Starting phenix.real_space_refine on Fri Aug 7 05:03:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vxh_43617/08_2026/8vxh_43617.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vxh_43617/08_2026/8vxh_43617.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8vxh_43617/08_2026/8vxh_43617.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vxh_43617/08_2026/8vxh_43617.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vxh_43617/08_2026/8vxh_43617.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vxh_43617/08_2026/8vxh_43617.map" } resolution = 2.79 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= 0.001 sd= 0.044 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 52 5.16 5 C 6212 2.51 5 N 1692 2.21 5 O 1756 1.98 5 H 9956 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19668 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 4917 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 13, 'TRANS': 298} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 14 Restraints were copied for chains: B, C, D Time building chain proxies: 4.54, per 1000 atoms: 0.23 Number of scatterers: 19668 At special positions: 0 Unit cell: (112.35, 112.35, 107.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 O 1756 8.00 N 1692 7.00 C 6212 6.00 H 9956 1.00 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: 1.53 Conformation dependent library (CDL) restraints added in 525.2 milliseconds 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2336 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 4 sheets defined 56.7% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 22 through 36 Processing helix chain 'A' and resid 53 through 64 Processing helix chain 'A' and resid 79 through 89 Processing helix chain 'A' and resid 106 through 108 No H-bonds generated for 'chain 'A' and resid 106 through 108' Processing helix chain 'A' and resid 109 through 118 Processing helix chain 'A' and resid 134 through 153 Processing helix chain 'A' and resid 168 through 175 Processing helix chain 'A' and resid 183 through 192 removed outlier: 3.677A pdb=" N PHE A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 229 Processing helix chain 'A' and resid 230 through 262 removed outlier: 3.715A pdb=" N ARG A 234 " --> pdb=" O THR A 230 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU A 236 " --> pdb=" O PRO A 232 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N SER A 237 " --> pdb=" O LEU A 233 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU A 238 " --> pdb=" O ARG A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 304 removed outlier: 3.710A pdb=" N TYR A 294 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG A 297 " --> pdb=" O GLU A 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 36 Processing helix chain 'B' and resid 53 through 64 Processing helix chain 'B' and resid 79 through 89 Processing helix chain 'B' and resid 106 through 108 No H-bonds generated for 'chain 'B' and resid 106 through 108' Processing helix chain 'B' and resid 109 through 118 Processing helix chain 'B' and resid 134 through 153 Processing helix chain 'B' and resid 168 through 175 Processing helix chain 'B' and resid 183 through 192 removed outlier: 3.677A pdb=" N PHE B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 229 Processing helix chain 'B' and resid 230 through 262 removed outlier: 3.715A pdb=" N ARG B 234 " --> pdb=" O THR B 230 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU B 236 " --> pdb=" O PRO B 232 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N SER B 237 " --> pdb=" O LEU B 233 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU B 238 " --> pdb=" O ARG B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 304 removed outlier: 3.711A pdb=" N TYR B 294 " --> pdb=" O LEU B 290 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG B 297 " --> pdb=" O GLU B 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 36 Processing helix chain 'C' and resid 53 through 64 Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 106 through 108 No H-bonds generated for 'chain 'C' and resid 106 through 108' Processing helix chain 'C' and resid 109 through 118 Processing helix chain 'C' and resid 134 through 153 Processing helix chain 'C' and resid 168 through 175 Processing helix chain 'C' and resid 183 through 192 removed outlier: 3.677A pdb=" N PHE C 191 " --> pdb=" O LEU C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 229 Processing helix chain 'C' and resid 230 through 262 removed outlier: 3.714A pdb=" N ARG C 234 " --> pdb=" O THR C 230 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU C 236 " --> pdb=" O PRO C 232 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N SER C 237 " --> pdb=" O LEU C 233 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU C 238 " --> pdb=" O ARG C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 304 removed outlier: 3.710A pdb=" N TYR C 294 " --> pdb=" O LEU C 290 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG C 297 " --> pdb=" O GLU C 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 36 Processing helix chain 'D' and resid 53 through 64 Processing helix chain 'D' and resid 79 through 89 Processing helix chain 'D' and resid 106 through 108 No H-bonds generated for 'chain 'D' and resid 106 through 108' Processing helix chain 'D' and resid 109 through 118 Processing helix chain 'D' and resid 134 through 153 Processing helix chain 'D' and resid 168 through 175 Processing helix chain 'D' and resid 183 through 192 removed outlier: 3.677A pdb=" N PHE D 191 " --> pdb=" O LEU D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 229 Processing helix chain 'D' and resid 230 through 262 removed outlier: 3.715A pdb=" N ARG D 234 " --> pdb=" O THR D 230 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU D 236 " --> pdb=" O PRO D 232 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N SER D 237 " --> pdb=" O LEU D 233 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU D 238 " --> pdb=" O ARG D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 304 removed outlier: 3.710A pdb=" N TYR D 294 " --> pdb=" O LEU D 290 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG D 297 " --> pdb=" O GLU D 293 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 195 through 200 removed outlier: 6.403A pdb=" N VAL A 123 " --> pdb=" O THR A 196 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N ILE A 198 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLY A 125 " --> pdb=" O ILE A 198 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N VAL A 200 " --> pdb=" O GLY A 125 