Starting phenix.real_space_refine on Sat Aug 23 12:39:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sgr_40465/08_2025/8sgr_40465.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sgr_40465/08_2025/8sgr_40465.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sgr_40465/08_2025/8sgr_40465.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sgr_40465/08_2025/8sgr_40465.map" model { file = "/net/cci-nas-00/data/ceres_data/8sgr_40465/08_2025/8sgr_40465.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sgr_40465/08_2025/8sgr_40465.cif" } resolution = 2.84 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= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 88 5.16 5 C 7720 2.51 5 N 2140 2.21 5 O 2296 1.98 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-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12252 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3010 Classifications: {'peptide': 393} Link IDs: {'PTRANS': 12, 'TRANS': 380} Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D Time building chain proxies: 2.69, per 1000 atoms: 0.22 Number of scatterers: 12252 At special positions: 0 Unit cell: (96.5835, 93.2815, 96.5835, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 88 16.00 P 8 15.00 O 2296 8.00 N 2140 7.00 C 7720 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.33 Conformation dependent library (CDL) restraints added in 625.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2808 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 12 sheets defined 63.4% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 39 through 44 removed outlier: 3.688A pdb=" N ASN A 43 " --> pdb=" O ASP A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 63 Processing helix chain 'A' and resid 64 through 66 No H-bonds generated for 'chain 'A' and resid 64 through 66' Processing helix chain 'A' and resid 67 through 75 Processing helix chain 'A' and resid 79 through 91 Processing helix chain 'A' and resid 98 through 102 Processing helix chain 'A' and resid 107 through 122 Processing helix chain 'A' and resid 122 through 134 Processing helix chain 'A' and resid 136 through 143 Processing helix chain 'A' and resid 145 through 159 Proline residue: A 154 - end of helix Processing helix chain 'A' and resid 175 through 179 Processing helix chain 'A' and resid 220 through 224 removed outlier: 3.955A pdb=" N GLY A 224 " --> pdb=" O PRO A 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 220 through 224' Processing helix chain 'A' and resid 274 through 291 removed outlier: 4.182A pdb=" N VAL A 278 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 310 removed outlier: 3.865A pdb=" N LEU A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) Proline residue: A 307 - end of helix Processing helix chain 'A' and resid 322 through 353 Processing helix chain 'A' and resid 356 through 383 removed outlier: 4.036A pdb=" N ILE A 364 " --> pdb=" O CYS A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 388 removed outlier: 3.515A pdb=" N ILE A 388 " --> pdb=" O ASN A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 401 Processing helix chain 'A' and resid 402 through 405 Processing helix chain 'A' and resid 409 through 424 removed outlier: 3.849A pdb=" N ASP A 424 " --> pdb=" O ALA A 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 44 removed outlier: 3.687A pdb=" N ASN B 43 " --> pdb=" O ASP B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 63 Processing helix chain 'B' and resid 64 through 66 No H-bonds generated for 'chain 'B' and resid 64 through 66' Processing helix chain 'B' and resid 67 through 75 Processing helix chain 'B' and resid 79 through 91 Processing helix chain 'B' and resid 98 through 102 Processing helix chain 'B' and resid 107 through 122 Processing helix chain 'B' and resid 122 through 134 Processing helix chain 'B' and resid 136 through 143 Processing helix chain 'B' and resid 145 through 159 Proline residue: B 154 - end of helix Processing helix chain 'B' and resid 175 through 179 Processing helix chain 'B' and resid 220 through 224 removed outlier: 3.954A pdb=" N GLY B 224 " --> pdb=" O PRO B 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 220 through 224' Processing helix chain 'B' and resid 274 through 291 removed outlier: 4.183A pdb=" N VAL B 278 " --> pdb=" O LYS B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 310 removed outlier: 3.865A pdb=" N LEU B 295 " --> pdb=" O ALA B 291 " (cutoff:3.500A) Proline residue: B 307 - end of helix Processing helix chain 'B' and resid 