Starting phenix.real_space_refine on Sat Jul 4 04:22:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pr6_71799/07_2026/9pr6_71799_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pr6_71799/07_2026/9pr6_71799.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9pr6_71799/07_2026/9pr6_71799.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pr6_71799/07_2026/9pr6_71799.map" model { file = "/net/cci-nas-00/data/ceres_data/9pr6_71799/07_2026/9pr6_71799_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pr6_71799/07_2026/9pr6_71799_trim.cif" } resolution = 3.9 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= 0.002 sd= 0.026 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: 6 Type Number sf(0) Gaussians P 12 5.49 5 S 76 5.16 5 C 5776 2.51 5 N 1452 2.21 5 O 1620 1.98 5 H 8760 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17696 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 4384 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 12, 'TRANS': 263} Chain breaks: 4 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Restraints were copied for chains: B, C, D Time building chain proxies: 3.67, per 1000 atoms: 0.21 Number of scatterers: 17696 At special positions: 0 Unit cell: (94.392, 95.22, 107.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 76 16.00 P 12 15.00 O 1620 8.00 N 1452 7.00 C 5776 6.00 H 8760 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: 1.51 Conformation dependent library (CDL) restraints added in 495.2 milliseconds 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2080 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 24 sheets defined 39.5% alpha, 36.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 35 through 43 removed outlier: 4.099A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU A 41 " --> pdb=" O GLY A 37 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP A 43 " --> pdb=" O ALA A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 51 removed outlier: 3.554A pdb=" N MET A 49 " --> pdb=" O TRP A 45 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASP A 50 " --> pdb=" O GLY A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 83 removed outlier: 3.850A pdb=" N PHE A 64 " --> pdb=" O PHE A 60 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N HIS A 67 " --> pdb=" O SER A 63 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A 74 " --> pdb=" O VAL A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 118 removed outlier: 3.506A pdb=" N LEU A 118 " --> pdb=" O LEU A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 161 removed outlier: 3.632A pdb=" N ILE A 135 " --> pdb=" O CYS A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 169 removed outlier: 4.074A pdb=" N ARG A 166 " --> pdb=" O ARG A 162 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE A 168 " --> pdb=" O LYS A 164 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N SER A 169 " --> pdb=" O ASN A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 291 No H-bonds generated for 'chain 'A' and resid 289 through 291' Processing helix chain 'A' and resid 316 through 318 No H-bonds generated for 'chain 'A' and resid 316 through 318' Processing helix chain 'B' and resid 35 through 43 removed outlier: 4.098A pdb=" N ALA B 39 " --> pdb=" O GLN B 35 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU B 41 " --> pdb=" O GLY B 37 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP B 43 " --> pdb=" O ALA B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 51 removed outlier: 3.554A pdb=" N MET B 49 " --> pdb=" O TRP B 45 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASP B 50 " --> pdb=" O GLY B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 83 removed outlier: 3.849A pdb=" N PHE B 64 " --> pdb=" O PHE B 60 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N HIS B 67 " --> pdb=" O SER B 63 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU B 74 " --> pdb=" O VAL B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 118 removed outlier: 3.506A pdb=" N LEU B 118 " --> pdb=" O LEU B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 161 removed outlier: 3.632A pdb=" N ILE B 135 " --> pdb=" O CYS B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 169 removed outlier: 4.075A pdb=" N ARG B 166 " --> pdb=" O ARG B 162 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE B 168 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N SER B 169 " --> pdb=" O ASN B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 291 No H-bonds generated for 'chain 'B' and resid 289 through 291' Processing helix chain 'B' and resid 316 through 318 No H-bonds generated for 'chain 'B' and resid 316 through 318' Processing helix chain 'C' and resid 35 through 43 removed outlier: 4.098A pdb=" N ALA C 39 " --> pdb=" O GLN C 35 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU C 41 " --> pdb=" O GLY C 37 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP C 43 " --> pdb=" O ALA C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 51 removed outlier: 3.553A pdb=" N MET C 49 " --> pdb=" O TRP C 45 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASP C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 83 removed outlier: 3.850A pdb=" N PHE C 64 " --> pdb=" O PHE C 60 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N HIS C 67 " --> pdb=" O SER C 63 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU C 74 " --> pdb=" O VAL C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 118 removed outlier: 3.506A pdb=" N LEU C 118 " --> pdb=" O LEU C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 161 removed outlier: 3.633A pdb=" N ILE C 135 " --> pdb=" O CYS C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 169 removed outlier: 4.075A pdb=" N ARG C 166 " --> pdb=" O ARG C 162 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE C 168 " --> pdb=" O LYS C 164 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N SER C 169 " --> pdb=" O ASN C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 291 No H-bonds generated for 'chain 'C' and resid 289 through 291' Processing helix chain 'C' and resid 316 through 318 No H-bonds