: 0.8444 (mt0) REVERT: C 330 ARG cc_start: 0.9124 (mmm160) cc_final: 0.8870 (ttp-170) REVERT: D 250 MET cc_start: 0.8752 (mmm) cc_final: 0.8485 (tpp) outliers start: 34 outliers final: 21 residues processed: 192 average time/residue: 0.0849 time to fit residues: 24.5264 Evaluate side-chains 179 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 158 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 80 HIS Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 343 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: [64, 116, 129, 32, 11, 31, 28, 89, 83, 87, 73] chunk 64 optimal weight: 6.9990 chunk 116 optimal weight: 3.9990 chunk 129 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 chunk 31 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 83 optimal weight: 0.0370 chunk 87 optimal weight: 0.0870 chunk 73 optimal weight: 1.9990 overall best weight: 0.8238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 60 GLN B 80 HIS ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 168 ASN ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 HIS C 168 ASN D 80 HIS ** D 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.094380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.073164 restraints weight = 29691.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.075609 restraints weight = 16422.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.077088 restraints weight = 11254.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.078024 restraints weight = 8861.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.078636 restraints weight = 7678.230| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.4539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10672 Z= 0.122 Angle : 0.617 12.348 14464 Z= 0.311 Chirality : 0.042 0.149 1644 Planarity : 0.004 0.056 1880 Dihedral : 4.055 18.307 1472 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.52 % Allowed : 19.69 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.92 (0.22), residues: 1364 helix: 1.74 (0.19), residues: 684 sheet: -0.93 (0.33), residues: 208 loop : -0.21 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 303 TYR 0.020 0.002 TYR B 203 PHE 0.016 0.001 PHE B 79 TRP 0.007 0.001 TRP B 313 HIS 0.005 0.000 HIS B 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (10672) covalent geometry : angle 0.61684 / 0.31 (14464) hydrogen bonds : bond 0.03337 / 2.30 ( 564) hydrogen bonds : angle 3.94206 / 2.83 ( 1608) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 165 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 134 CYS cc_start: 0.8307 (p) cc_final: 0.7894 (p) REVERT: B 250 MET cc_start: 0.8728 (tpt) cc_final: 0.8376 (tpp) REVERT: A 68 ARG cc_start: 0.8723 (mtm180) cc_final: 0.8477 (mtp180) REVERT: A 250 MET cc_start: 0.8729 (tpp) cc_final: 0.8506 (tpt) REVERT: A 252 THR cc_start: 0.8405 (OUTLIER) cc_final: 0.8150 (p) REVERT: A 311 LYS cc_start: 0.9620 (ttpp) cc_final: 0.9397 (ptmm) REVERT: A 326 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.8605 (pp20) REVERT: A 330 ARG cc_start: 0.9130 (mmm160) cc_final: 0.8808 (ttp-170) REVERT: D 60 GLN cc_start: 0.9112 (tt0) cc_final: 0.8883 (tt0) REVERT: D 229 LYS cc_start: 0.9303 (tttt) cc_final: 0.9054 (tptm) REVERT: D 330 ARG cc_start: 0.9081 (mmm160) cc_final: 0.8476 (ttp-170) outliers start: 28 outliers final: 14 residues processed: 184 average time/residue: 0.0881 time to fit residues: 23.7733 Evaluate side-chains 172 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 156 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 80 HIS Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 343 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: [129, 27, 0, 116, 115, 20, 7, 59, 74, 93, 117] chunk 129 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 116 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 117 optimal weight: 6.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 60 GLN B 80 HIS ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 168 ASN ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 HIS C 168 ASN D 80 HIS ** D 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.092126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.070974 restraints weight = 29968.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.073349 restraints weight = 16483.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.074794 restraints weight = 11310.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.075719 restraints weight = 8960.