322 through 353 Processing helix chain 'B' and resid 356 through 383 removed outlier: 4.036A pdb=" N ILE B 364 " --> pdb=" O CYS B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 388 removed outlier: 3.515A pdb=" N ILE B 388 " --> pdb=" O ASN B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 401 Processing helix chain 'B' and resid 402 through 405 Processing helix chain 'B' and resid 409 through 424 removed outlier: 3.850A pdb=" N ASP B 424 " --> pdb=" O ALA B 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 44 removed outlier: 3.687A pdb=" N ASN C 43 " --> pdb=" O ASP C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 63 Processing helix chain 'C' and resid 64 through 66 No H-bonds generated for 'chain 'C' and resid 64 through 66' Processing helix chain 'C' and resid 67 through 75 Processing helix chain 'C' and resid 79 through 91 Processing helix chain 'C' and resid 98 through 102 Processing helix chain 'C' and resid 107 through 122 Processing helix chain 'C' and resid 122 through 134 Processing helix chain 'C' and resid 136 through 143 Processing helix chain 'C' and resid 145 through 159 Proline residue: C 154 - end of helix Processing helix chain 'C' and resid 175 through 179 Processing helix chain 'C' and resid 220 through 224 removed outlier: 3.954A pdb=" N GLY C 224 " --> pdb=" O PRO C 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 220 through 224' Processing helix chain 'C' and resid 274 through 291 removed outlier: 4.182A pdb=" N VAL C 278 " --> pdb=" O LYS C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 310 removed outlier: 3.864A pdb=" N LEU C 295 " --> pdb=" O ALA C 291 " (cutoff:3.500A) Proline residue: C 307 - end of helix Processing helix chain 'C' and resid 322 through 353 Processing helix chain 'C' and resid 356 through 383 removed outlier: 4.036A pdb=" N ILE C 364 " --> pdb=" O CYS C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 388 removed outlier: 3.515A pdb=" N ILE C 388 " --> pdb=" O ASN C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 401 Processing helix chain 'C' and resid 402 through 405 Processing helix chain 'C' and resid 409 through 424 removed outlier: 3.850A pdb=" N ASP C 424 " --> pdb=" O ALA C 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 44 removed outlier: 3.687A pdb=" N ASN D 43 " --> pdb=" O ASP D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 63 Processing helix chain 'D' and resid 64 through 66 No H-bonds generated for 'chain 'D' and resid 64 through 66' Processing helix chain 'D' and resid 67 through 75 Processing helix chain 'D' and resid 79 through 91 Processing helix chain 'D' and resid 98 through 102 Processing helix chain 'D' and resid 107 through 122 Processing helix chain 'D' and resid 122 through 134 Processing helix chain 'D' and resid 136 through 143 Processing helix chain 'D' and resid 145 through 159 Proline residue: D 154 - end of helix Processing helix chain 'D' and resid 175 through 179 Processing helix chain 'D' and resid 220 through 224 removed outlier: 3.955A pdb=" N GLY D 224 " --> pdb=" O PRO D 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 220 through 224' Processing helix chain 'D' and resid 274 through 291 removed outlier: 4.182A pdb=" N VAL D 278 " --> pdb=" O LYS D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 310 removed outlier: 3.864A pdb=" N LEU D 295 " --> pdb=" O ALA D 291 " (cutoff:3.500A) Proline residue: D 307 - end of helix Processing helix chain 'D' and resid 322 through 353 Processing helix chain 'D' and resid 356 through 383 removed outlier: 4.036A pdb=" N ILE D 364 " --> pdb=" O CYS D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 388 removed outlier: 3.515A pdb=" N ILE D 388 " --> pdb=" O ASN D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 401 Processing helix chain 'D' and resid 402 through 405 Processing helix chain 'D' and resid 409 through 424 removed outlier: 3.849A pdb=" N ASP D 424 " --> pdb=" O ALA D 420 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 163 through 166 Processing sheet with id=AA2, first strand: chain 'A' and resid 182 through 186 removed outlier: 7.621A pdb=" N GLY A 194 " --> pdb=" O GLU A 259 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N GLU A 259 " --> pdb=" O GLY A 194 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N LYS A 196 " --> pdb=" O ILE A 257 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N ILE A 257 " --> pdb=" O LYS A 196 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N TRP A 198 " --> pdb=" O GLU A 255 