generated for 'chain 'C' and resid 316 through 318' Processing helix chain 'D' and resid 35 through 43 removed outlier: 4.099A pdb=" N ALA D 39 " --> pdb=" O GLN D 35 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU D 41 " --> pdb=" O GLY D 37 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP D 43 " --> pdb=" O ALA D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 51 removed outlier: 3.554A pdb=" N MET D 49 " --> pdb=" O TRP D 45 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASP D 50 " --> pdb=" O GLY D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 83 removed outlier: 3.850A pdb=" N PHE D 64 " --> pdb=" O PHE D 60 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N HIS D 67 " --> pdb=" O SER D 63 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU D 74 " --> pdb=" O VAL D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 118 removed outlier: 3.507A pdb=" N LEU D 118 " --> pdb=" O LEU D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 161 removed outlier: 3.632A pdb=" N ILE D 135 " --> pdb=" O CYS D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 169 removed outlier: 4.075A pdb=" N ARG D 166 " --> pdb=" O ARG D 162 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE D 168 " --> pdb=" O LYS D 164 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N SER D 169 " --> pdb=" O ASN D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 291 No H-bonds generated for 'chain 'D' and resid 289 through 291' Processing helix chain 'D' and resid 316 through 318 No H-bonds generated for 'chain 'D' and resid 316 through 318' Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 32 removed outlier: 6.894A pdb=" N GLN A 30 " --> pdb=" O ILE D 313 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 170 through 172 Processing sheet with id=AA3, first strand: chain 'A' and resid 170 through 172 removed outlier: 6.752A pdb=" N ALA A 176 " --> pdb=" O MET A 294 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 217 through 223 removed outlier: 4.042A pdb=" N LEU A 199 " --> pdb=" O PHE A 237 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 217 through 223 removed outlier: 5.685A pdb=" N SER A 201 " --> pdb=" O MET A 274 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N MET A 274 " --> pdb=" O SER A 201 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA A 273 " --> pdb=" O CYS A 282 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 297 through 299 Processing sheet with id=AA7, first strand: chain 'A' and resid 303 through 305 removed outlier: 3.673A pdb=" N GLN B 30 " --> pdb=" O TYR A 311 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE A 313 " --> pdb=" O GLN B 30 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP B 32 " --> pdb=" O ILE A 313 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 170 through 172 Processing sheet with id=AA9, first strand: chain 'B' and resid 170 through 172 removed outlier: 6.751A pdb=" N ALA B 176 " --> pdb=" O MET B 294 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 217 through 223 removed outlier: 4.041A pdb=" N LEU B 199 " --> pdb=" O PHE B 237 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 217 through 223 removed outlier: 5.685A pdb=" N SER B 201 " --> pdb=" O MET B 274 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N MET B 274 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA B 273 " --> pdb=" O CYS B 282 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 297 through 299 Processing sheet with id=AB4, first strand: chain 'B' and resid 303 through 305 removed outlier: 3.656A pdb=" N GLN C 30 " --> pdb=" O TYR B 311 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP C 32 " --> pdb=" O ILE B 313 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 170 through 172 Processing sheet with id=AB6, first strand: chain 'C' and resid 170 through 172 removed outlier: 6.751A pdb=" N ALA C 176 " --> pdb=" O MET C 294 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 217 through 223 removed outlier: 4.042A pdb=" N LEU C 199 " --> pdb=" O PHE C 237 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 217 through 223 removed outlier: 5.685A pdb=" N SER C 201 " --> pdb=" O MET C 274 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N MET C 274 " --> pdb=" O SER C 201 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA C 273 " --> pdb=" O CYS C 282 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 297 through 299 Processing sheet with id=AC1, first strand: chain 'C' and resid 303 through 305 removed outlier: 3.808A pdb=" N GLN D 30 " --> pdb=" O TYR C 311 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE C 313 " --> pdb=" O GLN D 30 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP D 32 " --> pdb=" O ILE C 313 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 170 through 172 Processing sheet with id=AC3, first strand: chain 'D' and resid 170 through 172 removed outlier: 6.752A pdb=" N ALA D 176 " --> pdb=" O MET D 294 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 217 through 223 removed outlier: 4.042A pdb=" N LEU D 199 " --> pdb=" O PHE D 237 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 217 through 223 removed outlier: 5.685A pdb=" N SER D 201 " --> pdb=" O MET D 274 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N MET D 274 " --> pdb=" O SER D 201 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA D 273 " --> pdb=" O CYS D 282 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 297 through 299 461 hydrogen bonds defined for protein. 