Starting phenix.real_space_refine on Sat Sep 12 07:13:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5ooe_3838/09_2026/5ooe_3838.cif Found real_map, /net/cci-nas-00/data/ceres_data/5ooe_3838/09_2026/5ooe_3838.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/5ooe_3838/09_2026/5ooe_3838.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5ooe_3838/09_2026/5ooe_3838.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5ooe_3838/09_2026/5ooe_3838.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5ooe_3838/09_2026/5ooe_3838.map" model { file = "/net/cci-nas-00/data/ceres_data/5ooe_3838/09_2026/5ooe_3838.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5ooe_3838/09_2026/5ooe_3838.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 15 5.49 5 Mg 5 5.21 5 S 95 5.16 5 C 9020 2.51 5 N 2405 2.21 5 O 2770 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 76 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14310 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2830 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 19, 'TRANS': 342} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B, C, D, E Time building chain proxies: 2.77, per 1000 atoms: 0.19 Number of scatterers: 14310 At special positions: 0 Unit cell: (99.18, 91.2, 193.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 95 16.00 P 15 15.00 Mg 5 11.99 O 2770 8.00 N 2405 7.00 C 9020 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.12 Conformation dependent library (CDL) restraints added in 606.4 milliseconds 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3360 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 30 sheets defined 50.3% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 97 through 101 Processing helix chain 'A' and resid 112 through 126 removed outlier: 4.002A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 181 through 193 Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 222 through 231 Processing helix chain 'A' and resid 252 through 260 Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 286 through 295 removed outlier: 4.272A pdb=" N LYS A 291 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ASP A 292 " --> pdb=" O ASP A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 306 Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 349 Processing helix chain 'A' and resid 350 through 356 removed outlier: 4.963A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 367 through 371 Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 112 through 126 removed outlier: 4.002A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 181 through 193 Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 222 through 231 Processing helix chain 'B' and resid 252 through 260 Proline residue: B 258 - end of helix Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 286 through 295 removed outlier: 4.272A pdb=" N LYS B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ASP B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 306 Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 349 Processing helix chain 'B' and resid 350 through 356 removed outlier: 4.963A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 112 through 126 removed outlier: 4.002A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 193 Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 222 through 231 Processing helix chain 'C' and resid 252 through 260 Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 286 through 295 removed outlier: 4.272A pdb=" N LYS C 291 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 306 Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 349 Processing helix chain 'C' and resid 350 through 356 removed outlier: 4.963A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 367 through 371 Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 97 through 101 Processing helix chain 'D' and resid 112 through 126 removed outlier: 4.003A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 Processing helix chain 'D' and resid 172 through 175 Processing helix chain 'D' and resid 181 through 193 Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 222 through 231 Processing helix chain 'D' and resid 252 through 260 Proline residue: D 258 - end of helix Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 286 through 295 removed outlier: 4.272A pdb=" N LYS D 291 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ASP D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 306 Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 349 Processing helix chain 'D' and resid 350 through 356 removed outlier: 4.963A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 367 through 371 Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 92 Processing helix chain 'E' and resid 97 through 101 Processing helix chain 'E' and resid 112 through 126 removed outlier: 4.003A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 146 Processing helix