Starting phenix.real_space_refine on Wed May 14 18:18:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sgr_40465/05_2025/8sgr_40465.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sgr_40465/05_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_40465/05_2025/8sgr_40465.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sgr_40465/05_2025/8sgr_40465.map" model { file = "/net/cci-nas-00/data/ceres_data/8sgr_40465/05_2025/8sgr_40465.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sgr_40465/05_2025/8sgr_40465.cif" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: C, B, D Time building chain proxies: 6.69, per 1000 atoms: 0.55 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: 3.15 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.33 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: 4.26 Time building geometry restraints manager: 3.67 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 2.600 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: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 29.240 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 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:10.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.620 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.010 0.001 TRP D 198 HIS 0.004 0.001 HIS B 304 PHE 0.005 0.001 PHE A 258 TYR 0.006 0.001 TYR A 366 ARG 0.002 0.000 ARG D 413 Details of bonding type rmsd hydrogen bonds : bond 0.14151 ( 740) hydrogen bonds : angle 5.00106 ( 2112) covalent geometry : bond 0.00551 (12488) covalent geometry : angle 0.61204 (16872) *********************** 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 : 1.286 Fit side-chains outliers start: 8 outliers final: 0 residues processed: 148 average time/residue: 1.3374 time to fit residues: 213.8515 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 : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.8980 chunk 118 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 63 optimal weight: 0.4980 chunk 122 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 74 optimal weight: 0.0270 chunk 91 optimal weight: 4.9990 chunk 141 optimal weight: 0.0070 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN A 139 GLN ** A 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 GLN ** A 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 GLN B 139 GLN ** B 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 GLN ** B 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 380 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN C 139 GLN ** C 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 GLN ** C 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 380 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 GLN D 139 GLN ** D 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 317 GLN ** D 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 380 GLN ** D 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.091484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.075656 restraints weight = 20928.399| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 2.47 r_work: 0.2762 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2624 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1459 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= 0.106 Angle : 0.473 4.764 16872 Z= 0.249 Chirality : 0.037 0.165 1836 Planarity : 0.004 0.040 2168 Dihedral : 9.743 107.788 1884 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.96 % Allowed : 7.40 % Favored : 91.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.21), residues: 1564 helix: 2.80 (0.18), residues: 848 sheet: -0.68 (0.35), residues: 140 loop : 0.35 (0.23), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 198 HIS 0.003 0.001 HIS D 304 PHE 0.005 0.001 PHE C 382 TYR 0.011 0.001 TYR A 277 ARG 0.002 0.000 ARG A 249 Details of bonding type rmsd hydrogen bonds : bond 0.04624 ( 740) hydrogen bonds : angle 3.84030 ( 2112) covalent geometry : bond 0.00223 (12488) covalent geometry : angle 0.47252 (16872) *********************** 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 109 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 1.350 Fit side-chains outliers start: 12 outliers final: 4 residues processed: 105 average time/residue: 1.1515 time to fit residues: 133.3223 Evaluate side-chains 84 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 ILE 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 96 optimal weight: 0.0030 chunk 84 optimal weight: 0.4980 chunk 65 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 21 optimal weight: 5.9990 chunk 149 optimal weight: 6.9990 chunk 88 optimal weight: 0.6980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 HIS ** A 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 HIS B 134 ASN ** 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 111 HIS D 134 ASN ** D 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.092366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.075866 restraints weight = 21587.131| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 2.51 r_work: 0.2776 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12488 Z= 0.106 Angle : 0.449 4.778 16872 Z= 0.238 Chirality : 0.037 0.166 1836 Planarity : 0.003 0.040 2168 Dihedral : 9.227 103.098 1884 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.32 % Allowed : 9.87 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.21), residues: 1564 helix: 2.84 (0.18), residues: 848 sheet: -0.56 (0.35), residues: 140 loop : 0.43 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 198 HIS 0.002 0.000 HIS D 304 PHE 0.004 0.001 PHE C 228 TYR 0.004 0.001 TYR A 277 ARG 0.001 0.000 ARG A 249 Details of bonding type rmsd hydrogen bonds : bond 0.04301 ( 740) hydrogen bonds : angle 3.65587 ( 2112) covalent geometry : bond 0.00235 (12488) covalent geometry : angle 0.44935 (16872) *********************** 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 99 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 95 time to evaluate : 1.363 Fit side-chains REVERT: A 262 LYS cc_start: 0.8484 (ptmm) cc_final: 0.8258 (tttp) outliers start: 4 outliers final: 0 residues processed: 99 average time/residue: 1.2757 time to fit residues: 137.6708 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 : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 44 optimal weight: 2.9990 chunk 91 optimal weight: 0.0980 chunk 54 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 74 optimal weight: 0.0010 chunk 87 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 149 optimal weight: 6.9990 chunk 86 optimal weight: 0.5980 overall best weight: 0.4586 ------------------------------------------------------------------------------- 