1347 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.96 Time building geometry restraints manager: 2.21 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: 8740 1.03 - 1.23: 28 1.23 - 1.42: 3880 1.42 - 1.61: 5120 1.61 - 1.81: 148 Bond restraints: 17916 Sorted by residual: bond pdb=" C1B PIO D 400 " pdb=" O3C PIO D 400 " ideal model delta sigma weight residual 1.331 1.402 -0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" C1B PIO C 400 " pdb=" O3C PIO C 400 " ideal model delta sigma weight residual 1.331 1.402 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" C1B PIO B 400 " pdb=" O3C PIO B 400 " ideal model delta sigma weight residual 1.331 1.402 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" C1B PIO A 400 " pdb=" O3C PIO A 400 " ideal model delta sigma weight residual 1.331 1.402 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" O53 PIO A 400 " pdb=" P5 PIO A 400 " ideal model delta sigma weight residual 1.528 1.458 0.070 2.00e-02 2.50e+03 1.24e+01 ... (remaining 17911 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.02: 32104 4.02 - 8.04: 45 8.04 - 12.06: 43 12.06 - 16.08: 8 16.08 - 20.10: 4 Bond angle restraints: 32204 Sorted by residual: angle pdb=" O11 PIO C 400 " pdb=" P1 PIO C 400 " pdb=" O12 PIO C 400 " ideal model delta sigma weight residual 121.09 100.99 20.10 3.00e+00 1.11e-01 4.49e+01 angle pdb=" O11 PIO D 400 " pdb=" P1 PIO D 400 " pdb=" O12 PIO D 400 " ideal model delta sigma weight residual 121.09 101.00 20.09 3.00e+00 1.11e-01 4.48e+01 angle pdb=" O11 PIO A 400 " pdb=" P1 PIO A 400 " pdb=" O12 PIO A 400 " ideal model delta sigma weight residual 121.09 101.01 20.08 3.00e+00 1.11e-01 4.48e+01 angle pdb=" O11 PIO B 400 " pdb=" P1 PIO B 400 " pdb=" O12 PIO B 400 " ideal model delta sigma weight residual 121.09 101.02 20.07 3.00e+00 1.11e-01 4.48e+01 angle pdb=" O1 PIO C 400 " pdb=" P1 PIO C 400 " pdb=" O13 PIO C 400 " ideal model delta sigma weight residual 97.64 111.17 -13.53 3.00e+00 1.11e-01 2.04e+01 ... (remaining 32199 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.84: 7566 11.84 - 23.68: 581 23.68 - 35.52: 173 35.52 - 47.35: 88 47.35 - 59.19: 56 Dihedral angle restraints: 8464 sinusoidal: 4484 harmonic: 3980 Sorted by residual: dihedral pdb=" CA LEU C 118 " pdb=" C LEU C 118 " pdb=" N THR C 119 " pdb=" CA THR C 119 " ideal model delta harmonic sigma weight residual 180.00 163.21 16.79 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA LEU A 118 " pdb=" C LEU A 118 " pdb=" N THR A 119 " pdb=" CA THR A 119 " ideal model delta harmonic sigma weight residual 180.00 163.23 16.77 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CA LEU D 118 " pdb=" C LEU D 118 " pdb=" N THR D 119 " pdb=" CA THR D 119 " ideal model delta harmonic sigma weight residual 180.00 163.26 16.74 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 8461 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 856 0.025 - 0.050: 353 0.050 - 0.075: 75 0.075 - 0.100: 56 0.100 - 0.125: 60 Chirality restraints: 1400 Sorted by residual: chirality pdb=" CA VAL C 100 " pdb=" N VAL C 100 " pdb=" C VAL C 100 " pdb=" CB VAL C 100 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.93e-01 chirality pdb=" CA VAL D 100 " pdb=" N VAL D 100 " pdb=" C VAL D 100 " pdb=" CB VAL D 100 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.74e-01 chirality pdb=" CA ILE A 313 " pdb=" N ILE A 313 " pdb=" C ILE A 313 " pdb=" CB ILE A 313 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.74e-01 ... (remaining 1397 not shown) Planarity restraints: 2552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 162 " -0.018 5.00e-02 4.00e+02 2.75e-02 1.21e+00 pdb=" N PRO B 163 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO B 163 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 163 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 162 " 0.018 5.00e-02 4.00e+02 2.75e-02 1.21e+00 pdb=" N PRO D 163 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO D 163 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO D 163 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 162 " -0.018 5.00e-02 4.00e+02 2.73e-02 1.19e+00 pdb=" N PRO C 163 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO C 163 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO C 163 " -0.015 5.00e-02 4.00e+02 ... (remaining 2549 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.48: 11939 2.48 - 3.01: 39869 3.01 - 3.54: 44603 3.54 - 4.07: 59604 4.07 - 4.60: 85839 Nonbonded interactions: 241854 Sorted by model distance: nonbonded pdb="HH22 ARG D 166 " pdb="HD21 ASN D 193 " model vdw 1.956 2.100 nonbonded pdb="HH22 ARG C 166 " pdb="HD21 ASN C 193 " model vdw 1.956 2.100 nonbonded pdb="HH22 ARG A 166 " pdb="HD21 ASN A 193 " model vdw 1.956 2.100 nonbonded pdb="HH22 ARG B 166 " pdb="HD21 ASN B 193 " model vdw 1.957 2.100 nonbonded pdb="HD11 ILE A 47 " pdb="HH12 ARG D 195 " model vdw 1.966 2.270 ... (remaining 241849 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain '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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.630 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: 0.130 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.900 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: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6623 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 : 0.005 0.071 9156 Z= 0.261 Angle : 0.939 20.101 12408 Z= 0.353 Chirality : 0.038 0.125 1400 Planarity : 0.003 0.028 1516 Dihedral : 10.652 59.193 3240 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.42 % Allowed : 4.20 % Favored : 95.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.26), residues: 1064 helix: 2.44 (0.29), residues: 336 sheet: 1.11 (0.37), residues: 228 loop : 0.30 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 162 TYR 0.006 0.001 TYR C 122 PHE 0.005 0.001 PHE C 71 TRP 0.002 0.001 TRP A 75 HIS 0.001 0.000 HIS D 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.26 ( 9156) covalent geometry : angle 0.93862 / 0.35 (12408) hydrogen bonds : bond 0.19003 / 12.39 ( 429) hydrogen bonds : angle 7.53448 / 5.39 ( 1347) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 204 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 MET cc_start: 0.5636 (tpp) cc_final: 0.5151 (mpp) REVERT: B 57 MET cc_start: 0.5956 (tpp) cc_final: 0.5242 (mpp) REVERT: C 125 MET cc_start: 0.7371 (OUTLIER) cc_final: 0.7104 (mpt) REVERT: C 241 LEU cc_start: 0.6034 (mt) cc_final: 0.5790 (mt) REVERT: C 270 PHE cc_start: 0.6192 (m-80) cc_final: 0.5984 (m-80) REVERT: D 57 MET cc_start: 0.5588 (tpp) cc_final: 0.5234 (mpp) REVERT: D 270 PHE cc_start: 0.6232 (m-80) cc_final: 0.5973 (m-80) outliers start: 4 outliers final: 1 residues processed: 204 average time/residue: 0.1607 time to fit residues: 48.6716 Evaluate side-chains 199 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 197 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain D residue 125 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.159144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.136074 restraints weight = 36381.