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N GLU A 255 " --> pdb=" O TRP A 198 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR A 200 " --> pdb=" O THR A 253 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N THR A 253 " --> pdb=" O THR A 200 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 313 through 314 Processing sheet with id=AA4, first strand: chain 'B' and resid 163 through 166 Processing sheet with id=AA5, first strand: chain 'B' and resid 182 through 186 removed outlier: 7.622A pdb=" N GLY B 194 " --> pdb=" O GLU B 259 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N GLU B 259 " --> pdb=" O GLY B 194 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N LYS B 196 " --> pdb=" O ILE B 257 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N ILE B 257 " --> pdb=" O LYS B 196 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N TRP B 198 " --> pdb=" O GLU B 255 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N GLU B 255 " --> pdb=" O TRP B 198 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR B 200 " --> pdb=" O THR B 253 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N THR B 253 " --> pdb=" O THR B 200 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 313 through 314 Processing sheet with id=AA7, first strand: chain 'C' and resid 163 through 166 Processing sheet with id=AA8, first strand: chain 'C' and resid 182 through 186 removed outlier: 7.622A pdb=" N GLY C 194 " --> pdb=" O GLU C 259 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N GLU C 259 " --> pdb=" O GLY C 194 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N LYS C 196 " --> pdb=" O ILE C 257 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N ILE C 257 " --> pdb=" O LYS C 196 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N TRP C 198 " --> pdb=" O GLU C 255 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N GLU C 255 " --> pdb=" O TRP C 198 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N THR C 200 " --> pdb=" O THR C 253 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N THR C 253 " --> pdb=" O THR C 200 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 313 through 314 Processing sheet with id=AB1, first strand: chain 'D' and resid 163 through 166 Processing sheet with id=AB2, first strand: chain 'D' and resid 182 through 186 removed outlier: 7.623A pdb=" N GLY D 194 " --> pdb=" O GLU D 259 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N GLU D 259 " --> pdb=" O GLY D 194 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N LYS D 196 " --> pdb=" O ILE D 257 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N ILE D 257 " --> pdb=" O LYS D 196 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N TRP D 198 " --> pdb=" O GLU D 255 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N GLU D 255 " --> pdb=" O TRP D 198 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N THR D 200 " --> pdb=" O THR D 253 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N THR D 253 " --> pdb=" O THR D 200 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 313 through 314 740 hydrogen bonds defined for protein. 2112 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: 2.59 Time building geometry restraints manager: 1.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4076 1.34 - 1.46: 2420 1.46 - 1.58: 5844 1.58 - 1.69: 8 1.69 - 1.81: 140 Bond restraints: 12488 Sorted by residual: bond pdb=" O3P FAD C1101 " pdb=" P FAD C1101 " ideal model delta sigma weight residual 1.660 1.576 0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" O3P FAD A1101 " pdb=" P FAD A1101 " ideal model delta sigma weight residual 1.660 1.576 0.084 2.00e-02 2.50e+03 1.76e+01 bond pdb=" O3P FAD B1101 " pdb=" P FAD B1101 " ideal model delta sigma weight residual 1.660 1.576 0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" O3P FAD D1101 " pdb=" P FAD D1101 " ideal model delta sigma weight residual 1.660 1.577 0.083 2.00e-02 2.50e+03 1.74e+01 bond pdb=" O5B FAD C1101 " pdb=" PA FAD C1101 " ideal model delta sigma weight residual 1.634 1.562 0.072 2.00e-02 2.50e+03 1.30e+01 ... (remaining 12483 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 16478 1.65 - 3.31: 314 3.31 - 4.96: 52 4.96 - 6.61: 20 6.61 - 8.27: 8 Bond angle restraints: 16872 Sorted by residual: angle pdb=" O1P FAD C1101 " pdb=" P FAD C1101 " pdb=" O2P FAD C1101 " ideal model delta sigma weight residual 122.50 114.23 8.27 3.00e+00 1.11e-01 7.59e+00 angle pdb=" O1P FAD D1101 " pdb=" P FAD D1101 " pdb=" O2P FAD D1101 " ideal model delta