Starting phenix.real_space_refine on Sat Nov 16 21:51:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgr_40465/11_2024/8sgr_40465.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgr_40465/11_2024/8sgr_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgr_40465/11_2024/8sgr_40465.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgr_40465/11_2024/8sgr_40465.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgr_40465/11_2024/8sgr_40465.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgr_40465/11_2024/8sgr_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-5513/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: 6.49, per 1000 atoms: 0.53 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: 2.86 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: 1.52 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: 3.94 Time building geometry restraints manager: 3.33 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.850 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: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 28.190 Find NCS groups from input model: 0.450 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:12.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.100 ------------------------------------------------------------------------------- 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= 0.362 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 *********************** 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 : 1.312 Fit side-chains outliers start: 8 outliers final: 0 residues processed: 148 average time/residue: 1.4856 time to fit residues: 236.8698 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 : 1.420 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 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= 0.148 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 *********************** 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 : 1.396 Fit side-chains outliers start: 12 outliers final: 4 residues processed: 105 average time/residue: 1.1992 time to fit residues: 138.8077 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 : 1.404 ------------------------------------------------------------------------------- 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 78 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 117 optimal weight: 7.9990 chunk 96 optimal weight: 0.0030 chunk 39 optimal weight: 6.9990 chunk 141 optimal weight: 1.9990 chunk 153 optimal weight: 0.8980 chunk 126 optimal weight: 0.9980 chunk 140 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 overall best weight: 0.9794 ------------------------------------------------------------------------------- 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** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12488 Z= 0.202 Angle : 0.468 4.847 16872 Z= 0.248 Chirality : 0.037 0.168 1836 Planarity : 0.003 0.040 2168 Dihedral : 9.311 103.769 1884 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.08 % Allowed : 10.03 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.81 (0.18), residues: 848 sheet: -0.61 (0.35), residues: 140 loop : 0.38 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 198 HIS 0.003 0.001 HIS C 304 PHE 0.004 0.001 PHE C 228 TYR 0.004 0.001 TYR A 403 ARG 0.001 0.000 ARG B 249 *********************** 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 88 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 87 time to evaluate : 1.518 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 88 average time/residue: 1.3898 time to fit residues: 133.3908 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 : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 15 optimal weight: 0.4980 chunk 67 optimal weight: 2.9990 chunk 95 optimal weight: 0.5980 chunk 142 optimal weight: 0.6980 chunk 150 optimal weight: 0.7980 chunk 74 optimal weight: 0.0070 chunk 134 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.1832 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= 0.137 Angle : 0.426 4.816 16872 Z= 0.223 Chirality : 0.036 0.152 1836 Planarity : 0.003 0.041 2168 Dihedral : 8.709 94.502 1884 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.72 % Allowed : 10.59 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.56 (0.21), residues: 1564 helix: 2.89 (0.18), residues: 848 sheet: -0.19 (0.36), residues: 140 loop : 0.42 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 198 HIS 0.002 0.000 HIS C 304 PHE 0.005 0.001 PHE C 382 TYR 0.009 0.001 TYR B 277 ARG 0.001 0.000 ARG A 223 *********************** 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 105 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 1.452 Fit side-chains outliers start: 9 outliers final: 1 residues processed: 100 average time/residue: 1.2349 time to fit residues: 135.7410 Evaluate side-chains 93 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 92 time to evaluate : 1.570 ------------------------------------------------------------------------------- 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 125 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 128 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 76 optimal weight: 0.0870 chunk 135 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.1362 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.1735 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= 0.218 Angle : 0.464 5.064 16872 Z= 0.241 Chirality : 0.037 0.151 1836 Planarity : 0.003 0.040 2168 Dihedral : 8.657 92.894 1884 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.40 % Allowed : 12.18 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.56 (0.21), residues: 1564 helix: 2.91 (0.18), residues: 848 sheet: -0.12 (0.36), residues: 140 loop : 0.36 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 198 HIS 0.003 0.001 HIS A 304 PHE 0.004 0.001 PHE C 258 TYR 0.005 0.001 TYR A 403 ARG 0.002 0.000 ARG B 223 *********************** 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 90 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 85 time to evaluate : 1.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 90 average time/residue: 1.4310 time to fit residues: 140.9108 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 : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 0.5980 chunk 135 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 88 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 150 optimal weight: 0.6980 chunk 125 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 79 optimal weight: 5.