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.140888 restraints weight = 15770.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.143806 restraints weight = 8699.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.145472 restraints weight = 5876.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.146409 restraints weight = 4628.731| |-----------------------------------------------------------------------------| r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6725 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 9156 Z= 0.261 Angle : 0.595 5.967 12408 Z= 0.307 Chirality : 0.043 0.144 1400 Planarity : 0.005 0.039 1516 Dihedral : 7.306 52.499 1226 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.74 % Allowed : 13.45 % Favored : 85.82 % 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: 0.96 (0.27), residues: 1064 helix: 1.76 (0.28), residues: 364 sheet: 0.36 (0.33), residues: 308 loop : -0.07 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 285 TYR 0.013 0.002 TYR C 311 PHE 0.018 0.002 PHE A 189 TRP 0.015 0.002 TRP C 45 HIS 0.008 0.001 HIS B 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00573 / 0.26 ( 9156) covalent geometry : angle 0.59471 / 0.31 (12408) hydrogen bonds : bond 0.04924 / 3.37 ( 429) hydrogen bonds : angle 5.73700 / 4.16 ( 1347) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 202 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 GLN cc_start: 0.6555 (mm-40) cc_final: 0.6350 (mm-40) REVERT: A 283 GLN cc_start: 0.8069 (tt0) cc_final: 0.7685 (tt0) REVERT: A 285 ARG cc_start: 0.8180 (mtt90) cc_final: 0.7792 (ptp90) REVERT: B 199 LEU cc_start: 0.8090 (mp) cc_final: 0.7835 (mt) REVERT: B 245 HIS cc_start: 0.7742 (t70) cc_final: 0.7314 (t70) REVERT: C 142 MET cc_start: 0.6931 (mtp) cc_final: 0.6569 (ttm) REVERT: C 190 GLN cc_start: 0.6530 (mm-40) cc_final: 0.6101 (mm-40) REVERT: C 270 PHE cc_start: 0.6157 (m-80) cc_final: 0.5930 (m-80) REVERT: C 285 ARG cc_start: 0.8246 (mtt90) cc_final: 0.7914 (ptp90) REVERT: D 269 VAL cc_start: 0.7191 (t) cc_final: 0.6975 (m) REVERT: D 285 ARG cc_start: 0.8208 (mtt90) cc_final: 0.7944 (ptp90) outliers start: 7 outliers final: 6 residues processed: 204 average time/residue: 0.1722 time to fit residues: 51.4385 Evaluate side-chains 201 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 195 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain D residue 125 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 1 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 96 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.156366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.133303 restraints weight = 36738.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.138155 restraints weight = 15894.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.141031 restraints weight = 8720.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.142802 restraints weight = 5881.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.143690 restraints weight = 4589.441| |-----------------------------------------------------------------------------| r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6729 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9156 Z= 0.199 Angle : 0.505 4.635 12408 Z= 0.261 Chirality : 0.040 0.129 1400 Planarity : 0.004 0.037 1516 Dihedral : 6.922 50.959 1226 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.89 % Allowed : 14.71 % Favored : 83.40 % 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: 1.04 (0.28), residues: 1064 helix: 2.02 (0.29), residues: 364 sheet: 0.29 (0.32), residues: 308 loop : -0.16 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 166 TYR 0.008 0.001 TYR C 311 PHE 0.020 0.002 PHE D 189 TRP 0.007 0.001 TRP B 45 HIS 0.007 0.001 HIS B 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.20 ( 9156) covalent geometry : angle 0.50497 / 0.26 (12408) hydrogen bonds : bond 0.04693 / 3.18 ( 429) hydrogen bonds : angle 5.36240 / 3.88 ( 1347) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 210 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ASP cc_start: 0.6219 (m-30) cc_final: 0.6013 (m-30) REVERT: A 190 GLN cc_start: 0.6607 (mm-40) cc_final: 0.6331 (mm-40) REVERT: A 199 LEU cc_start: 0.8011 (mp) cc_final: 0.7740 (mt) REVERT: A 245 HIS cc_start: 0.7491 (t70) cc_final: 0.7186 (t70) REVERT: A 283 GLN cc_start: 0.8087 (tt0) cc_final: 0.7726 (tt0) REVERT: A 285 ARG cc_start: 0.8111 (mtt90) cc_final: 0.7724 (ptp90) REVERT: B 84 ASP cc_start: 0.6169 (m-30) cc_final: 0.5951 (m-30) REVERT: B 285 ARG cc_start: 0.8132 (mtt90) cc_final: 0.7916 (ptp90) REVERT: B 315 MET cc_start: 0.7531 (mmm) cc_final: 0.7213 (mtt) REVERT: C 84 ASP cc_start: 0.6309 (m-30) cc_final: 0.6072 (m-30) REVERT: C 190 GLN cc_start: 0.6511 (mm-40) cc_final: 0.6167 (mm-40) REVERT: C 285 ARG cc_start: 0.8177 (mtt90) cc_final: 0.7842 (ptp90) REVERT: D 269 VAL cc_start: 0.7249 (t) cc_final: 0.6989 (m) REVERT: D 285 ARG cc_start: 0.8158 (mtt90) cc_final: 0.7839 (ptp90) outliers start: 18 outliers final: 13 residues processed: 218 average time/residue: 0.1626 time to fit residues: 52.1784 Evaluate side-chains 217 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 204 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 239 PHE Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 239 PHE Chi-restraints excluded: chain D residue 287 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 69 optimal weight: 0.0970 chunk 31 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 GLN ** D 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.153798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.131083 restraints weight = 36478.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.135775 restraints weight = 15834.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.138676 restraints weight = 8786.