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 134 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.093436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.076936 restraints weight = 21096.805| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 2.54 r_work: 0.2798 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12488 Z= 0.093 Angle : 0.429 4.776 16872 Z= 0.223 Chirality : 0.036 0.153 1836 Planarity : 0.003 0.041 2168 Dihedral : 8.735 95.168 1884 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.64 % Allowed : 10.27 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.57 (0.21), residues: 1564 helix: 2.91 (0.18), residues: 848 sheet: -0.32 (0.35), residues: 140 loop : 0.45 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 198 HIS 0.002 0.000 HIS D 304 PHE 0.004 0.001 PHE D 382 TYR 0.009 0.001 TYR A 277 ARG 0.002 0.000 ARG A 223 Details of bonding type rmsd hydrogen bonds : bond 0.03838 ( 740) hydrogen bonds : angle 3.54894 ( 2112) covalent geometry : bond 0.00203 (12488) covalent geometry : angle 0.42875 (16872) *********************** 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 94 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 1.450 Fit side-chains outliers start: 8 outliers final: 1 residues processed: 90 average time/residue: 1.2202 time to fit residues: 120.6077 Evaluate side-chains 85 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 84 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 33 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 18 optimal weight: 0.0870 chunk 8 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 137 optimal weight: 7.9990 chunk 141 optimal weight: 0.8980 overall best weight: 1.7162 ------------------------------------------------------------------------------- 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 111 HIS ** 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 = 0.3152 r_free = 0.3152 target = 0.088364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.072006 restraints weight = 21654.044| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 2.49 r_work: 0.2704 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2562 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12488 Z= 0.189 Angle : 0.494 5.065 16872 Z= 0.256 Chirality : 0.039 0.153 1836 Planarity : 0.003 0.040 2168 Dihedral : 8.750 93.954 1884 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.32 % Allowed : 11.86 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.21), residues: 1564 helix: 2.88 (0.18), residues: 848 sheet: -0.33 (0.36), residues: 140 loop : 0.28 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 198 HIS 0.004 0.001 HIS A 304 PHE 0.006 0.001 PHE A 258 TYR 0.006 0.001 TYR D 403 ARG 0.001 0.000 ARG B 398 Details of bonding type rmsd hydrogen bonds : bond 0.04997 ( 740) hydrogen bonds : angle 3.76483 ( 2112) covalent geometry : bond 0.00450 (12488) covalent geometry : angle 0.49418 (16872) *********************** 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 88 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 84 time to evaluate : 1.265 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 88 average time/residue: 1.3970 time to fit residues: 133.3714 Evaluate side-chains 83 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 91 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 120 optimal weight: 0.9990 chunk 127 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 149 optimal weight: 5.9990 chunk 140 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- 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 = 0.3173 r_free = 0.3173 target = 0.089986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.074174 restraints weight = 21492.575| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 2.47 r_work: 0.2729 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2588 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1764 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= 0.120 Angle : 0.450 4.898 16872 Z= 0.232 Chirality : 0.037 0.149 1836 Planarity : 0.003 0.040 2168 Dihedral : 8.512 89.557 1884 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.96 % Allowed : 12.82 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.21), residues: 1564 helix: 2.89 (0.18), residues: 848 sheet: -0.18 (0.38), residues: 140 loop : 0.30 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 198 HIS 0.002 0.001 HIS A 304 PHE 0.004 0.001 PHE A 258 TYR 0.008 0.001 TYR C 277 ARG 0.001 0.000 ARG B 223 Details of bonding type rmsd hydrogen bonds : bond 0.04411 ( 740) hydrogen bonds : angle 3.66655 ( 2112) covalent geometry : bond 0.00279 (12488) covalent geometry : angle 0.44978 (16872) *********************** 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 97 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 1.420 Fit side-chains outliers start: 12 outliers final: 0 residues processed: 97 average time/residue: 1.1596 time to fit residues: 123.9407 Evaluate side-chains 81 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 76 optimal weight: 0.8980 chunk 142 optimal weight: 0.7980 chunk 112 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 96 optimal weight: 0.0370 chunk 145 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 154 optimal weight: 0.0370 overall best weight: 0.4936 ------------------------------------------------------------------------------- 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 = 0.091985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.076651 restraints weight = 21079.881| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 2.51 r_work: 0.2765 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1953 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= 0.097 Angle : 0.437 4.829 16872 Z= 0.226 Chirality : 0.036 0.147 1836 Planarity : 0.003 0.040 2168 Dihedral : 8.338 85.493 1884 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.32 % Allowed : 14.17 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.61 (0.21), residues: 1564 helix: 2.94 (0.18), residues: 848 sheet: -0.05 (0.39), residues: 140 loop : 0.40 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 198 HIS 0.002 0.000 HIS D 304 PHE 0.005 0.001 PHE D 382 TYR 0.010 0.001 TYR D 277 ARG 0.001 0.000 ARG B 223 Details of bonding type rmsd hydrogen bonds : bond 0.03979 ( 740) hydrogen bonds : angle 3.63676 ( 2112) covalent geometry : bond 0.00210 (12488) covalent geometry : angle 0.43653 (16872) *********************** 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 91 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 87 time to evaluate : 1.293 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 91 average time/residue: 1.2741 time to fit residues: 127.4281 Evaluate side-chains 