Starting phenix.real_space_refine on Wed Jul 30 07:07:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sgr_40465/07_2025/8sgr_40465.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sgr_40465/07_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_40465/07_2025/8sgr_40465.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sgr_40465/07_2025/8sgr_40465.map" model { file = "/net/cci-nas-00/data/ceres_data/8sgr_40465/07_2025/8sgr_40465.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sgr_40465/07_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 7.23, per 1000 atoms: 0.59 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: 3.17 Conformation dependent library (CDL) restraints added in 1.8 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: 1.12 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: 5.14 Time building geometry restraints manager: 3.83 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: 0.15 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: 2.650 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: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 34.130 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.090 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: 0.020 Load rotamer database and sin/cos tables:17.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.170 ------------------------------------------------------------------------------- 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 : 1.672 Fit side-chains outliers start: 8 outliers final: 0 residues processed: 148 average time/residue: 1.4055 time to fit residues: 225.0987 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 : 1.306 ------------------------------------------------------------------------------- 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: 0.6980 chunk 74 optimal weight: 0.0270 chunk 91 optimal weight: 4.9990 chunk 141 optimal weight: 0.0070 overall best weight: 0.4056 ------------------------------------------------------------------------------- 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 = 0.3183 r_free = 0.3183 target = 0.090434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.074352 restraints weight = 20859.424| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 2.47 r_work: 0.2757 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1410 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= 0.108 Angle : 0.473 4.669 16872 Z= 0.250 Chirality : 0.037 0.171 1836 Planarity : 0.004 0.039 2168 Dihedral : 9.838 108.956 1884 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.72 % Allowed : 7.56 % Favored : 91.72 % 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: 2.39 (0.21), residues: 1564 helix: 2.81 (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 A 382 TYR 0.011 0.001 TYR A 277 ARG 0.002 0.000 ARG D 249 Details of bonding type rmsd hydrogen bonds : bond 0.04706 ( 740) hydrogen bonds : angle 3.86620 ( 2112) covalent geometry : bond 0.00223 (12488) covalent geometry : angle 0.47324 (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 107 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 1.476 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 106 average time/residue: 1.2374 time to fit residues: 144.2427 Evaluate side-chains 81 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 78 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A 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: 5.9990 chunk 84 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 149 optimal weight: 7.9990 chunk 88 optimal weight: 0.0870 overall best weight: 1.5162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 HIS A 134 ASN ** A 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 HIS B 134 ASN ** B 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 HIS C 134 ASN ** C 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 HIS D 134 ASN ** D 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.088698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.072100 restraints weight = 21931.222| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 2.52 r_work: 0.2700 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12488 Z= 0.178 Angle : 0.505 5.005 16872 Z= 0.266 Chirality : 0.039 0.176 1836 Planarity : 0.004 0.040 2168 Dihedral : 9.385 104.006 1884 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.08 % Allowed : 10.35 % Favored : 89.57 % 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: 2.32 (0.21), residues: 1564 helix: 2.76 (0.18), residues: 848 sheet: -0.70 (0.35), residues: 140 loop : 0.33 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 198 HIS 0.003 0.001 HIS B 304 PHE 0.005 0.001 PHE C 228 TYR 0.005 0.001 TYR A 403 ARG 0.001 0.000 ARG B 50 Details of bonding type rmsd hydrogen bonds : bond 0.05201 ( 740) hydrogen bonds : angle 3.83569 ( 2112) covalent geometry : bond 0.00424 (12488) covalent geometry : angle 0.50520 (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 85 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 84 time to evaluate : 1.348 Fit side-chains REVERT: B 262 LYS cc_start: 0.8464 (ptmm) cc_final: 0.8218 (tttp) REVERT: C 262 LYS cc_start: 0.8471 (ptmm) cc_final: 0.8225 (tttp) REVERT: D 262 LYS cc_start: 0.8468 (ptmm) cc_final: 0.8224 (tttp) outliers start: 1 outliers final: 0 residues processed: 85 average time/residue: 1.4530 time to fit residues: 134.3230 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 : 1.486 ------------------------------------------------------------------------------- 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: 5.9990 chunk 54 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 67 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 49 optimal weight: 0.3980 chunk 149 optimal weight: 5.9990 chunk 86 optimal weight: 0.5980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3164 r_free = 0.3164 target = 0.089110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.072448 restraints weight = 21390.716| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 2.51 r_work: 0.2709 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2567 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1599 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 : 0.476 5.093 16872 Z= 0.250 Chirality : 0.038 0.163 1836 Planarity : 0.003 0.039 2168 Dihedral : 8.955 97.105 1884 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.32 % Allowed : 11.15 % Favored : 88.54 % 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: 2.32 (0.21), residues: 1564 helix: 2.75 (0.18), residues: 848 sheet: -0.44 (0.36), residues: 