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N VAL A 127 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG A 164 " --> pdb=" O THR A 98 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N ILE A 70 " --> pdb=" O TRP A 41 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE A 43 " --> pdb=" O ILE A 70 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N ILE A 72 " --> pdb=" O ILE A 43 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LEU A 45 " --> pdb=" O ILE A 72 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N LEU A 74 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASP A 47 " --> pdb=" O LEU A 74 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N SER A 71 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N VAL B 313 " --> pdb=" O SER A 71 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LEU A 73 " --> pdb=" O GLN B 311 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 310 through 314 removed outlier: 6.976A pdb=" N LEU D 73 " --> pdb=" O GLN A 311 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N VAL A 313 " --> pdb=" O SER D 71 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N SER D 71 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N ILE D 70 " --> pdb=" O TRP D 41 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ILE D 43 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N ILE D 72 " --> pdb=" O ILE D 43 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N LEU D 45 " --> pdb=" O ILE D 72 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N LEU D 74 " --> pdb=" O LEU D 45 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASP D 47 " --> pdb=" O LEU D 74 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG D 164 " --> pdb=" O THR D 98 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL D 123 " --> pdb=" O THR D 196 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N ILE D 198 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLY D 125 " --> pdb=" O ILE D 198 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N VAL D 200 " --> pdb=" O GLY D 125 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N VAL D 127 " --> pdb=" O VAL D 200 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 195 through 200 removed outlier: 6.404A pdb=" N VAL B 123 " --> pdb=" O THR B 196 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N ILE B 198 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLY B 125 " --> pdb=" O ILE B 198 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N VAL B 200 " --> pdb=" O GLY B 125 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N VAL B 127 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG B 164 " --> pdb=" O THR B 98 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N ILE B 70 " --> pdb=" O TRP B 41 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE B 43 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N ILE B 72 " --> pdb=" O ILE B 43 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N LEU B 45 " --> pdb=" O ILE B 72 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N LEU B 74 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASP B 47 " --> pdb=" O LEU B 74 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N SER B 71 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL C 313 " --> pdb=" O SER B 71 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LEU B 73 " --> pdb=" O GLN C 311 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 195 through 200 removed outlier: 6.403A pdb=" N VAL C 123 " --> pdb=" O THR C 196 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N ILE C 198 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLY C 125 " --> pdb=" O ILE C 198 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N VAL C 200 " --> pdb=" O GLY C 125 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N VAL C 127 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG C 164 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N ILE C 70 " --> pdb=" O TRP C 41 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE C 43 " --> pdb=" O ILE C 70 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N ILE C 72 " --> pdb=" O ILE C 43 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LEU C 45 " --> pdb=" O ILE C 72 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N LEU C 74 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASP C 47 " --> pdb=" O LEU C 74 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N SER C 71 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N VAL D 313 " --> pdb=" O SER C 71 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LEU C 73 " --> pdb=" O GLN D 311 " (cutoff:3.500A) 576 hydrogen bonds defined for protein. 1716 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: 3.56 Time building geometry restraints manager: 2.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9940 1.03 - 1.23: 16 1.23 - 1.42: 4008 1.42 - 1.61: 5788 1.61 - 1.81: 88 Bond restraints: 19840 Sorted by residual: bond pdb=" CA ILE A 184 " pdb=" CB ILE A 184 " ideal model delta sigma weight residual 1.539 1.535 0.004 5.40e-03 3.43e+04 6.76e-01 bond pdb=" CA ILE B 184 " pdb=" CB ILE B 184 " ideal model delta sigma weight residual 1.539 1.535 0.004 5.40e-03 3.43e+04 6.64e-01 bond pdb=" CA ILE C 184 " pdb=" CB ILE C 184 " ideal model delta sigma weight residual 1.539 1.535 0.004 5.40e-03 3.43e+04 6.42e-01 bond pdb=" CA ILE D 184 " pdb=" CB ILE D 184 " ideal model delta sigma weight residual 1.539 1.535 0.004 5.40e-03 3.43e+04 5.05e-01 bond pdb=" CA ASP B 48 " pdb=" C ASP B 48 " ideal model delta sigma weight residual 1.530 1.523 0.007 1.14e-02 7.69e+03 4.02e-01 ... (remaining 19835 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.87: 32305 0.87 - 1.74: 3398 1.74 - 2.61: 149 2.61 - 3.49: 48 3.49 - 4.36: 20 Bond angle restraints: 35920 Sorted by residual: angle pdb=" C GLU A 109 " pdb=" N ILE A 110 " pdb=" CA ILE A 110 " ideal model delta sigma weight residual 120.33 122.74 -2.41 8.00e-01 1.56e+00 9.06e+00 angle pdb=" C GLU B 109 " pdb=" N ILE B 110 " pdb=" CA ILE B 110 " ideal model delta sigma weight residual 120.33 122.73 -2.40 8.00e-01 1.56e+00 8.97e+00 angle pdb=" C GLU C 109 " pdb=" N ILE C 110 " pdb=" CA ILE C 110 " ideal model delta sigma weight residual 120.33 122.72 -2.39 8.00e-01 1.56e+00 8.91e+00 angle pdb=" C GLU D 109 " pdb=" N ILE D 110 " pdb=" CA ILE D 110 " ideal model delta sigma weight residual 120.33 122.71 -2.38 8.00e-01 1.56e+00 8.87e+00 angle pdb=" C ILE A 110 " pdb=" CA ILE A 110 " pdb=" CB ILE A 110 " ideal model delta sigma weight residual 114.00 110.87 3.13 1.31e+00 5.83e-01 5.71e+00 ... (remaining 35915 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.13: 8657 16.13 - 32.26: 347 32.26 - 48.40: 151 48.40 - 64.53: 101 64.53 - 80.66: 8 Dihedral angle restraints: 9264 sinusoidal: 5128 harmonic: 4136 Sorted by residual: dihedral pdb=" CA ARG A 303 " pdb=" C ARG A 303 " pdb=" N ALA A 304 " pdb=" CA ALA A 304 " ideal model delta harmonic sigma weight residual 180.00 159.19 20.81 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA ARG B 303 " pdb=" C ARG B 303 " pdb=" N ALA B 304 " pdb=" CA ALA B 304 " ideal model delta harmonic sigma weight residual 180.00 159.19 20.81 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA ARG D 303 " pdb=" C ARG D 303 " pdb=" N ALA D 304 " pdb=" CA ALA D 304 " ideal model delta harmonic sigma weight residual 180.00 159.20 20.80 0 5.00e+00 4.00e-02 1.73e+01 ... (remaining 9261 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 982 0.025 - 0.051: 322 0.051 - 0.076: 156 0.076 - 0.102: 42 0.102 - 0.127: 78 Chirality restraints: 1580 Sorted by residual: chirality pdb=" CA ILE B 70 " pdb=" N ILE B 70 " pdb=" C ILE B 70 " pdb=" CB ILE B 70 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.03e-01 chirality pdb=" CA ILE D 70 " pdb=" N ILE D 70 " pdb=" C ILE D 70 " pdb=" CB ILE D 70 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.99e-01 chirality pdb=" CA ILE C 70 " pdb=" N ILE C 70 " pdb=" C ILE C 70 " pdb=" CB ILE C 70 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.97e-01 ... (remaining 1577 not shown) Planarity restraints: 2892 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 106 " -0.018 5.00e-02 4.00e+02 2.65e-02 1.12e+00 pdb=" N PRO A 107 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO A 107 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 107 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 106 " 0.017 5.00e-02 4.00e+02 2.64e-02 1.11e+00 pdb=" N PRO B 107 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO B 107 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 107 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 106 " -0.017 5.00e-02 4.00e+02 2.64e-02 1.11e+00 pdb=" N PRO D 107 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO D 107 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO D 107 " -0.015 5.00e-02 4.00e+02 ... (remaining 2889 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.22: 1319 2.22 - 2.81: 41355 2.81 - 3.41: 51167 3.41 - 4.00: 68161 4.00 - 4.60: 106876 Nonbonded interactions: 268878 Sorted by model distance: nonbonded pdb=" O MET A 215 " pdb="HD21 ASN A 219 " model vdw 1.622 2.450 nonbonded pdb=" O MET D 215 " pdb="HD21 ASN D 219 " model vdw 1.622 2.450 nonbonded pdb=" O MET C 215 " pdb="HD21 ASN C 219 " model vdw 1.622 2.450 nonbonded pdb=" O MET B 215 " pdb="HD21 ASN B 219 " model vdw 1.623 2.450 nonbonded pdb=" OD1 ASP B 223 " pdb="HH21 ARG C 297 " model vdw 1.649 2.450 ... (remaining 268873 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.570 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: 0.140 Extract box with map and model: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 18.030 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 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 : 0.002 0.018 9884 Z= 0.109 Angle : 0.462 4.356 13392 Z= 0.270 Chirality : 0.040 0.127 1580 Planarity : 0.003 0.026 1704 Dihedral : 9.660 80.662 3660 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 1.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.14 (0.25), residues: 1232 helix: 3.42 (0.21), residues: 676 sheet: 2.12 (0.39), residues: 204 loop : -0.85 (0.30), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 297 TYR 0.007 0.001 TYR A 299 PHE 0.006 0.001 PHE D 183 TRP 0.002 0.000 TRP D 41 HIS 0.002 0.001 HIS A 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.11 ( 9884) covalent geometry : angle 0.46179 / 0.27 (13392) hydrogen bonds : bond 0.13551 / 9.43 ( 576) hydrogen bonds : angle 6.03222 / 4.15 ( 1716) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 212 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Evaluate side-chains 220 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.6687 (tt0) cc_final: 0.6423 (mt-10) REVERT: A 122 ASP cc_start: 0.8922 (m-30) cc_final: 0.8702 (m-30) REVERT: A 149 GLN cc_start: 0.7414 (tt0) cc_final: 0.7090 (tp40) REVERT: A 221 MET cc_start: 0.7337 (mmp) cc_final: 0.6497 (tmt) REVERT: A 255 ILE cc_start: 0.8140 (mm) cc_final: 0.7893 (mp) REVERT: B 64 GLU cc_start: 0.6638 (tt0) cc_final: 0.6379 (mt-10) REVERT: B 149 GLN cc_start: 0.7354 (tt0) cc_final: 0.7092 (tp40) REVERT: B 221 MET cc_start: 0.7292 (mmp) cc_final: 0.6413 (tmt) REVERT: C 122 ASP cc_start: 0.8944 (m-30) cc_final: 0.8651 (m-30) REVERT: C 149 GLN cc_start: 0.7353 (tt0) cc_final: 0.7047 (tp40) REVERT: C 221 MET cc_start: 0.7312 (mmp) cc_final: 0.6462 (tmt) REVERT: D 64 GLU cc_start: 0.6609 (tt0) cc_final: 0.6362 (mt-10) REVERT: D 122 ASP cc_start: 0.8924 (m-30) cc_final: 0.8638 (m-30) REVERT: D 149 GLN cc_start: 0.7386 (tt0) cc_final: 0.7084 (tp40) REVERT: D 221 MET cc_start: 0.7364 (mmp) cc_final: 0.6504 (tmt) REVERT: D 255 ILE cc_start: 0.8104 (mm) cc_final: 0.7903 (mp) outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.9054 time to fit residues: 216.4319 Evaluate side-chains 162 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 0.0970 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 130 ASN A 132 GLN B 130 ASN B 132 GLN C 130 ASN C 132 GLN D 130 ASN D 132 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.151700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.117091 restraints weight = 31375.386| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.90 r_work: 0.3284 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9884 Z= 0.151 Angle : 0.507 4.559 13392 Z= 0.272 Chirality : 0.044 0.152 1580 Planarity : 0.005 0.031 1704 Dihedral : 3.814 24.557 1368 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 1.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.24 % Allowed : 5.63 % Favored : 93.