sigma weight residual 122.50 114.25 8.25 3.00e+00 1.11e-01 7.55e+00 angle pdb=" O1P FAD A1101 " pdb=" P FAD A1101 " pdb=" O2P FAD A1101 " ideal model delta sigma weight residual 122.50 114.27 8.23 3.00e+00 1.11e-01 7.53e+00 angle pdb=" O1P FAD B1101 " pdb=" P FAD B1101 " pdb=" O2P FAD B1101 " ideal model delta sigma weight residual 122.50 114.28 8.22 3.00e+00 1.11e-01 7.50e+00 angle pdb=" CA TRP A 198 " pdb=" C TRP A 198 " pdb=" N ILE A 199 " ideal model delta sigma weight residual 116.21 119.73 -3.52 1.29e+00 6.01e-01 7.43e+00 ... (remaining 16867 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.57: 7272 24.57 - 49.14: 216 49.14 - 73.71: 44 73.71 - 98.28: 0 98.28 - 122.86: 4 Dihedral angle restraints: 7536 sinusoidal: 3100 harmonic: 4436 Sorted by residual: dihedral pdb=" O5' FAD A1101 " pdb=" O3P FAD A1101 " pdb=" P FAD A1101 " pdb=" PA FAD A1101 " ideal model delta sinusoidal sigma weight residual 298.23 175.37 122.86 1 3.00e+01 1.11e-03 1.65e+01 dihedral pdb=" O5' FAD C1101 " pdb=" O3P FAD C1101 " pdb=" P FAD C1101 " pdb=" PA FAD C1101 " ideal model delta sinusoidal sigma weight residual 298.23 175.44 122.79 1 3.00e+01 1.11e-03 1.64e+01 dihedral pdb=" O5' FAD D1101 " pdb=" O3P FAD D1101 " pdb=" P FAD D1101 " pdb=" PA FAD D1101 " ideal model delta sinusoidal sigma weight residual 298.23 175.44 122.79 1 3.00e+01 1.11e-03 1.64e+01 ... (remaining 7533 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1246 0.033 - 0.067: 409 0.067 - 0.100: 134 0.100 - 0.133: 43 0.133 - 0.166: 4 Chirality restraints: 1836 Sorted by residual: chirality pdb=" C2B FAD B1101 " pdb=" C1B FAD B1101 " pdb=" C3B FAD B1101 " pdb=" O2B FAD B1101 " both_signs ideal model delta sigma weight residual False -2.53 -2.70 0.17 2.00e-01 2.50e+01 6.93e-01 chirality pdb=" C2B FAD C1101 " pdb=" C1B FAD C1101 " pdb=" C3B FAD C1101 " pdb=" O2B FAD C1101 " both_signs ideal model delta sigma weight residual False -2.53 -2.70 0.16 2.00e-01 2.50e+01 6.79e-01 chirality pdb=" C2B FAD D1101 " pdb=" C1B FAD D1101 " pdb=" C3B FAD D1101 " pdb=" O2B FAD D1101 " both_signs ideal model delta sigma weight residual False -2.53 -2.70 0.16 2.00e-01 2.50e+01 6.79e-01 ... (remaining 1833 not shown) Planarity restraints: 2168 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 293 " -0.024 5.00e-02 4.00e+02 3.57e-02 2.04e+00 pdb=" N PRO C 294 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO C 294 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 294 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 293 " 0.024 5.00e-02 4.00e+02 3.57e-02 2.04e+00 pdb=" N PRO D 294 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO D 294 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 294 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 293 " -0.024 5.00e-02 4.00e+02 3.55e-02 2.02e+00 pdb=" N PRO B 294 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 294 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 294 " -0.020 5.00e-02 4.00e+02 ... (remaining 2165 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 279 2.69 - 3.25: 12280 3.25 - 3.80: 19901 3.80 - 4.35: 26930 4.35 - 4.90: 45392 Nonbonded interactions: 104782 Sorted by model distance: nonbonded pdb=" O3' FAD D1101 " pdb=" O5' FAD D1101 " model vdw 2.143 3.040 nonbonded pdb=" O3' FAD C1101 " pdb=" O5' FAD C1101 " model vdw 2.143 3.040 nonbonded pdb=" O3' FAD A1101 " pdb=" O5' FAD A1101 " model vdw 2.143 3.040 nonbonded pdb=" O3' FAD B1101 " pdb=" O5' FAD B1101 " model vdw 2.143 3.040 nonbonded pdb=" OE2 GLU D 70 " pdb=" OG SER D 74 " model vdw 2.216 3.040 ... (remaining 104777 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.800 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: 0.020 Extract box with map and model: 0.190 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.570 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 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 : 0.006 0.084 12488 Z= 0.255 Angle : 0.612 8.266 16872 Z= 0.320 Chirality : 0.039 0.166 1836 Planarity : 0.003 0.036 2168 Dihedral : 11.942 122.856 4728 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.64 % Allowed : 5.10 % Favored : 94.27 % 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 aren not related in a simple way. whole: 2.16 (0.20), residues: 1564 helix: 2.67 (0.18), residues: 844 sheet: -0.73 (0.34), residues: 140 loop : 0.17 (0.23), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 413 TYR 0.006 0.001 TYR A 366 PHE 0.005 0.001 PHE A 258 TRP 0.010 0.001 TRP D 198 HIS 0.004 0.001 HIS B 304 Details of bonding