chain 'E' and resid 172 through 175 Processing helix chain 'E' and resid 181 through 193 Processing helix chain 'E' and resid 202 through 217 Processing helix chain 'E' and resid 222 through 231 Processing helix chain 'E' and resid 252 through 260 Proline residue: E 258 - end of helix Processing helix chain 'E' and resid 273 through 284 Processing helix chain 'E' and resid 286 through 295 removed outlier: 4.271A pdb=" N LYS E 291 " --> pdb=" O ILE E 287 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N ASP E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 306 Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 334 through 336 No H-bonds generated for 'chain 'E' and resid 334 through 336' Processing helix chain 'E' and resid 337 through 349 Processing helix chain 'E' and resid 350 through 356 removed outlier: 4.964A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 367 through 371 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.939A pdb=" N THR A 106 " --> pdb=" O CYS A 10 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N ASN A 12 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 170 removed outlier: 6.426A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 32 removed outlier: 3.940A pdb=" N THR B 106 " --> pdb=" O CYS B 10 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N ASN B 12 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AB2, first strand: chain 'B' and resid 169 through 170 removed outlier: 6.427A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 32 removed outlier: 3.939A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N ASN C 12 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB8, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.426A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 32 removed outlier: 3.940A pdb=" N THR D 106 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N ASN D 12 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AC5, first strand: chain 'D' and resid 169 through 170 removed outlier: 6.427A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC7, first strand: chain 'E' and resid 29 through 32 removed outlier: 3.939A pdb=" N THR E 106 " --> pdb=" O CYS E 10 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N ASN E 12 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC9, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AD1, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AD2, first strand: chain 'E' and resid 169 through 170 removed outlier: 6.426A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 238 through 241 760 hydrogen bonds defined for protein. 1935 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.76 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3628 1.32 - 1.44: 3102 1.44 - 1.56: 7690 1.56 - 1.68: 30 1.68 - 1.81: 170 Bond restraints: 14620 Sorted by residual: bond pdb=" N3B ANP E 401 " pdb=" PG ANP E 401 " ideal model delta sigma weight residual 1.795 1.618 0.177 2.00e-02 2.50e+03 7.87e+01 bond pdb=" N3B ANP C 401 " pdb=" PG ANP C 401 " ideal model delta sigma weight residual 1.795 1.618 0.177 2.00e-02 2.50e+03 7.87e+01 bond pdb=" N3B ANP D 401 " pdb=" PG ANP D 401 " ideal model delta sigma weight residual 1.795 1.618 0.177 2.00e-02 2.50e+03 7.84e+01 bond pdb=" N3B ANP B 401 " pdb=" PG ANP B 401 " ideal model delta sigma weight residual 1.795 1.618 0.177 2.00e-02 2.50e+03 7.82e+01 bond pdb=" N3B ANP A 401 " pdb=" PG ANP A 401 " ideal model delta sigma weight residual 1.795 1.618 0.177 2.00e-02 2.50e+03 7.80e+01 ... (remaining 14615 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.39: 19055 3.39 - 6.79: 660 6.79 - 10.18: 105 10.18 - 13.57: 30 13.57 - 16.96: 10 Bond angle restraints: 19860 Sorted by residual: angle pdb=" C GLN E 263 " pdb=" N PRO E 264 " pdb=" CA PRO E 264 " ideal model delta sigma weight residual 119.84 128.62 -8.78 1.25e+00 6.40e-01 4.93e+01 angle pdb=" C GLN A 263 " pdb=" N PRO A 264 " pdb=" CA PRO A 264 " ideal model delta sigma weight residual 119.84 128.61 -8.77 1.25e+00 6.40e-01 4.92e+01 angle pdb=" C GLN B 263 " pdb=" N PRO B 264 " pdb=" CA PRO B 264 " ideal model delta sigma weight residual 119.84 128.59 -8.75 1.25e+00 6.40e-01 4.90e+01 angle pdb=" C GLN C 263 " pdb=" N PRO C 264 " pdb=" CA PRO C 264 " ideal model delta sigma weight residual 119.84 128.56 -8.72 1.25e+00 6.40e-01 4.87e+01 angle pdb=" C GLN D 263 " pdb=" N PRO D 264 " pdb=" CA PRO D 264 " ideal model delta sigma weight residual 119.84 128.55 -8.71 1.25e+00 6.40e-01 4.85e+01 ... (remaining 19855 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.67: 8375 16.67 - 33.33: 251 33.33 - 50.00: 79 50.00 - 66.67: 25 66.67 - 83.33: 10 Dihedral angle restraints: 8740 sinusoidal: 3500 harmonic: 5240 Sorted by residual: dihedral pdb=" CB MET C 123 " pdb=" CG MET C 123 " pdb=" SD MET C 123 " pdb=" CE MET C 123 " ideal model delta sinusoidal sigma weight residual 60.00 100.38 -40.38 3 1.50e+01 4.44e-03 7.19e+00 dihedral pdb=" CB