140 loop : 0.25 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 198 HIS 0.003 0.001 HIS A 304 PHE 0.004 0.001 PHE A 258 TYR 0.007 0.001 TYR A 277 ARG 0.002 0.000 ARG B 223 Details of bonding type rmsd hydrogen bonds : bond 0.04876 ( 740) hydrogen bonds : angle 3.75070 ( 2112) covalent geometry : bond 0.00368 (12488) covalent geometry : angle 0.47571 (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 93 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 89 time to evaluate : 1.387 Fit side-chains REVERT: B 262 LYS cc_start: 0.8411 (ptmm) cc_final: 0.8197 (tttp) REVERT: C 262 LYS cc_start: 0.8423 (ptmm) cc_final: 0.8213 (tttp) REVERT: D 262 LYS cc_start: 0.8422 (ptmm) cc_final: 0.8209 (tttp) outliers start: 4 outliers final: 1 residues processed: 90 average time/residue: 1.7872 time to fit residues: 174.8976 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 : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 225 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 33 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 78 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 123 optimal weight: 0.6980 chunk 137 optimal weight: 0.5980 chunk 141 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3192 r_free = 0.3192 target = 0.090764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.074216 restraints weight = 21417.803| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 2.52 r_work: 0.2746 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1771 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= 0.109 Angle : 0.448 4.873 16872 Z= 0.233 Chirality : 0.037 0.155 1836 Planarity : 0.003 0.040 2168 Dihedral : 8.615 91.923 1884 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.32 % Allowed : 12.74 % Favored : 86.94 % 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: 2.47 (0.21), residues: 1564 helix: 2.87 (0.18), residues: 848 sheet: -0.26 (0.36), residues: 140 loop : 0.29 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 198 HIS 0.002 0.000 HIS C 304 PHE 0.004 0.001 PHE A 228 TYR 0.009 0.001 TYR D 277 ARG 0.002 0.000 ARG C 223 Details of bonding type rmsd hydrogen bonds : bond 0.04295 ( 740) hydrogen bonds : angle 3.64425 ( 2112) covalent geometry : bond 0.00248 (12488) covalent geometry : angle 0.44819 (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 97 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 93 time to evaluate : 1.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 97 average time/residue: 1.6014 time to fit residues: 169.1538 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 : 2.293 ------------------------------------------------------------------------------- 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: 1.9990 chunk 88 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 127 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 149 optimal weight: 6.9990 chunk 140 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.086764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.071182 restraints weight = 21518.301| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 2.48 r_work: 0.2691 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2551 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12488 Z= 0.160 Angle : 0.484 5.145 16872 Z= 0.250 Chirality : 0.038 0.151 1836 Planarity : 0.003 0.040 2168 Dihedral : 8.564 90.461 1884 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.19 % Allowed : 13.22 % Favored : 85.59 % 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: 2.45 (0.21), residues: 1564 helix: 2.84 (0.18), residues: 848 sheet: -0.13 (0.37), residues: 140 loop : 0.25 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 198 HIS 0.003 0.001 HIS A 189 PHE 0.005 0.001 PHE A 258 TYR 0.005 0.001 TYR A 403 ARG 0.002 0.000 ARG A 223 Details of bonding type rmsd hydrogen bonds : bond 0.04865 ( 740) hydrogen bonds : angle 3.73211 ( 2112) covalent geometry : bond 0.00380 (12488) covalent geometry : angle 0.48419 (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 96 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 1.628 Fit side-chains outliers start: 15 outliers final: 0 residues processed: 96 average time/residue: 1.3434 time to fit residues: 141.8519 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 : 1.307 ------------------------------------------------------------------------------- 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: 4.9990 chunk 112 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 120 optimal weight: 0.0010 chunk 96 optimal weight: 0.0970 chunk 145 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 154 optimal weight: 0.7980 overall best weight: 0.4984 ------------------------------------------------------------------------------- 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 = 0.3192 r_free = 0.3192 target = 0.091056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.075248 restraints weight = 21054.180| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 2.52 r_work: 0.2754 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1955 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= 0.096 Angle : 0.438 4.832 16872 Z= 0.227 Chirality : 0.036 0.147 1836 Planarity : 0.003 0.040 2168 Dihedral : 8.327 85.051 1884 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.64 % Allowed : 13.85 % 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: 2.57 (0.21), residues: 1564 helix: 2.90 (0.18), residues: 848 sheet: 0.10 (0.38), residues: 140 loop : 0.32 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 198 HIS 0.004 0.001 HIS D 189 PHE 0.004 0.001 PHE B 382 TYR 0.008 0.001 TYR A 277 ARG 0.002 0.000 ARG A 53 Details of bonding type rmsd hydrogen bonds : bond 0.04001 ( 740) hydrogen bonds : angle 3.52051 ( 2112) covalent geometry : bond 0.00212 (12488) covalent geometry : angle 0.43845 (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 97 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 1.381 Fit side-chains outliers start: 8 outliers final: 0 residues processed: 97 average time/residue: 1.4435 time to fit residues: 153.7421 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 : 2.448 ------------------------------------------------------------------------------- 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: 0.4980 chunk 83 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 117 optimal weight: 6.9990 chunk 85 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- 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** ** D 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.086051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.070384 