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.076218 restraints weight = 7780.540| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.4652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10672 Z= 0.173 Angle : 0.644 12.083 14464 Z= 0.327 Chirality : 0.043 0.155 1644 Planarity : 0.004 0.057 1880 Dihedral : 4.136 19.143 1472 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.43 % Allowed : 20.41 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.98 (0.22), residues: 1364 helix: 1.74 (0.19), residues: 684 sheet: -0.91 (0.33), residues: 208 loop : -0.12 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 303 TYR 0.038 0.002 TYR B 137 PHE 0.016 0.002 PHE B 79 TRP 0.010 0.001 TRP C 147 HIS 0.004 0.001 HIS B 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (10672) covalent geometry : angle 0.64435 / 0.33 (14464) hydrogen bonds : bond 0.03632 / 2.50 ( 564) hydrogen bonds : angle 4.06010 / 2.94 ( 1608) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 150 time to evaluate : 0.407 Fit side-chains revert: symmetry clash REVERT: B 79 PHE cc_start: 0.9007 (t80) cc_final: 0.8804 (t80) REVERT: B 134 CYS cc_start: 0.8335 (p) cc_final: 0.8050 (p) REVERT: B 250 MET cc_start: 0.8741 (tpt) cc_final: 0.8395 (tpp) REVERT: A 250 MET cc_start: 0.8746 (tpp) cc_final: 0.8522 (tpt) REVERT: A 311 LYS cc_start: 0.9630 (ttpp) cc_final: 0.9378 (ttpp) REVERT: A 330 ARG cc_start: 0.9098 (mmm160) cc_final: 0.8894 (ttp-170) REVERT: C 67 ASP cc_start: 0.9073 (p0) cc_final: 0.8800 (t0) REVERT: D 250 MET cc_start: 0.8785 (mmm) cc_final: 0.8556 (tpp) REVERT: D 330 ARG cc_start: 0.9111 (mmm160) cc_final: 0.8493 (ttp-170) outliers start: 27 outliers final: 20 residues processed: 168 average time/residue: 0.0888 time to fit residues: 22.0203 Evaluate side-chains 161 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 217 SER Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 217 SER Chi-restraints excluded: chain D residue 343 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: [45, 27, 5, 115, 122, 51, 92, 124, 128, 133, 58] chunk 45 optimal weight: 0.0970 chunk 27 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 115 optimal weight: 0.7980 chunk 122 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 128 optimal weight: 0.6980 chunk 133 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 60 GLN B 80 HIS ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 HIS D 60 GLN D 80 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.094293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.072997 restraints weight = 29956.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.075431 restraints weight = 16416.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.076920 restraints weight = 11198.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.077869 restraints weight = 8839.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.078364 restraints weight = 7660.929| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.4846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10672 Z= 0.119 Angle : 0.636 12.537 14464 Z= 0.319 Chirality : 0.043 0.199 1644 Planarity : 0.004 0.056 1880 Dihedral : 4.067 18.962 1472 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.71 % Allowed : 21.13 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.91 (0.22), residues: 1364 helix: 1.73 (0.19), residues: 684 sheet: -0.77 (0.30), residues: 256 loop : -0.23 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 59 TYR 0.046 0.002 TYR B 137 PHE 0.021 0.002 PHE B 79 TRP 0.008 0.001 TRP B 313 HIS 0.004 0.000 HIS C 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (10672) covalent geometry : angle 0.63573 / 0.32 (14464) hydrogen bonds : bond 0.03308 / 2.29 ( 564) hydrogen bonds : angle 4.04246 / 2.92 ( 1608) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 169 time to evaluate : 0.407 Fit side-chains revert: symmetry clash REVERT: B 79 PHE cc_start: 0.8994 (t80) cc_final: 0.8732 (t80) REVERT: B 134 CYS cc_start: 0.8287 (p) cc_final: 0.7968 (p) REVERT: B 250 MET cc_start: 0.8749 (tpt) cc_final: 0.8409 (tpp) REVERT: A 67 ASP cc_start: 0.8926 (p0) cc_final: 0.8448 (t0) REVERT: A 250 MET cc_start: 0.8738 (tpp) cc_final: 0.8513 (tpt) REVERT: A 311 LYS cc_start: 0.9657 (ttpp) cc_final: 0.9391 (ttpp) REVERT: A 326 GLU cc_start: 0.8905 (OUTLIER) cc_final: 0.8533 (pp20) REVERT: C 67 ASP cc_start: 0.9011 (p0) cc_final: 0.8760 (t0) REVERT: D 229 LYS cc_start: 0.9318 (tttt) cc_final: 0.8963 (tptt) REVERT: D 250 MET cc_start: 0.8766 (mmm) cc_final: 0.8536 (tpp) REVERT: D 330 ARG cc_start: 0.9134 (mmm160) cc_final: 0.8552 (ttp-170) outliers start: 19 outliers final: 14 residues processed: 180 average time/residue: 0.0948 time to fit residues: 24.7706 Evaluate side-chains 164 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 149 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 343 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: [41, 94, 68, 131, 16, 25, 92, 132, 86, 125, 15] chunk 41 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 68 optimal weight: 0.2980 chunk 131 optimal weight: 0.0570 chunk 16 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 15 optimal weight: 0.0050 overall best weight: 0.3512 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 60 GLN B 80 HIS ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 GLN C 80 HIS D 60 GLN D 80 HIS ** D 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.094643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.073804 restraints weight = 29629.