type rmsd covalent geometry : bond 0.00551 (12488) covalent geometry : angle 0.61204 (16872) hydrogen bonds : bond 0.14151 ( 740) hydrogen bonds : angle 5.00106 ( 2112) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 140 time to evaluate : 0.521 Fit side-chains outliers start: 8 outliers final: 0 residues processed: 148 average time/residue: 0.7354 time to fit residues: 117.3193 Evaluate side-chains 87 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 0.8980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN A 111 HIS A 139 GLN ** A 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 GLN A 380 GLN B 69 GLN B 111 HIS B 134 ASN B 139 GLN ** B 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 GLN B 380 GLN C 69 GLN C 111 HIS C 139 GLN ** C 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 GLN C 380 GLN D 69 GLN D 111 HIS D 134 ASN D 139 GLN ** D 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 317 GLN D 380 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.088624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.072758 restraints weight = 21345.450| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 2.47 r_work: 0.2708 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2569 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12488 Z= 0.153 Angle : 0.504 4.886 16872 Z= 0.265 Chirality : 0.038 0.171 1836 Planarity : 0.004 0.039 2168 Dihedral : 9.830 108.743 1884 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.96 % Allowed : 7.64 % Favored : 91.40 % 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 aren not related in a simple way. whole: 2.29 (0.21), residues: 1564 helix: 2.75 (0.18), residues: 848 sheet: -0.73 (0.35), residues: 140 loop : 0.26 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 249 TYR 0.011 0.001 TYR A 277 PHE 0.004 0.001 PHE C 258 TRP 0.013 0.001 TRP D 198 HIS 0.004 0.001 HIS D 304 Details of bonding type rmsd covalent geometry : bond 0.00358 (12488) covalent geometry : angle 0.50403 (16872) hydrogen bonds : bond 0.05246 ( 740) hydrogen bonds : angle 3.93740 ( 2112) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.515 Fit side-chains outliers start: 12 outliers final: 1 residues processed: 96 average time/residue: 0.6864 time to fit residues: 71.6750 Evaluate side-chains 77 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 76 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 21 optimal weight: 4.9990 chunk 10 optimal weight: 0.2980 chunk 83 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 chunk 150 optimal weight: 0.9980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN ** A 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 ASN ** C 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.089215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.072717 restraints weight = 21635.539| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 2.50 r_work: 0.2715 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2574 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12488 Z= 0.151 Angle : 0.487 4.966 16872 Z= 0.258 Chirality : 0.038 0.170 1836 Planarity : 0.003 0.040 2168 Dihedral : 9.340 103.453 1884 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.40 % Allowed : 9.71 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.32 (0.21), residues: 1564 helix: 2.75 (0.18), residues: 848 sheet: -0.66 (0.35), residues: 140 loop : 0.32 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 223 TYR 0.006 0.001 TYR D 277 PHE 0.005 0.001 PHE A 228 TRP 0.013 0.002 TRP D 198 HIS 0.003 0.001 HIS C 304 Details of bonding type rmsd covalent geometry : bond 0.00355 (12488) covalent geometry : angle 0.48721 (16872) hydrogen bonds : bond 0.04980 ( 740) hydrogen bonds : angle 3.82307 ( 2112) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 88 time to evaluate : 0.535 Fit side-chains REVERT: B 262 LYS cc_start: 0.8497 (ptmm) cc_final: 0.8246 (tttp) REVERT: C 262 LYS cc_start: 0.8490 (ptmm) cc_final: 0.8225 (tttp) REVERT: D 262 LYS cc_start: 0.8503 (ptmm) cc_final: 0.8251 (tttp) outliers start: 5 outliers final: 3 residues processed: 92 average time/residue: 0.7091 time to fit residues: 70.8768 Evaluate side-chains 88 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 85 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain D residue 225 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 4 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 88 optimal weight: 0.5980 chunk 107 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 150 optimal weight: 0.6980 chunk 