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.140418 restraints weight = 5877.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.141444 restraints weight = 4566.032| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9156 Z= 0.237 Angle : 0.538 4.563 12408 Z= 0.279 Chirality : 0.041 0.129 1400 Planarity : 0.004 0.036 1516 Dihedral : 6.892 54.904 1226 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.63 % Allowed : 15.13 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.28), residues: 1064 helix: 1.87 (0.29), residues: 364 sheet: 0.40 (0.32), residues: 304 loop : -0.51 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 19 TYR 0.010 0.001 TYR B 288 PHE 0.014 0.002 PHE C 126 TRP 0.010 0.002 TRP B 45 HIS 0.008 0.001 HIS C 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.24 ( 9156) covalent geometry : angle 0.53792 / 0.28 (12408) hydrogen bonds : bond 0.04529 / 3.09 ( 429) hydrogen bonds : angle 5.31437 / 3.84 ( 1347) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 208 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLN cc_start: 0.7353 (mt0) cc_final: 0.7082 (mt0) REVERT: A 285 ARG cc_start: 0.8071 (mtt90) cc_final: 0.7822 (ptp90) REVERT: A 315 MET cc_start: 0.7548 (mmm) cc_final: 0.7321 (mtt) REVERT: B 104 THR cc_start: 0.8278 (p) cc_final: 0.8025 (m) REVERT: B 269 VAL cc_start: 0.7325 (t) cc_final: 0.7004 (m) REVERT: B 285 ARG cc_start: 0.8093 (mtt90) cc_final: 0.7767 (ptp90) REVERT: C 84 ASP cc_start: 0.6285 (m-30) cc_final: 0.6019 (m-30) REVERT: C 168 PHE cc_start: 0.6812 (t80) cc_final: 0.6601 (t80) REVERT: C 199 LEU cc_start: 0.8150 (mt) cc_final: 0.7880 (mt) REVERT: C 245 HIS cc_start: 0.7700 (t70) cc_final: 0.7293 (t70) REVERT: C 269 VAL cc_start: 0.7384 (t) cc_final: 0.7087 (m) REVERT: C 285 ARG cc_start: 0.8107 (mtt90) cc_final: 0.7778 (ptp90) REVERT: D 269 VAL cc_start: 0.7284 (t) cc_final: 0.7010 (m) REVERT: D 285 ARG cc_start: 0.8135 (mtt90) cc_final: 0.7827 (ptp90) REVERT: D 312 GLN cc_start: 0.5226 (mm-40) cc_final: 0.4988 (mm-40) REVERT: D 315 MET cc_start: 0.7580 (mmm) cc_final: 0.7322 (mtt) outliers start: 25 outliers final: 20 residues processed: 215 average time/residue: 0.1623 time to fit residues: 51.2151 Evaluate side-chains 226 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 206 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 239 PHE Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain B residue 53 TRP Chi-restraints excluded: chain B residue 96 HIS Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain C residue 53 TRP Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 239 PHE Chi-restraints excluded: chain C residue 270 PHE Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 239 PHE Chi-restraints excluded: chain D residue 270 PHE Chi-restraints excluded: chain D residue 287 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 37 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 GLN D 30 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.153677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.131277 restraints weight = 36181.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.136080 restraints weight = 15336.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.138947 restraints weight = 8277.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.140600 restraints weight = 5474.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.141617 restraints weight = 4276.556| |-----------------------------------------------------------------------------| r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6755 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9156 Z= 0.238 Angle : 0.532 4.580 12408 Z= 0.277 Chirality : 0.041 0.137 1400 Planarity : 0.004 0.034 1516 Dihedral : 6.592 59.861 1220 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.57 % Allowed : 15.44 % Favored : 80.99 % 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: 0.58 (0.28), residues: 1064 helix: 1.82 (0.29), residues: 364 sheet: 0.19 (0.29), residues: 348 loop : -0.88 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 19 TYR 0.011 0.002 TYR B 243 PHE 0.017 0.002 PHE B 126 TRP 0.010 0.002 TRP B 45 HIS 0.007 0.001 HIS B 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.24 ( 9156) covalent geometry : angle 0.53240 / 0.28 (12408) hydrogen bonds : bond 0.04504 / 3.08 ( 429) hydrogen bonds : angle 5.24008 / 3.78 ( 1347) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 208 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLN cc_start: 0.7401 (mt0) cc_final: 0.7075 (mt0) REVERT: A 84 ASP cc_start: 0.6153 (m-30) cc_final: 0.5820 (m-30) REVERT: A 285 ARG cc_start: 0.8094 (mtt90) cc_final: 0.7848 (ptp90) REVERT: A 312 GLN cc_start: 0.5199 (mm-40) cc_final: 0.4899 (mm-40) REVERT: B 104 THR cc_start: 0.8274 (p) cc_final: 0.7996 (m) REVERT: B 168 PHE cc_start: 0.6856 (t80) cc_final: 0.6627 (t80) REVERT: B 269 VAL cc_start: 0.7379 (t) cc_final: 0.7130 (m) REVERT: B 285 ARG cc_start: 0.8106 (mtt90) cc_final: 0.7816 (ptp90) REVERT: C 84 ASP cc_start: 0.6432 (m-30) cc_final: 0.6167 (m-30) REVERT: C 168 PHE cc_start: 0.6799 (t80) cc_final: 0.6587 (t80) REVERT: C 269 VAL cc_start: 0.7410 (t) cc_final: 0.7133 (m) REVERT: C 285 ARG cc_start: 0.8104 (mtt90) cc_final: 0.7820 (ptp90) REVERT: D 30 GLN cc_start: 0.7282 (mt0) cc_final: 0.6995 (mt0) REVERT: D 84 ASP cc_start: 0.6059 (m-30) cc_final: 0.5832 (m-30) REVERT: D 168 PHE cc_start: 0.6847 (t80) cc_final: 0.6615 (t80) REVERT: D 269 VAL cc_start: 0.7318 (t) cc_final: 0.7064 (m) REVERT: D 285 ARG cc_start: 0.8158 (mtt90) cc_final: 0.7894 (ptp90) REVERT: D 312 GLN cc_start: 0.5139 (mm-40) cc_final: 0.4928 (mm-40) REVERT: D 315 MET cc_start: 0.7681 (mmm) cc_final: 0.7352 (mtt) outliers start: 34 outliers final: 26 residues processed: 221 average time/residue: 0.1641 time to fit residues: 53.0846 Evaluate side-chains 231 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 205 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 53 TRP Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 239 PHE Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 53 TRP Chi-restraints excluded: chain B residue 96 HIS Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 53 TRP Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 239 PHE Chi-restraints excluded: chain C residue 270 PHE Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 53 TRP Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 239 PHE Chi-restraints excluded: chain D residue 270 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 80 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.151888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.129033 restraints weight = 35793.