restraints weight = 22019.692| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 2.49 r_work: 0.2662 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2521 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 12488 Z= 0.228 Angle : 0.536 5.262 16872 Z= 0.278 Chirality : 0.040 0.153 1836 Planarity : 0.004 0.041 2168 Dihedral : 8.506 88.097 1884 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % 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: 2.39 (0.21), residues: 1564 helix: 2.81 (0.18), residues: 848 sheet: -0.08 (0.38), residues: 140 loop : 0.19 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 198 HIS 0.004 0.001 HIS A 304 PHE 0.006 0.001 PHE A 258 TYR 0.007 0.001 TYR C 403 ARG 0.004 0.000 ARG B 223 Details of bonding type rmsd hydrogen bonds : bond 0.05330 ( 740) hydrogen bonds : angle 3.75827 ( 2112) covalent geometry : bond 0.00550 (12488) covalent geometry : angle 0.53582 (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 89 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 1.402 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 1.3770 time to fit residues: 133.7234 Evaluate side-chains 82 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 1.458 ------------------------------------------------------------------------------- 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: 0.7980 chunk 2 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 117 optimal weight: 0.9990 chunk 103 optimal weight: 0.4980 chunk 147 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.3160 r_free = 0.3160 target = 0.088922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.073239 restraints weight = 21450.042| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 2.51 r_work: 0.2714 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2573 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1943 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= 0.122 Angle : 0.468 5.009 16872 Z= 0.246 Chirality : 0.037 0.150 1836 Planarity : 0.003 0.040 2168 Dihedral : 8.330 84.197 1884 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.08 % Allowed : 14.97 % 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 (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: 2.43 (0.21), residues: 1564 helix: 2.79 (0.18), residues: 848 sheet: 0.04 (0.38), residues: 140 loop : 0.26 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 198 HIS 0.003 0.001 HIS A 189 PHE 0.004 0.001 PHE B 382 TYR 0.009 0.001 TYR A 277 ARG 0.003 0.000 ARG B 223 Details of bonding type rmsd hydrogen bonds : bond 0.04458 ( 740) hydrogen bonds : angle 3.62422 ( 2112) covalent geometry : bond 0.00281 (12488) covalent geometry : angle 0.46795 (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 87 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 86 time to evaluate : 1.576 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 87 average time/residue: 1.7283 time to fit residues: 163.6998 Evaluate side-chains 86 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 1.610 ------------------------------------------------------------------------------- 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: 0.6980 chunk 18 optimal weight: 0.0470 chunk 58 optimal weight: 0.7980 chunk 146 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 150 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 141 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- 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 = 0.3192 r_free = 0.3192 target = 0.091038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.075662 restraints weight = 21234.569| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 2.49 r_work: 0.2753 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2614 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2054 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 : 0.451 4.849 16872 Z= 0.238 Chirality : 0.036 0.143 1836 Planarity : 0.003 0.040 2168 Dihedral : 8.229 79.760 1884 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.00 % Allowed : 15.21 % 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 (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: 2.84 (0.18), residues: 848 sheet: 0.17 (0.38), residues: 140 loop : 0.33 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 198 HIS 0.003 0.001 HIS C 304 PHE 0.005 0.001 PHE B 382 TYR 0.004 0.001 TYR A 366 ARG 0.003 0.000 ARG B 223 Details of bonding type rmsd hydrogen bonds : bond 0.04030 ( 740) hydrogen bonds : angle 3.50537 ( 2112) covalent geometry : bond 0.00239 (12488) covalent geometry : angle 0.45067 (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 88 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 1.337 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 1.3898 time to fit residues: 133.0788 Evaluate side-chains 86 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 1.334 ------------------------------------------------------------------------------- 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: 0.9980 chunk 119 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 150 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 142 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 59 optimal weight: 0.0870 overall best weight: 0.7558 ------------------------------------------------------------------------------- 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 = 0.3177 r_free = 0.3177 target = 0.089394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.074057 restraints weight = 21169.650| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 2.51 r_work: 0.2748 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2611 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12488 Z= 0.112 Angle : 0.453 4.912 16872 Z= 0.238 Chirality : 0.037 0.136 1836 Planarity : 0.003 0.040 2168 Dihedral : 8.247 77.615 1884 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.00 % Allowed : 15.45 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.58 (0.21), residues: 1564 helix: 2.84 (0.18), residues: 848 sheet: 0.25 (0.39), residues: 148 loop : 0.43 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 198 HIS 0.004 0.001 HIS A 189 PHE 0.005 0.001 PHE B 382 TYR 0.010 0.001 TYR C 277 ARG 0.001 0.000 ARG B 223 Details of bonding type rmsd hydrogen bonds : bond 0.04110 ( 740) hydrogen bonds : angle 3.51431 ( 2112) covalent geometry : bond 0.00256 (12488) covalent geometry : angle 0.45269 (16872) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6684.97 seconds wall clock time: 119 minutes 56.91 seconds (7196.91 seconds total)