54 optimal weight: 4.9990 chunk 92 optimal weight: 0.0980 chunk 140 optimal weight: 6.9990 chunk 147 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 310 HIS ** 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 = 0.3209 r_free = 0.3209 target = 0.091761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.075321 restraints weight = 21388.309| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 2.53 r_work: 0.2768 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12488 Z= 0.102 Angle : 0.437 4.783 16872 Z= 0.229 Chirality : 0.036 0.157 1836 Planarity : 0.003 0.040 2168 Dihedral : 8.740 94.693 1884 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.56 % Allowed : 10.75 % Favored : 88.69 % 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 aren not related in a simple way. whole: 2.49 (0.21), residues: 1564 helix: 2.87 (0.18), residues: 848 sheet: -0.33 (0.36), residues: 140 loop : 0.37 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 223 TYR 0.008 0.001 TYR C 277 PHE 0.004 0.001 PHE A 382 TRP 0.012 0.001 TRP A 198 HIS 0.002 0.000 HIS D 304 Details of bonding type rmsd covalent geometry : bond 0.00226 (12488) covalent geometry : angle 0.43725 (16872) hydrogen bonds : bond 0.04154 ( 740) hydrogen bonds : angle 3.61403 ( 2112) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 103 time to evaluate : 0.519 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 0 residues processed: 107 average time/residue: 0.6497 time to fit residues: 75.8957 Evaluate side-chains 87 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 123 optimal weight: 4.9990 chunk 37 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 154 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 143 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 chunk 141 optimal weight: 6.9990 chunk 148 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 310 HIS ** 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 = 0.3191 r_free = 0.3191 target = 0.090675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.075219 restraints weight = 21564.669| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 2.50 r_work: 0.2747 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12488 Z= 0.111 Angle : 0.446 4.990 16872 Z= 0.230 Chirality : 0.036 0.139 1836 Planarity : 0.003 0.040 2168 Dihedral : 8.576 91.655 1884 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.96 % Allowed : 12.26 % Favored : 86.78 % 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 aren not related in a simple way. whole: 2.54 (0.21), residues: 1564 helix: 2.91 (0.18), residues: 848 sheet: -0.22 (0.37), residues: 140 loop : 0.36 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 223 TYR 0.010 0.001 TYR D 277 PHE 0.004 0.001 PHE C 258 TRP 0.008 0.001 TRP B 198 HIS 0.003 0.001 HIS D 304 Details of bonding type rmsd covalent geometry : bond 0.00254 (12488) covalent geometry : angle 0.44589 (16872) hydrogen bonds : bond 0.04195 ( 740) hydrogen bonds : angle 3.63289 ( 2112) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.522 Fit side-chains outliers start: 12 outliers final: 0 residues processed: 96 average time/residue: 0.6610 time to fit residues: 69.3329 Evaluate side-chains 85 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 104 optimal weight: 0.5980 chunk 142 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 150 optimal weight: 0.6980 chunk 112 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 126 optimal weight: 0.7980 chunk 132 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 62 optimal weight: 0.0060 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 310 HIS ** 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 = 0.3211 r_free = 0.3211 target = 0.092001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.075774 restraints weight = 21412.632| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 2.51 r_work: 0.2777 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12488 Z= 0.101 Angle : 0.436 4.835 16872 Z= 0.225 Chirality : 0.036 0.145 1836 Planarity : 0.003 0.040 2168 Dihedral : 8.371 86.479 1884 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.88 % Allowed : 12.34 % Favored : 86.78 % 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 aren not related in a simple way. whole: 2.61 (0.21), residues: 1564 helix: 2.95 (0.18), residues: 848 sheet: -0.15 (0.37), residues: 140 loop : 0.40 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 223 TYR 0.008 0.001 TYR A 277 PHE 0.003 0.001 PHE B 391 TRP 0.009 0.001 TRP C 198 HIS 0.002 0.000 