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.47 (0.24), residues: 1232 helix: 2.86 (0.20), residues: 688 sheet: 2.32 (0.40), residues: 168 loop : -1.20 (0.28), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 176 TYR 0.007 0.001 TYR C 166 PHE 0.008 0.001 PHE B 88 TRP 0.004 0.001 TRP A 41 HIS 0.002 0.001 HIS C 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 9884) covalent geometry : angle 0.50659 / 0.27 (13392) hydrogen bonds : bond 0.06114 / 4.20 ( 576) hydrogen bonds : angle 4.74880 / 3.27 ( 1716) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 212 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Evaluate side-chains 172 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 159 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8246 (ptmt) cc_final: 0.7436 (pttt) REVERT: A 64 GLU cc_start: 0.6895 (tt0) cc_final: 0.6455 (mt-10) REVERT: A 122 ASP cc_start: 0.9091 (m-30) cc_final: 0.8807 (m-30) REVERT: A 149 GLN cc_start: 0.7269 (tt0) cc_final: 0.6808 (tp40) REVERT: A 221 MET cc_start: 0.7450 (mmp) cc_final: 0.6457 (tmt) REVERT: A 251 SER cc_start: 0.8433 (OUTLIER) cc_final: 0.8210 (m) REVERT: B 8 LYS cc_start: 0.8134 (ptmt) cc_final: 0.7353 (pttt) REVERT: B 64 GLU cc_start: 0.6897 (tt0) cc_final: 0.6450 (mt-10) REVERT: B 122 ASP cc_start: 0.9077 (m-30) cc_final: 0.8864 (m-30) REVERT: B 149 GLN cc_start: 0.7129 (tt0) cc_final: 0.6697 (tp40) REVERT: B 221 MET cc_start: 0.7558 (mmp) cc_final: 0.6600 (tmt) REVERT: B 251 SER cc_start: 0.8185 (OUTLIER) cc_final: 0.7965 (m) REVERT: C 8 LYS cc_start: 0.8192 (ptmt) cc_final: 0.7415 (pttt) REVERT: C 142 LYS cc_start: 0.7363 (mptm) cc_final: 0.7130 (mptm) REVERT: C 149 GLN cc_start: 0.7231 (tt0) cc_final: 0.6755 (tp40) REVERT: C 215 MET cc_start: 0.6020 (mmp) cc_final: 0.5726 (mmt) REVERT: C 221 MET cc_start: 0.7498 (mmp) cc_final: 0.6535 (tmt) REVERT: C 251 SER cc_start: 0.8220 (OUTLIER) cc_final: 0.7976 (m) REVERT: D 8 LYS cc_start: 0.8159 (ptmt) cc_final: 0.7381 (pttt) REVERT: D 64 GLU cc_start: 0.6898 (tt0) cc_final: 0.6456 (mt-10) REVERT: D 149 GLN cc_start: 0.7226 (tt0) cc_final: 0.6792 (tp40) REVERT: D 221 MET cc_start: 0.7459 (mmp) cc_final: 0.6465 (tmt) REVERT: D 251 SER cc_start: 0.8244 (OUTLIER) cc_final: 0.7988 (m) outliers start: 13 outliers final: 4 residues processed: 162 average time/residue: 0.8470 time to fit residues: 151.0048 Evaluate side-chains 168 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 160 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 251 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 92 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 63.9499 > 50:) chunk 37 optimal weight: 2.9990 chunk 20 optimal weight: 0.2980 chunk 2 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 132 GLN A 300 ASN B 132 GLN B 300 ASN C 132 GLN C 300 ASN D 132 GLN D 300 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.149451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.114582 restraints weight = 31284.630| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.90 r_work: 0.3253 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 9884 Z= 0.153 Angle : 0.504 4.366 13392 Z= 0.269 Chirality : 0.043 0.143 1580 Planarity : 0.005 0.035 1704 Dihedral : 3.964 25.461 1368 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.24 % Allowed : 6.97 % Favored : 91.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.13 (0.25), residues: 1232 helix: 2.66 (0.20), residues: 680 sheet: 2.18 (0.41), residues: 168 loop : -1.41 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 128 TYR 0.006 0.001 TYR C 315 PHE 0.007 0.001 PHE D 309 TRP 0.004 0.001 TRP B 41 HIS 0.002 0.001 HIS B 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 ( 9884) covalent geometry : angle 0.50412 / 0.27 (13392) hydrogen bonds : bond 0.06346 / 4.36 ( 576) hydrogen bonds : angle 4.46932 / 3.09 ( 1716) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 212 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Evaluate side-chains 184 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 171 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8306 (ptmt) cc_final: 0.7504 (pttt) REVERT: A 64 GLU cc_start: 0.7082 (tt0) cc_final: 0.6561 (mt-10) REVERT: A 122 ASP cc_start: 0.9096 (m-30) cc_final: 0.8807 (m-30) REVERT: A 132 GLN cc_start: 0.6658 (mt0) cc_final: 0.6417 (pp30) REVERT: A 149 GLN cc_start: 0.7345 (tt0) cc_final: 0.6792 (tp40) REVERT: A 221 MET cc_start: 0.7452 (mmp) cc_final: 0.6503 (tmm) REVERT: A 251 SER cc_start: 0.8315 (OUTLIER) cc_final: 0.7513 (p) REVERT: B 8 LYS cc_start: 0.8287 (ptmt) cc_final: 0.7478 (pttt) REVERT: B 64 GLU cc_start: 0.7037 (tt0) cc_final: 0.6519 (mt-10) REVERT: B 122 ASP cc_start: 0.9070 (m-30) cc_final: 0.8843 (m-30) REVERT: B 142 LYS cc_start: 0.7392 (mptm) cc_final: 0.7073 (mptm) REVERT: B 149 GLN cc_start: 0.7202 (tt0) cc_final: 0.6665 (tp40) REVERT: B 251 SER cc_start: 0.8237 (OUTLIER) cc_final: 0.7655 (p) REVERT: B 272 MET cc_start: 0.6906 (ttp) cc_final: 0.6416 (mmm) REVERT: C 8 LYS cc_start: 0.8321 (ptmt) cc_final: 0.7512 (pttt) REVERT: C 144 ILE cc_start: 0.7557 (mm) cc_final: 0.7314 (mt) REVERT: C 149 GLN cc_start: 0.7388 (tt0) cc_final: 0.6828 (tp40) REVERT: C 251 SER cc_start: 0.8245 (OUTLIER) cc_final: 0.7640 (p) REVERT: C 272 MET cc_start: 0.6868 (ttp) cc_final: 0.6372 (mmm) REVERT: D 8 LYS cc_start: 0.8283 (ptmt) cc_final: 0.7478 (pttt) REVERT: D 64 GLU cc_start: 0.7034 (tt0) cc_final: 0.6530 (mt-10) REVERT: D 132 GLN cc_start: 0.6748 (mt0) cc_final: 0.6414 (pp30) REVERT: D 149 GLN cc_start: 0.7197 (tt0) cc_final: 0.6657 (tp40) REVERT: D 251 SER cc_start: 0.8267 (OUTLIER) cc_final: 0.7460 (p) outliers start: 13 outliers final: 4 residues processed: 175 average time/residue: 0.9608 time to fit residues: 184.7970 Evaluate side-chains 167 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 159 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 251 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 300 ASN B 132 GLN B 300 ASN C 132 GLN C 300 ASN D 300 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.151109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.115948 restraints weight = 31334.792| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.93 r_work: 0.3271 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 9884 Z= 0.113 Angle : 0.462 4.301 13392 Z= 0.244 Chirality : 0.041 0.140 1580 Planarity : 0.004 0.036 1704 Dihedral : 3.803 24.631 1368 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 1.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.86 % Allowed : 7.92 % Favored : 91.