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.076257 restraints weight = 16313.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.077768 restraints weight = 11138.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.078745 restraints weight = 8761.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.079340 restraints weight = 7544.078| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.5026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10672 Z= 0.121 Angle : 0.666 12.224 14464 Z= 0.336 Chirality : 0.043 0.196 1644 Planarity : 0.005 0.093 1880 Dihedral : 4.058 20.021 1472 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.53 % Allowed : 22.21 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.93 (0.23), residues: 1364 helix: 1.74 (0.19), residues: 680 sheet: -0.42 (0.32), residues: 232 loop : -0.45 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 56 TYR 0.055 0.002 TYR B 137 PHE 0.024 0.002 PHE D 79 TRP 0.011 0.001 TRP A 313 HIS 0.008 0.001 HIS D 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (10672) covalent geometry : angle 0.66594 / 0.34 (14464) hydrogen bonds : bond 0.03298 / 2.26 ( 564) hydrogen bonds : angle 4.10011 / 2.96 ( 1608) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 169 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 79 PHE cc_start: 0.8956 (t80) cc_final: 0.8741 (t80) REVERT: B 134 CYS cc_start: 0.8261 (p) cc_final: 0.7876 (p) REVERT: B 164 MET cc_start: 0.8540 (tmm) cc_final: 0.8194 (ptt) REVERT: B 250 MET cc_start: 0.8749 (tpt) cc_final: 0.8403 (tpp) REVERT: B 301 TYR cc_start: 0.6822 (m-80) cc_final: 0.6508 (m-10) REVERT: B 306 GLN cc_start: 0.7392 (pp30) cc_final: 0.7076 (pp30) REVERT: A 67 ASP cc_start: 0.8907 (p0) cc_final: 0.8410 (t0) REVERT: A 68 ARG cc_start: 0.8784 (mtm180) cc_final: 0.8408 (mtm180) REVERT: A 250 MET cc_start: 0.8741 (tpp) cc_final: 0.8514 (tpt) REVERT: C 67 ASP cc_start: 0.8914 (p0) cc_final: 0.8690 (t0) REVERT: C 130 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8743 (tt) REVERT: D 229 LYS cc_start: 0.9306 (tttt) cc_final: 0.8949 (tptt) REVERT: D 250 MET cc_start: 0.8755 (mmm) cc_final: 0.8529 (tpp) outliers start: 17 outliers final: 13 residues processed: 178 average time/residue: 0.0830 time to fit residues: 22.1675 Evaluate side-chains 170 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 156 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain C residue 60 GLN Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 343 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: [87, 63, 33, 47, 73, 88, 19, 101, 21, 67, 54] chunk 87 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 33 optimal weight: 0.3980 chunk 47 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 54 optimal weight: 0.3980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 60 GLN B 80 HIS ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 168 ASN ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 GLN C 60 GLN C 80 HIS C 168 ASN D 80 HIS ** D 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.094178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.073442 restraints weight = 29960.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.075899 restraints weight = 16402.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.077403 restraints weight = 11164.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.078374 restraints weight = 8771.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.078884 restraints weight = 7543.288| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.5124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10672 Z= 0.125 Angle : 0.669 12.335 14464 Z= 0.337 Chirality : 0.042 0.181 1644 Planarity : 0.005 0.092 1880 Dihedral : 4.032 19.887 1472 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.53 % Allowed : 22.66 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.96 (0.23), residues: 1364 helix: 1.78 (0.19), residues: 680 sheet: -0.60 (0.31), residues: 252 loop : -0.33 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 59 TYR 0.053 0.002 TYR B 137 PHE 0.019 0.002 PHE B 79 TRP 0.012 0.001 TRP A 313 HIS 0.002 0.000 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (10672) covalent geometry : angle 0.66874 / 0.34 (14464) hydrogen bonds : bond 0.03326 / 2.28 ( 564) hydrogen bonds : angle 4.09011 / 2.96 ( 1608) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1749.26 seconds wall clock time: 31 minutes 10.40 seconds (1870.40 seconds total)