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12488 Z= 0.193 Angle : 0.451 5.053 16872 Z= 0.234 Chirality : 0.037 0.149 1836 Planarity : 0.003 0.040 2168 Dihedral : 8.464 88.278 1884 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.96 % Allowed : 12.98 % Favored : 86.07 % 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: 2.90 (0.18), residues: 848 sheet: 0.02 (0.37), residues: 140 loop : 0.37 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 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 A 277 ARG 0.001 0.000 ARG B 223 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 1.334 Fit side-chains outliers start: 12 outliers final: 0 residues processed: 100 average time/residue: 1.1528 time to fit residues: 127.4977 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 : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 127 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 150 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 69 optimal weight: 0.5980 chunk 93 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12488 Z= 0.180 Angle : 0.456 4.935 16872 Z= 0.238 Chirality : 0.037 0.148 1836 Planarity : 0.003 0.040 2168 Dihedral : 8.393 86.098 1884 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.32 % Allowed : 13.85 % Favored : 85.83 % 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: 2.62 (0.21), residues: 1564 helix: 2.93 (0.18), residues: 848 sheet: 0.06 (0.38), residues: 140 loop : 0.40 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 198 HIS 0.002 0.001 HIS A 304 PHE 0.004 0.001 PHE C 382 TYR 0.007 0.001 TYR B 108 ARG 0.001 0.000 ARG D 223 *********************** 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 92 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 88 time to evaluate : 1.284 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 92 average time/residue: 1.2830 time to fit residues: 129.4828 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 : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 0.9980 chunk 89 optimal weight: 0.0670 chunk 45 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 74 optimal weight: 0.2980 chunk 14 optimal weight: 0.0270 chunk 118 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12488 Z= 0.157 Angle : 0.448 4.910 16872 Z= 0.236 Chirality : 0.037 0.146 1836 Planarity : 0.003 0.040 2168 Dihedral : 8.286 82.378 1884 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.24 % Allowed : 14.81 % 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: 2.63 (0.21), residues: 1564 helix: 2.90 (0.18), residues: 848 sheet: 0.18 (0.39), residues: 140 loop : 0.43 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 198 HIS 0.002 0.000 HIS C 304 PHE 0.004 0.001 PHE B 382 TYR 0.009 0.001 TYR A 277 ARG 0.001 0.000 ARG A 223 *********************** 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 91 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 88 time to evaluate : 1.329 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 91 average time/residue: 1.3692 time to fit residues: 136.0200 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 : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 6.9990 chunk 140 optimal weight: 5.9990 chunk 144 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 110 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 126 optimal weight: 0.5980 chunk 132 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 92 optimal weight: 0.0370 overall best weight: 1.0660 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.1917 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= 0.209 Angle : 0.481 6.120 16872 Z= 0.250 Chirality : 0.037 0.148 1836 Planarity : 0.003 0.040 2168 Dihedral : 8.305 81.664 1884 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.00 % Allowed : 15.05 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.87 (0.18), residues: 848 sheet: 0.23 (0.39), residues: 140 loop : 0.37 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 198 HIS 0.003 0.001 HIS A 189 PHE 0.004 0.001 PHE A 258 TYR 0.005 0.001 TYR B 108 ARG 0.002 0.000 ARG B 223 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 1.388 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 1.4466 time to fit residues: 138.4796 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 : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 143 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 95 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.2004 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= 0.175 Angle : 0.463 4.944 16872 Z= 0.242 Chirality : 0.037 0.146 1836 Planarity : 0.003 0.040 2168 Dihedral : 8.271 78.940 1884 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.00 % Allowed : 15.05 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.87 (0.18), residues: 848 sheet: 0.27 (0.39), residues: 140 loop : 0.36 (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 C 304 PHE 0.005 0.001 PHE B 382 TYR 0.010 0.001 TYR A 277 ARG 0.001 0.000 ARG A 223 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 1.401 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 1.3596 time to fit residues: 124.9262 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 : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 114 optimal weight: 0.2980 chunk 18 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 127 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3140 r_free = 0.3140 target = 0.087752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.071945 restraints weight = 21334.211| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 2.48 r_work: 0.2713 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2572 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12488 Z= 0.232 Angle : 0.487 5.050 16872 Z= 0.254 Chirality : 0.038 0.149 1836 Planarity : 0.003 0.040 2168 Dihedral : 8.313 79.488 1884 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.24 % Allowed : 14.81 % 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: 2.52 (0.21), residues: 1564 helix: 2.84 (0.18), residues: 848 sheet: 0.24 (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 0.003 0.001 HIS A 304 PHE 0.005 0.001 PHE C 258 TYR 0.005 0.001 TYR D 403 ARG 0.001 0.000 ARG D 223 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3442.16 seconds wall clock time: 63 minutes 23.27 seconds (3803.27 seconds total)