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.23 (0.25), residues: 1232 helix: 2.85 (0.20), residues: 676 sheet: 2.00 (0.43), residues: 168 loop : -1.44 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 128 TYR 0.006 0.001 TYR D 159 PHE 0.006 0.001 PHE C 309 TRP 0.001 0.000 TRP D 41 HIS 0.002 0.001 HIS C 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 ( 9884) covalent geometry : angle 0.46156 / 0.24 (13392) hydrogen bonds : bond 0.05280 / 3.64 ( 576) hydrogen bonds : angle 4.31964 / 2.99 ( 1716) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 212 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Evaluate side-chains 178 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 169 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8264 (ptmt) cc_final: 0.7478 (pttt) REVERT: A 60 LYS cc_start: 0.8310 (ttmt) cc_final: 0.7864 (ttpp) REVERT: A 64 GLU cc_start: 0.7063 (tt0) cc_final: 0.6515 (mt-10) REVERT: A 122 ASP cc_start: 0.9092 (m-30) cc_final: 0.8885 (m-30) REVERT: A 132 GLN cc_start: 0.6699 (mt0) cc_final: 0.6416 (pp30) REVERT: A 149 GLN cc_start: 0.7344 (tt0) cc_final: 0.6754 (tp40) REVERT: A 251 SER cc_start: 0.8386 (OUTLIER) cc_final: 0.7570 (p) REVERT: B 8 LYS cc_start: 0.8207 (ptmt) cc_final: 0.7410 (pttt) REVERT: B 60 LYS cc_start: 0.8244 (ttmt) cc_final: 0.7843 (ttpp) REVERT: B 64 GLU cc_start: 0.7028 (tt0) cc_final: 0.6495 (mt-10) REVERT: B 122 ASP cc_start: 0.9044 (m-30) cc_final: 0.8808 (m-30) REVERT: B 149 GLN cc_start: 0.7173 (tt0) cc_final: 0.6639 (tp40) REVERT: B 251 SER cc_start: 0.8205 (OUTLIER) cc_final: 0.7610 (p) REVERT: B 272 MET cc_start: 0.6840 (ttp) cc_final: 0.6365 (mmm) REVERT: C 8 LYS cc_start: 0.8243 (ptmt) cc_final: 0.7454 (pttt) REVERT: C 144 ILE cc_start: 0.7553 (mm) cc_final: 0.7314 (mt) REVERT: C 149 GLN cc_start: 0.7354 (tt0) cc_final: 0.6794 (tp40) REVERT: C 215 MET cc_start: 0.6055 (mmp) cc_final: 0.5636 (mmt) REVERT: C 251 SER cc_start: 0.8217 (OUTLIER) cc_final: 0.7408 (p) REVERT: D 8 LYS cc_start: 0.8213 (ptmt) cc_final: 0.7414 (pttt) REVERT: D 60 LYS cc_start: 0.8286 (ttmt) cc_final: 0.7833 (ttpp) REVERT: D 64 GLU cc_start: 0.7025 (tt0) cc_final: 0.6523 (mt-10) REVERT: D 132 GLN cc_start: 0.6740 (mt0) cc_final: 0.6404 (pp30) REVERT: D 149 GLN cc_start: 0.7291 (tt0) cc_final: 0.6765 (tp40) REVERT: D 251 SER cc_start: 0.8223 (OUTLIER) cc_final: 0.7431 (p) outliers start: 9 outliers final: 4 residues processed: 173 average time/residue: 0.8734 time to fit residues: 166.3450 Evaluate side-chains 170 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 162 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 251 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 107 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 111 optimal weight: 0.6980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 300 ASN B 300 ASN C 300 ASN D 300 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.149486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.114475 restraints weight = 31255.891| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.92 r_work: 0.3257 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9884 Z= 0.130 Angle : 0.469 4.219 13392 Z= 0.249 Chirality : 0.042 0.143 1580 Planarity : 0.005 0.037 1704 Dihedral : 3.865 25.385 1368 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.15 % Allowed : 8.11 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.25), residues: 1232 helix: 2.74 (0.20), residues: 676 sheet: 1.65 (0.42), residues: 176 loop : -1.50 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 128 TYR 0.007 0.001 TYR B 159 PHE 0.006 0.001 PHE A 309 TRP 0.003 0.001 TRP D 41 HIS 0.002 0.001 HIS A 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 9884) covalent geometry : angle 0.46912 / 0.25 (13392) hydrogen bonds : bond 0.05673 / 3.90 ( 576) hydrogen bonds : angle 4.27883 / 2.96 ( 1716) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 212 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Evaluate side-chains 184 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 172 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8261 (ptmt) cc_final: 0.7469 (pttt) REVERT: A 64 GLU cc_start: 0.7169 (tt0) cc_final: 0.6629 (mt-10) REVERT: A 122 ASP cc_start: 0.9098 (m-30) cc_final: 0.8816 (m-30) REVERT: A 132 GLN cc_start: 0.6700 (mt0) cc_final: 0.6433 (pp30) REVERT: A 144 ILE cc_start: 0.7486 (mm) cc_final: 0.7250 (mt) REVERT: A 149 GLN cc_start: 0.7278 (tt0) cc_final: 0.6699 (tp40) REVERT: A 251 SER cc_start: 0.8357 (OUTLIER) cc_final: 0.7750 (p) REVERT: A 272 MET cc_start: 0.6778 (ttm) cc_final: 0.6520 (mmm) REVERT: B 8 LYS cc_start: 0.8210 (ptmt) cc_final: 0.7412 (pttt) REVERT: B 64 GLU cc_start: 0.7122 (tt0) cc_final: 0.6548 (mt-10) REVERT: B 142 LYS cc_start: 0.7378 (mptm) cc_final: 0.7139 (mptm) REVERT: B 149 GLN cc_start: 0.7076 (tt0) cc_final: 0.6515 (tp40) REVERT: B 251 SER cc_start: 0.8181 (OUTLIER) cc_final: 0.7551 (p) REVERT: B 272 MET cc_start: 0.6886 (ttp) cc_final: 0.6429 (mmm) REVERT: C 8 LYS cc_start: 0.8235 (ptmt) cc_final: 0.7450 (pttt) REVERT: C 149 GLN cc_start: 0.7326 (tt0) cc_final: 0.6734 (tp40) REVERT: C 251 SER cc_start: 0.8249 (OUTLIER) cc_final: 0.7625 (p) REVERT: C 272 MET cc_start: 0.6871 (ttp) cc_final: 0.6399 (mmm) REVERT: D 8 LYS cc_start: 0.8210 (ptmt) cc_final: 0.7418 (pttt) REVERT: D 64 GLU cc_start: 0.7144 (tt0) cc_final: 0.6561 (mt-10) REVERT: D 144 ILE cc_start: 0.7487 (mm) cc_final: 0.7246 (mt) REVERT: D 149 GLN cc_start: 0.7263 (tt0) cc_final: 0.6708 (tp40) REVERT: D 251 SER cc_start: 0.8262 (OUTLIER) cc_final: 0.7656 (p) REVERT: D 272 MET cc_start: 0.6870 (ttm) cc_final: 0.6599 (mmm) outliers start: 12 outliers final: 4 residues processed: 176 average time/residue: 0.9630 time to fit residues: 186.1151 Evaluate side-chains 170 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 162 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 251 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 0 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 118 optimal weight: 0.0670 chunk 68 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 109 optimal weight: 0.4980 overall best weight: 1.1122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 300 ASN B 132 GLN B 300 ASN C 300 ASN D 132 GLN D 300 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.149611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.114638 restraints weight = 31405.163| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.92 r_work: 0.3260 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 9884 Z= 0.128 Angle : 0.470 4.201 13392 Z= 0.249 Chirality : 0.041 0.142 1580 Planarity : 0.005 0.038 1704 Dihedral : 3.849 24.980 1368 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.15 % Allowed : 8.30 % Favored : 90.