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.134266 restraints weight = 13965.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.137282 restraints weight = 7029.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.139059 restraints weight = 4428.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.140075 restraints weight = 3342.944| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6756 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 9156 Z= 0.292 Angle : 0.580 4.762 12408 Z= 0.304 Chirality : 0.043 0.135 1400 Planarity : 0.005 0.034 1516 Dihedral : 6.110 45.824 1220 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.26 % Allowed : 17.02 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.27), residues: 1064 helix: 1.82 (0.29), residues: 356 sheet: 0.11 (0.30), residues: 332 loop : -1.13 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 19 TYR 0.014 0.002 TYR C 243 PHE 0.017 0.002 PHE B 151 TRP 0.013 0.002 TRP A 45 HIS 0.007 0.001 HIS B 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00641 / 0.29 ( 9156) covalent geometry : angle 0.58040 / 0.30 (12408) hydrogen bonds : bond 0.04745 / 3.23 ( 429) hydrogen bonds : angle 5.36627 / 3.86 ( 1347) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 208 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 PHE cc_start: 0.6887 (t80) cc_final: 0.6665 (t80) REVERT: B 104 THR cc_start: 0.8285 (p) cc_final: 0.8054 (m) REVERT: B 168 PHE cc_start: 0.6947 (t80) cc_final: 0.6701 (t80) REVERT: B 269 VAL cc_start: 0.7319 (t) cc_final: 0.7066 (m) REVERT: B 285 ARG cc_start: 0.8066 (mtt90) cc_final: 0.7764 (ptp90) REVERT: C 168 PHE cc_start: 0.6934 (t80) cc_final: 0.6724 (t80) REVERT: C 269 VAL cc_start: 0.7356 (t) cc_final: 0.7100 (m) REVERT: C 283 GLN cc_start: 0.8192 (tt0) cc_final: 0.7831 (tt0) REVERT: C 285 ARG cc_start: 0.8054 (mtt90) cc_final: 0.7750 (ptp90) REVERT: C 312 GLN cc_start: 0.5155 (mm-40) cc_final: 0.4620 (mm-40) REVERT: D 84 ASP cc_start: 0.6154 (m-30) cc_final: 0.5919 (m-30) REVERT: D 168 PHE cc_start: 0.6917 (t80) cc_final: 0.6675 (t80) REVERT: D 269 VAL cc_start: 0.7240 (t) cc_final: 0.6981 (m) REVERT: D 285 ARG cc_start: 0.8138 (mtt90) cc_final: 0.7803 (ptp90) REVERT: D 312 GLN cc_start: 0.5301 (mm-40) cc_final: 0.4946 (mm-40) REVERT: D 315 MET cc_start: 0.7588 (mmm) cc_final: 0.7262 (mtt) outliers start: 31 outliers final: 26 residues processed: 219 average time/residue: 0.1561 time to fit residues: 50.0163 Evaluate side-chains 233 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 207 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 TRP Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 239 PHE Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 53 TRP Chi-restraints excluded: chain B residue 96 HIS Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 53 TRP Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 239 PHE Chi-restraints excluded: chain C residue 270 PHE Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 53 TRP Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain D residue 239 PHE Chi-restraints excluded: chain D residue 270 PHE Chi-restraints excluded: chain D residue 301 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 36 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 283 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.154859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.131926 restraints weight = 35667.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.137263 restraints weight = 13820.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.140353 restraints weight = 6884.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.142189 restraints weight = 4303.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.143257 restraints weight = 3223.567| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6707 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9156 Z= 0.164 Angle : 0.508 5.216 12408 Z= 0.258 Chirality : 0.040 0.140 1400 Planarity : 0.004 0.034 1516 Dihedral : 5.427 42.950 1220 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.94 % Allowed : 18.28 % Favored : 78.78 % 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: 0.66 (0.28), residues: 1064 helix: 1.98 (0.30), residues: 364 sheet: 0.19 (0.29), residues: 348 loop : -0.88 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 19 TYR 0.009 0.001 TYR B 209 PHE 0.015 0.001 PHE C 151 TRP 0.006 0.001 TRP A 45 HIS 0.005 0.001 HIS D 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 ( 9156) covalent geometry : angle 0.50838 / 0.26 (12408) hydrogen bonds : bond 0.04066 / 2.78 ( 429) hydrogen bonds : angle 5.01811 / 3.62 ( 1347) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 210 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLN cc_start: 0.7503 (mt0) cc_final: 0.7226 (mt0) REVERT: A 168 PHE cc_start: 0.6887 (t80) cc_final: 0.6633 (t80) REVERT: A 285 ARG cc_start: 0.8044 (mtt90) cc_final: 0.7734 (ptp90) REVERT: B 168 PHE cc_start: 0.6933 (t80) cc_final: 0.6698 (t80) REVERT: B 283 GLN cc_start: 0.8228 (tt0) cc_final: 0.7969 (tt0) REVERT: B 285 ARG cc_start: 0.8034 (mtt90) cc_final: 0.7689 (ptp90) REVERT: C 168 PHE cc_start: 0.6900 (t80) cc_final: 0.6699 (t80) REVERT: C 269 VAL cc_start: 0.7341 (t) cc_final: 0.7080 (m) REVERT: C 283 GLN cc_start: 0.8113 (tt0) cc_final: 0.7800 (tt0) REVERT: C 285 ARG cc_start: 0.8042 (mtt90) cc_final: 0.7750 (ptp90) REVERT: C 312 GLN cc_start: 0.5212 (mm-40) cc_final: 0.4645 (mm-40) REVERT: D 84 ASP cc_start: 0.6038 (m-30) cc_final: 0.5774 (m-30) REVERT: D 168 PHE cc_start: 0.6916 (t80) cc_final: 0.6691 (t80) REVERT: D 269 VAL cc_start: 0.7223 (t) cc_final: 0.7003 (m) REVERT: D 285 ARG cc_start: 0.8082 (mtt90) cc_final: 0.7745 (ptp90) REVERT: D 312 GLN cc_start: 0.5316 (mm-40) cc_final: 0.4623 (mm-40) REVERT: D 315 MET cc_start: 0.7519 (mmm) cc_final: 0.7216 (mtt) outliers start: 28 outliers final: 27 residues processed: 220 average time/residue: 0.1545 time to fit residues: 49.9465 Evaluate side-chains 234 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 207 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 53 TRP Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 239 PHE Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 53 TRP Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 239 PHE Chi-restraints excluded: chain C residue 270 PHE Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 53 TRP Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain D residue 239 PHE Chi-restraints excluded: chain D residue 270 PHE Chi-restraints excluded: chain D residue 301 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 33 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 107 optimal weight: 0.1980 chunk 76 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.153511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.132412 restraints weight = 36082.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.136967 restraints weight = 14930.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.139646 restraints weight = 7871.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.141295 restraints weight = 5157.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.142135 restraints weight = 3979.176| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6741 moved from start: 0.4232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9156 Z= 0.202 Angle : 0.526 6.005 12408 Z= 0.270 Chirality : 0.040 0.137 1400 Planarity : 0.004 0.033 1516 Dihedral : 5.399 41.614 1220 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.26 % Allowed : 19.01 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.28), residues: 1064 helix: 2.13 (0.30), residues: 356 sheet: 0.18 (0.29), residues: 348 loop : -1.11 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 19 TYR 0.009 0.001 TYR B 288 PHE 0.015 0.001 PHE A 172 TRP 0.009 0.002 TRP A 45 HIS 0.004 0.001 HIS B 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.20 ( 9156) covalent geometry : angle 0.52587 / 0.27 (12408) hydrogen bonds : bond 0.04221 / 2.89 ( 429) hydrogen bonds : angle 5.04773 / 3.63 ( 1347) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 205 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLN cc_start: 0.7470 (mt0) cc_final: 0.7226 (mt0) REVERT: A 168 PHE cc_start: 0.6841 (t80) cc_final: 0.6611 (t80) REVERT: A 285 ARG cc_start: 0.8088 (mtt90) cc_final: 0.7785 (ptp90) REVERT: B 168 PHE cc_start: 0.6915 (t80) cc_final: 0.6683 (t80) REVERT: B 285 ARG cc_start: 0.8096 (mtt90) cc_final: 0.7886 (ptp90) REVERT: C 269 VAL cc_start: 0.7415 (t) cc_final: 0.7163 (m) REVERT: C 283 GLN cc_start: 0.8108 (tt0) cc_final: 0.7843 (tt0) REVERT: C 285 ARG cc_start: 0.8058 (mtt90) cc_final: 0.7789 (ptp90) REVERT: C 312 GLN cc_start: 0.5126 (mm-40) cc_final: 0.4559 (mm-40) REVERT: D 84 ASP cc_start: 0.6098 (m-30) cc_final: 0.5830 (m-30) REVERT: D 168 PHE cc_start: 0.6879 (t80) cc_final: 0.6665 (t80) REVERT: D 269 VAL cc_start: 0.7278 (t) cc_final: 0.7047 (m) REVERT: D 285 ARG cc_start: 0.8098 (mtt90) cc_final: 0.7794 (ptp90) REVERT: D 312 GLN cc_start: 0.5237 (mm-40) cc_final: 0.4535 (mm-40) REVERT: D 315 MET cc_start: 0.7584 (mmm) cc_final: 0.7288 (mtt) outliers start: 31 outliers final: 28 residues processed: 219 average time/residue: 0.1740 time to fit residues: 56.2325 Evaluate side-chains 233 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 205 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 53 TRP Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 239 PHE Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 53 TRP Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 239 PHE Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 53 TRP Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 239 PHE Chi-restraints excluded: chain D residue 270 PHE Chi-restraints excluded: chain D residue 301 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 44 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 96 optimal weight: 6.9990 chunk 104 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.151826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.130832 restraints weight = 36430.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.135284 restraints weight = 15170.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.137922 restraints weight = 8048.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.139435 restraints weight = 5296.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.140345 restraints weight = 4151.595| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6770 moved from start: 0.4504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 9156 Z= 0.296 Angle : 0.599 8.173 12408 Z= 0.313 Chirality : 0.043 0.138 1400 Planarity : 0.005 0.032 1516 Dihedral : 5.634 39.543 1220 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 3.05 % Allowed : 19.12 % Favored : 77.84 % 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: 0.35 (0.27), residues: 1064 helix: 1.87 (0.30), residues: 356 sheet: 0.17 (0.29), residues: 324 loop : -1.27 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 19 TYR 0.016 0.002 TYR D 243 PHE 0.022 0.002 PHE A 172 TRP 0.014 0.002 TRP B 45 HIS 0.005 0.001 HIS D 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00649 / 0.30 ( 9156) covalent geometry : angle 0.59906 / 0.31 (12408) hydrogen bonds : bond 0.04714 / 3.21 ( 429) hydrogen bonds : angle 5.29755 / 3.81 ( 1347) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 208 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 PHE cc_start: 0.6883 (t80) cc_final: 0.6663 (t80) REVERT: A 285 ARG cc_start: 0.8087 (mtt90) cc_final: 0.7808 (ptp90) REVERT: B 168 PHE cc_start: 0.6964 (t80) cc_final: 0.6730 (t80) REVERT: B 283 GLN cc_start: 0.8268 (tt0) cc_final: 0.8054 (tt0) REVERT: B 285 ARG cc_start: 0.8096 (mtt90) cc_final: 0.7890 (ptp90) REVERT: C 269 VAL cc_start: 0.7429 (t) cc_final: 0.7164 (m) REVERT: C 283 GLN cc_start: 0.8165 (tt0) cc_final: 0.7840 (tt0) REVERT: C 285 ARG cc_start: 0.8082 (mtt90) cc_final: 0.7785 (ptp90) REVERT: C 312 GLN cc_start: 0.5191 (mm-40) cc_final: 0.4640 (mm-40) REVERT: D 168 PHE cc_start: 0.6909 (t80) cc_final: 0.6687 (t80) REVERT: D 269 VAL cc_start: 0.7310 (t) cc_final: 0.7093 (m) REVERT: D 285 ARG cc_start: 0.8129 (mtt90) cc_final: 0.7814 (ptp90) REVERT: D 312 GLN cc_start: 0.5297 (mm-40) cc_final: 0.4619 (mm-40) outliers start: 29 outliers final: 24 residues processed: 218 average time/residue: 0.1640 time to fit residues: 52.7461 Evaluate side-chains 230 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 206 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 TRP Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 239 PHE Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 53 TRP Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 53 TRP Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 239 PHE Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain D residue 53 TRP Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain D residue 239 PHE Chi-restraints excluded: chain D residue 301 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 5 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 79 optimal weight: 7.9990 chunk 10 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 106 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.155668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.134680 restraints weight = 35540.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.139041 restraints weight = 14933.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.141692 restraints weight = 8074.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.143247 restraints weight = 5378.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.144133 restraints weight = 4232.297| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6710 moved from start: 0.4462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9156 Z= 0.152 Angle : 0.509 7.246 12408 Z= 0.257 Chirality : 0.039 0.137 1400 Planarity : 0.004 0.036 1516 Dihedral : 5.157 37.074 1220 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.52 % Allowed : 19.96 % Favored : 77.52 % 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: 0.69 (0.28), residues: 1064 helix: 2.20 (0.30), residues: 356 sheet: 0.27 (0.30), residues: 324 loop : -1.03 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 19 TYR 0.009 0.001 TYR B 209 PHE 0.020 0.001 PHE A 172 TRP 0.007 0.001 TRP C 53 HIS 0.004 0.001 HIS D 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 ( 9156) covalent geometry : angle 0.50853 / 0.26 (12408) hydrogen bonds : bond 0.03983 / 2.72 ( 429) hydrogen bonds : angle 4.94299 / 3.56 ( 1347) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 203 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLN cc_start: 0.7546 (mt0) cc_final: 0.7301 (mt0) REVERT: A 168 PHE cc_start: 0.6919 (t80) cc_final: 0.6693 (t80) REVERT: A 285 ARG cc_start: 0.8061 (mtt90) cc_final: 0.7748 (ptp90) REVERT: B 168 PHE cc_start: 0.6953 (t80) cc_final: 0.6732 (t80) REVERT: B 283 GLN cc_start: 0.8234 (tt0) cc_final: 0.7948 (tt0) REVERT: B 285 ARG cc_start: 0.8079 (mtt90) cc_final: 0.7774 (ptp90) REVERT: C 269 VAL cc_start: 0.7349 (t) cc_final: 0.7081 (m) REVERT: C 285 ARG cc_start: 0.8037 (mtt90) cc_final: 0.7726 (ptp90) REVERT: C 312 GLN cc_start: 0.5272 (mm-40) cc_final: 0.4712 (mm-40) REVERT: D 269 VAL cc_start: 0.7223 (t) cc_final: 0.6991 (m) REVERT: D 285 ARG cc_start: 0.8085 (mtt90) cc_final: 0.7752 (ptp90) REVERT: D 312 GLN cc_start: 0.5359 (mm-40) cc_final: 0.4605 (mm-40) REVERT: D 315 MET cc_start: 0.7504 (mmm) cc_final: 0.7202 (mtt) outliers start: 24 outliers final: 24 residues processed: 212 average time/residue: 0.1807 time to fit residues: 56.1294 Evaluate side-chains 226 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 202 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 53 TRP Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 239 PHE Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 53 TRP Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 53 TRP Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 239 PHE Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain D residue 53 TRP Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain D residue 239 PHE Chi-restraints excluded: chain D residue 287 SER Chi-restraints excluded: chain D residue 301 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 75 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.153983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.131924 restraints weight = 35727.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.136873 restraints weight = 14330.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.139715 restraints weight = 7386.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.141381 restraints weight = 4772.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.142365 restraints weight = 3680.146| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6706 moved from start: 0.4502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9156 Z= 0.164 Angle : 0.512 7.499 12408 Z= 0.258 Chirality : 0.039 0.137 1400 Planarity : 0.004 0.042 1516 Dihedral : 5.121 36.172 1220 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.42 % Allowed : 20.17 % Favored : 77.42 % 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: 0.72 (0.28), residues: 1064 helix: 2.22 (0.30), residues: 356 sheet: 0.31 (0.30), residues: 324 loop : -1.03 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 19 TYR 0.009 0.001 TYR B 209 PHE 0.022 0.001 PHE A 172 TRP 0.006 0.001 TRP D 45 HIS 0.004 0.000 HIS B 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 ( 9156) covalent geometry : angle 0.51242 / 0.26 (12408) hydrogen bonds : bond 0.03952 / 2.70 ( 429) hydrogen bonds : angle 4.90640 / 3.55 ( 1347) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2678.92 seconds wall clock time: 46 minutes 29.70 seconds (2789.70 seconds total)