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00225 (12488) covalent geometry : angle 0.43570 (16872) hydrogen bonds : bond 0.03961 ( 740) hydrogen bonds : angle 3.57380 ( 2112) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.380 Fit side-chains outliers start: 11 outliers final: 0 residues processed: 97 average time/residue: 0.5854 time to fit residues: 62.2614 Evaluate side-chains 84 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 103 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 136 optimal weight: 3.9990 chunk 128 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 57 optimal weight: 0.0170 chunk 86 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 310 HIS ** 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 = 0.3207 r_free = 0.3207 target = 0.091641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.075433 restraints weight = 21485.649| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 2.53 r_work: 0.2769 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12488 Z= 0.107 Angle : 0.445 4.921 16872 Z= 0.231 Chirality : 0.036 0.142 1836 Planarity : 0.003 0.040 2168 Dihedral : 8.317 84.225 1884 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.00 % Allowed : 14.73 % Favored : 85.27 % 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 aren not related in a simple way. whole: 2.65 (0.21), residues: 1564 helix: 2.96 (0.18), residues: 848 sheet: -0.07 (0.38), residues: 140 loop : 0.43 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 223 TYR 0.008 0.001 TYR D 277 PHE 0.004 0.001 PHE A 382 TRP 0.009 0.001 TRP D 198 HIS 0.003 0.000 HIS C 304 Details of bonding type rmsd covalent geometry : bond 0.00240 (12488) covalent geometry : angle 0.44462 (16872) hydrogen bonds : bond 0.04019 ( 740) hydrogen bonds : angle 3.59850 ( 2112) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.538 Fit side-chains outliers start: 0 outliers final: 3 residues processed: 88 average time/residue: 0.6297 time to fit residues: 60.7566 Evaluate side-chains 87 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 84 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain D residue 225 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 6 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 50 optimal weight: 0.0470 chunk 18 optimal weight: 0.0000 chunk 124 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 138 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 97 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 overall best weight: 0.5884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 310 HIS ** 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 = 0.3219 r_free = 0.3219 target = 0.092432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.076289 restraints weight = 21374.196| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 2.54 r_work: 0.2784 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12488 Z= 0.100 Angle : 0.440 4.848 16872 Z= 0.232 Chirality : 0.036 0.141 1836 Planarity : 0.003 0.040 2168 Dihedral : 8.250 80.087 1884 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.32 % Allowed : 14.81 % Favored : 84.87 % 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 aren not related in a simple way. whole: 2.65 (0.21), residues: 1564 helix: 2.92 (0.18), residues: 848 sheet: 0.06 (0.38), residues: 140 loop : 0.47 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 223 TYR 0.011 0.001 TYR C 277 PHE 0.005 0.001 PHE A 382 TRP 0.009 0.001 TRP C 198 HIS 0.002 0.000 HIS D 304 Details of bonding type rmsd covalent geometry : bond 0.00222 (12488) covalent geometry : angle 0.44049 (16872) hydrogen bonds : bond 0.03882 ( 740) hydrogen bonds : angle 3.58267 ( 2112) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 95 time to evaluate : 0.465 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 99 average time/residue: 0.6499 time to fit residues: 70.2598 Evaluate side-chains 87 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 84 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain D residue 225 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 111 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 17 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 121 optimal weight: 4.9990 chunk 51 optimal weight: 0.0470 chunk 117 optimal weight: 5.9990 chunk 144 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 overall best weight: 0.8880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 310 HIS ** 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 = 0.3170 r_free = 0.3170 target = 0.089657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.073877 restraints weight = 21223.060| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 2.52 r_work: 0.2748 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2608 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12488 Z= 0.120 Angle : 0.469 6.026 16872 Z= 0.242 Chirality : 0.037 0.143 1836 Planarity : 0.003 0.040 2168 Dihedral : 8.280 78.663 1884 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.00 % Allowed : 15.05 % Favored : 84.95 % 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 aren not related in a simple way. whole: 2.62 (0.21), residues: 1564 helix: 2.90 (0.18), residues: 848 sheet: 0.18 (0.39), residues: 140 loop : 0.43 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 223 TYR 0.010 0.001 TYR D 277 PHE 0.004 0.001 PHE A 382 TRP 0.008 0.001 TRP D 198 HIS 0.003 0.001 HIS D 304 Details of bonding type rmsd covalent geometry : bond 0.00279 (12488) covalent geometry : angle 0.46869 (16872) hydrogen bonds : bond 0.04195 ( 740) hydrogen bonds : angle 3.62379 ( 2112) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.524 Fit side-chains outliers start: 0 outliers final: 3 residues processed: 88 average time/residue: 0.6229 time to fit residues: 59.6353 Evaluate side-chains 87 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 84 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain D residue 225 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 27 optimal weight: 0.0170 chunk 19 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 101 optimal weight: 0.8980 chunk 52 optimal weight: 6.9990 chunk 154 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 422 ASN ** 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 = 0.3180 r_free = 0.3180 target = 0.090298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.074527 restraints weight = 21329.653| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 2.54 r_work: 0.2759 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12488 Z= 0.109 Angle : 0.457 4.877 16872 Z= 0.237 Chirality : 0.037 0.140 1836 Planarity : 0.003 0.040 2168 Dihedral : 8.292 75.942 1884 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.00 % Allowed : 15.05 % Favored : 84.95 % 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 aren not related in a simple way. whole: 2.63 (0.21), residues: 1564 helix: 2.89 (0.18), residues: 848 sheet: 0.27 (0.39), residues: 140 loop : 0.43 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 223 TYR 0.010 0.001 TYR A 277 PHE 0.005 0.001 PHE B 382 TRP 0.009 0.001 TRP D 198 HIS 0.003 0.001 HIS D 304 Details of bonding type rmsd covalent geometry : bond 0.00247 (12488) covalent geometry : angle 0.45662 (16872) hydrogen bonds : bond 0.04040 ( 740) hydrogen bonds : angle 3.51366 ( 2112) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.528 Fit side-chains outliers start: 0 outliers final: 3 residues processed: 84 average time/residue: 0.6679 time to fit residues: 61.1581 Evaluate side-chains 87 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 84 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain D residue 225 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 67 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 131 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 310 HIS ** 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 = 0.3130 r_free = 0.3130 target = 0.087256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.071360 restraints weight = 21417.000| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 2.52 r_work: 0.2698 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2558 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12488 Z= 0.162 Angle : 0.497 5.068 16872 Z= 0.259 Chirality : 0.038 0.144 1836 Planarity : 0.003 0.040 2168 Dihedral : 8.356 78.418 1884 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.32 % Allowed : 14.89 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.52 (0.21), residues: 1564 helix: 2.84 (0.18), residues: 848 sheet: 0.19 (0.39), residues: 140 loop : 0.31 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 223 TYR 0.012 0.001 TYR D 277 PHE 0.005 0.001 PHE A 258 TRP 0.008 0.001 TRP D 198 HIS 0.003 0.001 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00386 (12488) covalent geometry : angle 0.49680 (16872) hydrogen bonds : bond 0.04769 ( 740) hydrogen bonds : angle 3.62414 ( 2112) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3020.13 seconds wall clock time: 52 minutes 51.25 seconds (3171.25 seconds total)