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.25), residues: 1232 helix: 2.75 (0.20), residues: 676 sheet: 1.60 (0.42), residues: 176 loop : -1.57 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 128 TYR 0.007 0.001 TYR D 159 PHE 0.005 0.001 PHE A 309 TRP 0.002 0.001 TRP D 41 HIS 0.002 0.001 HIS A 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 9884) covalent geometry : angle 0.47049 / 0.25 (13392) hydrogen bonds : bond 0.05585 / 3.84 ( 576) hydrogen bonds : angle 4.24645 / 2.94 ( 1716) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 212 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Evaluate side-chains 179 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 167 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8277 (ptmt) cc_final: 0.7502 (pttt) REVERT: A 64 GLU cc_start: 0.7243 (tt0) cc_final: 0.6662 (mt-10) REVERT: A 122 ASP cc_start: 0.9111 (m-30) cc_final: 0.8823 (m-30) REVERT: A 132 GLN cc_start: 0.6728 (mt0) cc_final: 0.6439 (pp30) REVERT: A 144 ILE cc_start: 0.7546 (mm) cc_final: 0.7305 (mt) REVERT: A 149 GLN cc_start: 0.7294 (tt0) cc_final: 0.6729 (tp40) REVERT: A 251 SER cc_start: 0.8397 (OUTLIER) cc_final: 0.7806 (p) REVERT: A 272 MET cc_start: 0.6882 (ttm) cc_final: 0.6630 (mmm) REVERT: B 8 LYS cc_start: 0.8237 (ptmt) cc_final: 0.7455 (pttt) REVERT: B 60 LYS cc_start: 0.8139 (ttpt) cc_final: 0.7630 (ttpp) REVERT: B 64 GLU cc_start: 0.7241 (tt0) cc_final: 0.6672 (mt-10) REVERT: B 132 GLN cc_start: 0.6967 (mt0) cc_final: 0.6561 (pp30) REVERT: B 149 GLN cc_start: 0.7118 (tt0) cc_final: 0.6565 (tp40) REVERT: B 251 SER cc_start: 0.8290 (OUTLIER) cc_final: 0.7686 (p) REVERT: B 272 MET cc_start: 0.6920 (ttp) cc_final: 0.6470 (mmm) REVERT: C 8 LYS cc_start: 0.8264 (ptmt) cc_final: 0.7506 (pttt) REVERT: C 60 LYS cc_start: 0.8270 (ttmt) cc_final: 0.7957 (ttpp) REVERT: C 132 GLN cc_start: 0.6917 (mt0) cc_final: 0.6539 (pp30) REVERT: C 142 LYS cc_start: 0.7411 (mptm) cc_final: 0.7075 (mptm) REVERT: C 149 GLN cc_start: 0.7172 (tt0) cc_final: 0.6586 (tp40) REVERT: C 251 SER cc_start: 0.8294 (OUTLIER) cc_final: 0.7673 (p) REVERT: C 272 MET cc_start: 0.6907 (ttp) cc_final: 0.6462 (mmm) REVERT: D 8 LYS cc_start: 0.8238 (ptmt) cc_final: 0.7466 (pttt) REVERT: D 60 LYS cc_start: 0.8104 (ttpt) cc_final: 0.7566 (ttpp) REVERT: D 64 GLU cc_start: 0.7247 (tt0) cc_final: 0.6680 (mt-10) REVERT: D 144 ILE cc_start: 0.7545 (mm) cc_final: 0.7302 (mt) REVERT: D 149 GLN cc_start: 0.7149 (tt0) cc_final: 0.6588 (tp40) REVERT: D 251 SER cc_start: 0.8307 (OUTLIER) cc_final: 0.7718 (p) REVERT: D 272 MET cc_start: 0.6918 (ttm) cc_final: 0.6646 (mmm) outliers start: 12 outliers final: 4 residues processed: 171 average time/residue: 0.9620 time to fit residues: 180.2086 Evaluate side-chains 171 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 163 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 251 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 18 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 87 optimal weight: 0.5980 chunk 77 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 109 optimal weight: 0.0070 chunk 27 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 overall best weight: 1.1002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 300 ASN B 300 ASN C 300 ASN D 300 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.149395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.114429 restraints weight = 31324.366| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.92 r_work: 0.3259 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 9884 Z= 0.127 Angle : 0.468 4.789 13392 Z= 0.247 Chirality : 0.041 0.142 1580 Planarity : 0.005 0.037 1704 Dihedral : 3.850 25.273 1368 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.24 % Allowed : 9.16 % Favored : 89.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.25), residues: 1232 helix: 2.77 (0.20), residues: 676 sheet: 1.53 (0.41), residues: 176 loop : -1.58 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 128 TYR 0.007 0.001 TYR B 159 PHE 0.006 0.001 PHE A 309 TRP 0.002 0.001 TRP D 41 HIS 0.002 0.001 HIS A 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 9884) covalent geometry : angle 0.46768 / 0.25 (13392) hydrogen bonds : bond 0.05585 / 3.84 ( 576) hydrogen bonds : angle 4.21583 / 2.92 ( 1716) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 212 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Evaluate side-chains 176 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 163 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8266 (ptmt) cc_final: 0.7523 (pttt) REVERT: A 64 GLU cc_start: 0.7337 (tt0) cc_final: 0.6732 (mt-10) REVERT: A 122 ASP cc_start: 0.9102 (m-30) cc_final: 0.8818 (m-30) REVERT: A 132 GLN cc_start: 0.6729 (mt0) cc_final: 0.6429 (pp30) REVERT: A 144 ILE cc_start: 0.7462 (mm) cc_final: 0.7219 (mt) REVERT: A 149 GLN cc_start: 0.7132 (tt0) cc_final: 0.6606 (tp40) REVERT: A 251 SER cc_start: 0.8452 (OUTLIER) cc_final: 0.7840 (p) REVERT: A 272 MET cc_start: 0.6916 (ttm) cc_final: 0.6661 (mmm) REVERT: B 8 LYS cc_start: 0.8242 (ptmt) cc_final: 0.7473 (pttt) REVERT: B 60 LYS cc_start: 0.8146 (ttpt) cc_final: 0.7631 (ttpp) REVERT: B 64 GLU cc_start: 0.7297 (tt0) cc_final: 0.6686 (mt-10) REVERT: B 118 ASP cc_start: 0.8047 (OUTLIER) cc_final: 0.7838 (m-30) REVERT: B 132 GLN cc_start: 0.6949 (mt0) cc_final: 0.6565 (pp30) REVERT: B 142 LYS cc_start: 0.7423 (mptm) cc_final: 0.7098 (mptm) REVERT: B 149 GLN cc_start: 0.7157 (tt0) cc_final: 0.6594 (tp40) REVERT: B 251 SER cc_start: 0.8271 (OUTLIER) cc_final: 0.7664 (p) REVERT: B 272 MET cc_start: 0.6969 (ttp) cc_final: 0.6550 (mmm) REVERT: C 8 LYS cc_start: 0.8271 (ptmt) cc_final: 0.7516 (pttt) REVERT: C 60 LYS cc_start: 0.8233 (ttmt) cc_final: 0.7906 (ttpp) REVERT: C 132 GLN cc_start: 0.6894 (mt0) cc_final: 0.6527 (pp30) REVERT: C 142 LYS cc_start: 0.7384 (mptm) cc_final: 0.7037 (mptm) REVERT: C 144 ILE cc_start: 0.7571 (mm) cc_final: 0.7307 (mt) REVERT: C 149 GLN cc_start: 0.7174 (tt0) cc_final: 0.6590 (tp40) REVERT: C 251 SER cc_start: 0.8271 (OUTLIER) cc_final: 0.7661 (p) REVERT: C 272 MET cc_start: 0.6937 (ttp) cc_final: 0.6494 (mmm) REVERT: D 8 LYS cc_start: 0.8254 (ptmt) cc_final: 0.7492 (pttt) REVERT: D 60 LYS cc_start: 0.8133 (ttpt) cc_final: 0.7618 (ttpp) REVERT: D 64 GLU cc_start: 0.7307 (tt0) cc_final: 0.6721 (mt-10) REVERT: D 149 GLN cc_start: 0.7166 (tt0) cc_final: 0.6650 (tp40) REVERT: D 251 SER cc_start: 0.8305 (OUTLIER) cc_final: 0.7702 (p) REVERT: D 272 MET cc_start: 0.6927 (ttm) cc_final: 0.6678 (mmm) outliers start: 13 outliers final: 4 residues processed: 168 average time/residue: 1.0118 time to fit residues: 186.1013 Evaluate side-chains 172 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 163 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 251 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 44 optimal weight: 7.9990 chunk 122 optimal weight: 0.0000 chunk 61 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 109 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 300 ASN B 300 ASN C 300 ASN D 300 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.150016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.115057 restraints weight = 31368.588| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.92 r_work: 0.3269 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 9884 Z= 0.115 Angle : 0.457 4.281 13392 Z= 0.241 Chirality : 0.041 0.141 1580 Planarity : 0.005 0.037 1704 Dihedral : 3.791 24.901 1368 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.95 % Allowed : 9.64 % Favored : 89.