80 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 97 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 chunk 117 optimal weight: 5.9990 chunk 85 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 98 optimal weight: 0.0770 overall best weight: 1.0740 ------------------------------------------------------------------------------- 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 = 0.3154 r_free = 0.3154 target = 0.088641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.072778 restraints weight = 21602.666| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 2.50 r_work: 0.2724 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2583 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1882 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= 0.134 Angle : 0.467 4.983 16872 Z= 0.244 Chirality : 0.037 0.149 1836 Planarity : 0.003 0.040 2168 Dihedral : 8.332 84.593 1884 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.24 % Allowed : 14.65 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.21), residues: 1564 helix: 2.86 (0.18), residues: 848 sheet: -0.03 (0.39), residues: 140 loop : 0.37 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 198 HIS 0.002 0.001 HIS B 304 PHE 0.004 0.001 PHE A 258 TYR 0.009 0.001 TYR C 277 ARG 0.001 0.000 ARG D 223 Details of bonding type rmsd hydrogen bonds : bond 0.04430 ( 740) hydrogen bonds : angle 3.68314 ( 2112) covalent geometry : bond 0.00315 (12488) covalent geometry : angle 0.46690 (16872) *********************** 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 83 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 80 time to evaluate : 1.275 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 83 average time/residue: 1.3355 time to fit residues: 121.0237 Evaluate side-chains 80 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 12 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 113 optimal weight: 0.0770 chunk 58 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 147 optimal weight: 1.9990 chunk 63 optimal weight: 0.3980 chunk 122 optimal weight: 2.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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** ** 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 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 = 0.3205 r_free = 0.3205 target = 0.092034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.076450 restraints weight = 21182.357| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 2.50 r_work: 0.2766 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2020 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 : 0.438 4.763 16872 Z= 0.230 Chirality : 0.036 0.144 1836 Planarity : 0.003 0.040 2168 Dihedral : 8.245 80.025 1884 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.00 % Allowed : 14.89 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.59 (0.21), residues: 1564 helix: 2.89 (0.18), residues: 848 sheet: 0.07 (0.40), residues: 140 loop : 0.41 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 198 HIS 0.003 0.001 HIS D 189 PHE 0.004 0.001 PHE C 382 TYR 0.008 0.001 TYR D 277 ARG 0.001 0.000 ARG A 223 Details of bonding type rmsd hydrogen bonds : bond 0.03967 ( 740) hydrogen bonds : angle 3.55300 ( 2112) covalent geometry : bond 0.00228 (12488) covalent geometry : angle 0.43831 (16872) *********************** 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 81 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 1.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 1.3685 time to fit residues: 121.1646 Evaluate side-chains 80 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 89 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 150 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 overall best weight: 1.2982 ------------------------------------------------------------------------------- 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 = 0.3139 r_free = 0.3139 target = 0.087646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.071836 restraints weight = 21348.377| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 2.47 r_work: 0.2709 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2570 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12488 Z= 0.154 Angle : 0.479 5.052 16872 Z= 0.251 Chirality : 0.038 0.149 1836 Planarity : 0.003 0.040 2168 Dihedral : 8.308 81.160 1884 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.00 % Allowed : 14.81 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.21), residues: 1564 helix: 2.84 (0.18), residues: 848 sheet: 0.07 (0.39), residues: 140 loop : 0.29 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 198 HIS 0.004 0.001 HIS A 304 PHE 0.005 0.001 PHE A 258 TYR 0.010 0.001 TYR A 277 ARG 0.001 0.000 ARG D 223 Details of bonding type rmsd hydrogen bonds : bond 0.04661 ( 740) hydrogen bonds : angle 3.61361 ( 2112) covalent geometry : bond 0.00368 (12488) covalent geometry : angle 0.47934 (16872) ********************** 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 80 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 1.3530 time to fit residues: 118.0721 Evaluate side-chains 80 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 118 optimal weight: 6.9990 chunk 139 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 150 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 overall best weight: 1.3388 ------------------------------------------------------------------------------- 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 = 0.3133 r_free = 0.3133 target = 0.087336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.071497 restraints weight = 21464.948| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 2.49 r_work: 0.2700 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2561 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1896 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= 0.155 Angle : 0.479 5.017 16872 Z= 0.251 Chirality : 0.038 0.150 1836 Planarity : 0.003 0.040 2168 Dihedral : 8.315 80.988 1884 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.00 % Allowed : 14.97 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.21), residues: 1564 helix: 2.78 (0.18), residues: 848 sheet: 0.08 (0.39), residues: 140 loop : 0.24 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 198 HIS 0.003 0.001 HIS A 304 PHE 0.005 0.001 PHE D 258 TYR 0.012 0.001 TYR D 277 ARG 0.001 0.000 ARG B 223 Details of bonding type rmsd hydrogen bonds : bond 0.04714 ( 740) hydrogen bonds : angle 3.64283 ( 2112) covalent geometry : bond 0.00369 (12488) covalent geometry : angle 0.47873 (16872) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6357.35 seconds wall clock time: 111 minutes 12.84 seconds (6672.84 seconds total)