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.09 (0.25), residues: 1232 helix: 2.85 (0.20), residues: 676 sheet: 1.54 (0.41), residues: 176 loop : -1.59 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 76 TYR 0.007 0.001 TYR B 159 PHE 0.007 0.001 PHE B 309 TRP 0.002 0.000 TRP A 41 HIS 0.002 0.001 HIS A 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 ( 9884) covalent geometry : angle 0.45682 / 0.24 (13392) hydrogen bonds : bond 0.05291 / 3.64 ( 576) hydrogen bonds : angle 4.18014 / 2.89 ( 1716) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 212 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Evaluate side-chains 177 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 167 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8250 (ptmt) cc_final: 0.7515 (pttt) REVERT: A 60 LYS cc_start: 0.8078 (ttpt) cc_final: 0.7554 (ttpp) REVERT: A 64 GLU cc_start: 0.7346 (tt0) cc_final: 0.6710 (mt-10) REVERT: A 122 ASP cc_start: 0.9102 (m-30) cc_final: 0.8821 (m-30) REVERT: A 144 ILE cc_start: 0.7535 (mm) cc_final: 0.7289 (mt) REVERT: A 149 GLN cc_start: 0.7120 (tt0) cc_final: 0.6597 (tp40) REVERT: A 251 SER cc_start: 0.8435 (OUTLIER) cc_final: 0.7823 (p) REVERT: A 265 TRP cc_start: 0.5988 (m-90) cc_final: 0.5742 (m-90) REVERT: A 272 MET cc_start: 0.6868 (ttm) cc_final: 0.6632 (mmm) REVERT: B 8 LYS cc_start: 0.8233 (ptmt) cc_final: 0.7467 (pttt) REVERT: B 60 LYS cc_start: 0.8165 (ttpt) cc_final: 0.7662 (ttpp) REVERT: B 64 GLU cc_start: 0.7336 (tt0) cc_final: 0.6711 (mt-10) REVERT: B 118 ASP cc_start: 0.8032 (OUTLIER) cc_final: 0.7829 (m-30) REVERT: B 132 GLN cc_start: 0.7041 (mt0) cc_final: 0.6565 (pp30) REVERT: B 149 GLN cc_start: 0.7153 (tt0) cc_final: 0.6583 (tp40) REVERT: B 215 MET cc_start: 0.5995 (mmp) cc_final: 0.5648 (mmt) REVERT: B 251 SER cc_start: 0.8192 (OUTLIER) cc_final: 0.7574 (p) REVERT: B 272 MET cc_start: 0.6915 (ttp) cc_final: 0.6500 (mmm) REVERT: C 8 LYS cc_start: 0.8259 (ptmt) cc_final: 0.7512 (pttt) REVERT: C 60 LYS cc_start: 0.8146 (ttmt) cc_final: 0.7854 (ttpp) REVERT: C 132 GLN cc_start: 0.6961 (mt0) cc_final: 0.6533 (pp30) REVERT: C 142 LYS cc_start: 0.7401 (mptm) cc_final: 0.7055 (mptm) REVERT: C 144 ILE cc_start: 0.7556 (mm) cc_final: 0.7302 (mt) REVERT: C 149 GLN cc_start: 0.7164 (tt0) cc_final: 0.6581 (tp40) REVERT: C 251 SER cc_start: 0.8263 (OUTLIER) cc_final: 0.7653 (p) REVERT: C 272 MET cc_start: 0.6884 (ttp) cc_final: 0.6445 (mmm) REVERT: D 8 LYS cc_start: 0.8241 (ptmt) cc_final: 0.7482 (pttt) REVERT: D 60 LYS cc_start: 0.8129 (ttpt) cc_final: 0.7616 (ttpp) REVERT: D 64 GLU cc_start: 0.7345 (tt0) cc_final: 0.6743 (mt-10) REVERT: D 132 GLN cc_start: 0.6870 (mt0) cc_final: 0.6560 (pp30) REVERT: D 144 ILE cc_start: 0.7547 (mm) cc_final: 0.7301 (mt) REVERT: D 149 GLN cc_start: 0.7153 (tt0) cc_final: 0.6640 (tp40) REVERT: D 251 SER cc_start: 0.8273 (OUTLIER) cc_final: 0.7679 (p) REVERT: D 272 MET cc_start: 0.6898 (ttm) cc_final: 0.6641 (mmm) outliers start: 10 outliers final: 4 residues processed: 173 average time/residue: 0.9830 time to fit residues: 186.4866 Evaluate side-chains 174 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 165 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 251 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 49 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 120 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 300 ASN B 300 ASN C 300 ASN D 300 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.146647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.111543 restraints weight = 31388.329| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.93 r_work: 0.3224 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9884 Z= 0.176 Angle : 0.522 4.369 13392 Z= 0.277 Chirality : 0.043 0.145 1580 Planarity : 0.005 0.038 1704 Dihedral : 4.068 26.387 1368 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.81 % Allowed : 9.06 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.25), residues: 1232 helix: 2.42 (0.20), residues: 680 sheet: 1.36 (0.40), residues: 176 loop : -1.74 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 29 TYR 0.008 0.002 TYR B 315 PHE 0.008 0.001 PHE C 309 TRP 0.007 0.001 TRP C 41 HIS 0.003 0.001 HIS B 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 ( 9884) covalent geometry : angle 0.52165 / 0.28 (13392) hydrogen bonds : bond 0.06613 / 4.52 ( 576) hydrogen bonds : angle 4.28374 / 2.98 ( 1716) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 212 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Evaluate side-chains 180 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 161 time to evaluate : 0.704 Fit side-chains revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8306 (ptmt) cc_final: 0.7565 (pttt) REVERT: A 60 LYS cc_start: 0.8117 (ttpt) cc_final: 0.7606 (ttpp) REVERT: A 64 GLU cc_start: 0.7518 (tt0) cc_final: 0.6873 (mt-10) REVERT: A 132 GLN cc_start: 0.6938 (mt0) cc_final: 0.6531 (pp30) REVERT: A 144 ILE cc_start: 0.7467 (mm) cc_final: 0.7208 (mt) REVERT: A 149 GLN cc_start: 0.7143 (tt0) cc_final: 0.6621 (tp40) REVERT: A 251 SER cc_start: 0.8404 (OUTLIER) cc_final: 0.7827 (p) REVERT: A 265 TRP cc_start: 0.6068 (m-90) cc_final: 0.5867 (m-90) REVERT: B 8 LYS cc_start: 0.8310 (ptmt) cc_final: 0.7544 (pttt) REVERT: B 60 LYS cc_start: 0.8198 (ttpt) cc_final: 0.7697 (ttpp) REVERT: B 64 GLU cc_start: 0.7507 (tt0) cc_final: 0.6872 (mt-10) REVERT: B 118 ASP cc_start: 0.8041 (OUTLIER) cc_final: 0.7826 (m-30) REVERT: B 132 GLN cc_start: 0.6997 (mt0) cc_final: 0.6568 (pp30) REVERT: B 142 LYS cc_start: 0.7458 (mptm) cc_final: 0.7135 (mptm) REVERT: B 149 GLN cc_start: 0.6984 (tt0) cc_final: 0.6458 (tp40) REVERT: B 250 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7666 (mm) REVERT: B 251 SER cc_start: 0.8220 (OUTLIER) cc_final: 0.7612 (p) REVERT: B 272 MET cc_start: 0.7142 (ttp) cc_final: 0.6739 (mmm) REVERT: C 8 LYS cc_start: 0.8302 (ptmt) cc_final: 0.7558 (pttt) REVERT: C 60 LYS cc_start: 0.8215 (ttmt) cc_final: 0.7897 (ttpp) REVERT: C 132 GLN cc_start: 0.6926 (mt0) cc_final: 0.6564 (pp30) REVERT: C 142 LYS cc_start: 0.7432 (mptm) cc_final: 0.7094 (mptm) REVERT: C 144 ILE cc_start: 0.7449 (mm) cc_final: 0.7197 (mt) REVERT: C 149 GLN cc_start: 0.7142 (tt0) cc_final: 0.6618 (tp40) REVERT: C 250 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7664 (mm) REVERT: C 251 SER cc_start: 0.8278 (OUTLIER) cc_final: 0.7682 (p) REVERT: C 272 MET cc_start: 0.7111 (ttp) cc_final: 0.6671 (mmm) REVERT: D 8 LYS cc_start: 0.8306 (ptmt) cc_final: 0.7547 (pttt) REVERT: D 60 LYS cc_start: 0.8177 (ttpt) cc_final: 0.7668 (ttpp) REVERT: D 64 GLU cc_start: 0.7522 (tt0) cc_final: 0.6857 (mt-10) REVERT: D 132 GLN cc_start: 0.6912 (mt0) cc_final: 0.6570 (pp30) REVERT: D 144 ILE cc_start: 0.7414 (mm) cc_final: 0.7161 (mt) REVERT: D 149 GLN cc_start: 0.7136 (tt0) cc_final: 0.6607 (tp40) REVERT: D 251 SER cc_start: 0.8290 (OUTLIER) cc_final: 0.7696 (p) outliers start: 19 outliers final: 4 residues processed: 169 average time/residue: 1.0246 time to fit residues: 189.7121 Evaluate side-chains 172 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 161 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 251 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 7 optimal weight: 1.9990 chunk 82 optimal weight: 7.9990 chunk 109 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 10 optimal weight: 0.0970 chunk 94 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 300 ASN B 300 ASN C 300 ASN D 300 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.144592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.106767 restraints weight = 31025.742| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.09 r_work: 0.3100 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 9884 Z= 0.121 Angle : 0.473 5.451 13392 Z= 0.249 Chirality : 0.041 0.142 1580 Planarity : 0.005 0.039 1704 Dihedral : 3.895 25.516 1368 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.15 % Allowed : 9.64 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.25), residues: 1232 helix: 2.74 (0.20), residues: 676 sheet: 1.36 (0.40), residues: 176 loop : -1.64 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 128 TYR 0.006 0.001 TYR B 159 PHE 0.008 0.001 PHE C 309 TRP 0.002 0.001 TRP A 41 HIS 0.002 0.001 HIS B 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 9884) covalent geometry : angle 0.47290 / 0.25 (13392) hydrogen bonds : bond 0.05593 / 3.85 ( 576) hydrogen bonds : angle 4.19839 / 2.91 ( 1716) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 212 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Evaluate side-chains 180 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 168 time to evaluate : 0.581 Fit side-chains REVERT: A 8 LYS cc_start: 0.8141 (ptmt) cc_final: 0.7363 (pttt) REVERT: A 60 LYS cc_start: 0.7900 (ttpt) cc_final: 0.7353 (ttpp) REVERT: A 64 GLU cc_start: 0.7340 (tt0) cc_final: 0.6636 (mt-10) REVERT: A 122 ASP cc_start: 0.9095 (m-30) cc_final: 0.8854 (m-30) REVERT: A 132 GLN cc_start: 0.6971 (mt0) cc_final: 0.6567 (pp30) REVERT: A 144 ILE cc_start: 0.7217 (mm) cc_final: 0.6973 (mt) REVERT: A 149 GLN cc_start: 0.6947 (tt0) cc_final: 0.6376 (tp40) REVERT: A 265 TRP cc_start: 0.6034 (m-90) cc_final: 0.5832 (m-90) REVERT: B 8 LYS cc_start: 0.8132 (ptmt) cc_final: 0.7324 (pttt) REVERT: B 60 LYS cc_start: 0.7940 (ttpt) cc_final: 0.7400 (ttpp) REVERT: B 64 GLU cc_start: 0.7320 (tt0) cc_final: 0.6615 (mt-10) REVERT: B 118 ASP cc_start: 0.7848 (OUTLIER) cc_final: 0.7642 (m-30) REVERT: B 132 GLN cc_start: 0.6995 (mt0) cc_final: 0.6552 (pp30) REVERT: B 142 LYS cc_start: 0.7227 (mptm) cc_final: 0.6895 (mptm) REVERT: B 144 ILE cc_start: 0.7343 (mm) cc_final: 0.7103 (mt) REVERT: B 149 GLN cc_start: 0.6807 (tt0) cc_final: 0.6244 (tp40) REVERT: B 250 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7418 (mm) REVERT: B 251 SER cc_start: 0.7872 (OUTLIER) cc_final: 0.7249 (p) REVERT: B 272 MET cc_start: 0.6766 (ttp) cc_final: 0.6323 (mmm) REVERT: C 8 LYS cc_start: 0.8124 (ptmt) cc_final: 0.7355 (pttt) REVERT: C 60 LYS cc_start: 0.7900 (ttmt) cc_final: 0.7630 (ttpp) REVERT: C 132 GLN cc_start: 0.6984 (mt0) cc_final: 0.6556 (pp30) REVERT: C 142 LYS cc_start: 0.7187 (mptm) cc_final: 0.6851 (mptm) REVERT: C 144 ILE cc_start: 0.7357 (mm) cc_final: 0.7114 (mt) REVERT: C 149 GLN cc_start: 0.7006 (tt0) cc_final: 0.6363 (tp40) REVERT: C 250 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7432 (mm) REVERT: C 251 SER cc_start: 0.7892 (OUTLIER) cc_final: 0.7267 (p) REVERT: C 272 MET cc_start: 0.6739 (ttp) cc_final: 0.6259 (mmm) REVERT: D 8 LYS cc_start: 0.8135 (ptmt) cc_final: 0.7337 (pttt) REVERT: D 60 LYS cc_start: 0.7951 (ttpt) cc_final: 0.7402 (ttpp) REVERT: D 64 GLU cc_start: 0.7355 (tt0) cc_final: 0.6650 (mt-10) REVERT: D 132 GLN cc_start: 0.6915 (mt0) cc_final: 0.6566 (pp30) REVERT: D 144 ILE cc_start: 0.7242 (mm) cc_final: 0.6994 (mt) REVERT: D 149 GLN cc_start: 0.6969 (tt0) cc_final: 0.6399 (tp40) outliers start: 12 outliers final: 7 residues processed: 173 average time/residue: 0.9827 time to fit residues: 186.5309 Evaluate side-chains 179 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 167 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 251 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 113 optimal weight: 7.9990 chunk 60 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 61 optimal weight: 0.0270 chunk 34 optimal weight: 0.9980 chunk 43 optimal weight: 0.0770 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 300 ASN B 300 ASN C 300 ASN D 300 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.146156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.108514 restraints weight = 30922.437| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.08 r_work: 0.3124 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 9884 Z= 0.105 Angle : 0.450 5.308 13392 Z= 0.236 Chirality : 0.041 0.141 1580 Planarity : 0.005 0.039 1704 Dihedral : 3.759 25.112 1368 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.34 % Allowed : 9.64 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.07 (0.26), residues: 1232 helix: 2.77 (0.20), residues: 696 sheet: 1.41 (0.41), residues: 176 loop : -1.64 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 128 TYR 0.007 0.001 TYR B 159 PHE 0.008 0.001 PHE C 309 TRP 0.001 0.000 TRP C 41 HIS 0.002 0.001 HIS D 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 ( 9884) covalent geometry : angle 0.44971 / 0.24 (13392) hydrogen bonds : bond 0.04983 / 3.44 ( 576) hydrogen bonds : angle 4.12687 / 2.86 ( 1716) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6545.88 seconds wall clock time: 111 minutes 20.54 seconds (6680.54 seconds total)