MET B 123 " pdb=" CG MET B 123 " pdb=" SD MET B 123 " pdb=" CE MET B 123 " ideal model delta sinusoidal sigma weight residual 60.00 100.37 -40.37 3 1.50e+01 4.44e-03 7.19e+00 dihedral pdb=" CB MET E 123 " pdb=" CG MET E 123 " pdb=" SD MET E 123 " pdb=" CE MET E 123 " ideal model delta sinusoidal sigma weight residual 60.00 100.36 -40.36 3 1.50e+01 4.44e-03 7.19e+00 ... (remaining 8737 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 1712 0.085 - 0.169: 468 0.169 - 0.254: 30 0.254 - 0.339: 0 0.339 - 0.423: 5 Chirality restraints: 2215 Sorted by residual: chirality pdb=" C3' ANP C 401 " pdb=" C2' ANP C 401 " pdb=" C4' ANP C 401 " pdb=" O3' ANP C 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.78 0.42 2.00e-01 2.50e+01 4.48e+00 chirality pdb=" C3' ANP E 401 " pdb=" C2' ANP E 401 " pdb=" C4' ANP E 401 " pdb=" O3' ANP E 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.78 0.42 2.00e-01 2.50e+01 4.43e+00 chirality pdb=" C3' ANP A 401 " pdb=" C2' ANP A 401 " pdb=" C4' ANP A 401 " pdb=" O3' ANP A 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.78 0.42 2.00e-01 2.50e+01 4.41e+00 ... (remaining 2212 not shown) Planarity restraints: 2525 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ANP D 401 " 0.404 2.00e-02 2.50e+03 1.59e-01 6.95e+02 pdb=" C2 ANP D 401 " -0.042 2.00e-02 2.50e+03 pdb=" C4 ANP D 401 " -0.118 2.00e-02 2.50e+03 pdb=" C5 ANP D 401 " -0.030 2.00e-02 2.50e+03 pdb=" C6 ANP D 401 " 0.059 2.00e-02 2.50e+03 pdb=" C8 ANP D 401 " -0.132 2.00e-02 2.50e+03 pdb=" N1 ANP D 401 " 0.047 2.00e-02 2.50e+03 pdb=" N3 ANP D 401 " -0.120 2.00e-02 2.50e+03 pdb=" N6 ANP D 401 " 0.160 2.00e-02 2.50e+03 pdb=" N7 ANP D 401 " -0.047 2.00e-02 2.50e+03 pdb=" N9 ANP D 401 " -0.181 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ANP E 401 " 0.404 2.00e-02 2.50e+03 1.59e-01 6.95e+02 pdb=" C2 ANP E 401 " -0.042 2.00e-02 2.50e+03 pdb=" C4 ANP E 401 " -0.118 2.00e-02 2.50e+03 pdb=" C5 ANP E 401 " -0.030 2.00e-02 2.50e+03 pdb=" C6 ANP E 401 " 0.059 2.00e-02 2.50e+03 pdb=" C8 ANP E 401 " -0.132 2.00e-02 2.50e+03 pdb=" N1 ANP E 401 " 0.048 2.00e-02 2.50e+03 pdb=" N3 ANP E 401 " -0.120 2.00e-02 2.50e+03 pdb=" N6 ANP E 401 " 0.160 2.00e-02 2.50e+03 pdb=" N7 ANP E 401 " -0.047 2.00e-02 2.50e+03 pdb=" N9 ANP E 401 " -0.181 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ANP A 401 " 0.404 2.00e-02 2.50e+03 1.59e-01 6.95e+02 pdb=" C2 ANP A 401 " -0.042 2.00e-02 2.50e+03 pdb=" C4 ANP A 401 " -0.118 2.00e-02 2.50e+03 pdb=" C5 ANP A 401 " -0.030 2.00e-02 2.50e+03 pdb=" C6 ANP A 401 " 0.059 2.00e-02 2.50e+03 pdb=" C8 ANP A 401 " -0.132 2.00e-02 2.50e+03 pdb=" N1 ANP A 401 " 0.047 2.00e-02 2.50e+03 pdb=" N3 ANP A 401 " -0.120 2.00e-02 2.50e+03 pdb=" N6 ANP A 401 " 0.160 2.00e-02 2.50e+03 pdb=" N7 ANP A 401 " -0.048 2.00e-02 2.50e+03 pdb=" N9 ANP A 401 " -0.181 2.00e-02 2.50e+03 ... (remaining 2522 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 62 2.53 - 3.12: 12458 3.12 - 3.72: 21765 3.72 - 4.31: 34713 4.31 - 4.90: 53192 Nonbonded interactions: 122190 Sorted by model distance: nonbonded pdb=" O1G ANP A 401 " pdb="MG MG A 402 " model vdw 1.939 2.170 nonbonded pdb=" O1G ANP E 401 " pdb="MG MG E 402 " model vdw 1.939 2.170 nonbonded pdb=" O1G ANP D 401 " pdb="MG MG D 402 " model vdw 1.940 2.170 nonbonded pdb=" O1G ANP C 401 " pdb="MG MG C 402 " model vdw 1.940 2.170 nonbonded pdb=" O1G ANP B 401 " pdb="MG MG B 402 " model vdw 1.940 2.170 ... (remaining 122185 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.270 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: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 13.390 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 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 : 0.016 0.177 14620 Z= 0.987 Angle : 1.635 16.965 19860 Z= 1.009 Chirality : 0.075 0.423 2215 Planarity : 0.019 0.159 2525 Dihedral : 10.520 83.334 5380 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 1.97 % Allowed : 4.79 % Favored : 93.24 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.19), residues: 1775 helix: -1.35 (0.16), residues: 745 sheet: -0.63 (0.29), residues: 285 loop : -0.29 (0.25), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 196 TYR 0.032 0.006 TYR B 166 PHE 0.009 0.003 PHE E 352 TRP 0.026 0.006 TRP B 340 HIS 0.006 0.002 HIS E 88 Details of bonding type rmsd/Z covalent geometry : bond 0.01609 / 0.99 (14620) covalent geometry : angle 1.63510 / 1.01 (19860) hydrogen bonds : bond 0.16496 / 11.33 ( 750) hydrogen bonds : angle 7.19826 / 5.08 ( 1935) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 466 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ASP cc_start: 0.8025 (p0) cc_final: 0.7804 (p0) REVERT: A 62 ARG cc_start: 0.8394 (ttp-110) cc_final: 0.8176 (ttm170) REVERT: A 176 MET cc_start: 0.8631 (mmm) cc_final: 0.8427 (mmt) REVERT: A 191 LYS cc_start: 0.8783 (tttt) cc_final: 0.8206 (ttmm) REVERT: A 270 GLU cc_start: 0.5932 (pt0) cc_final: 0.5433 (mm-30) REVERT: A 355 MET cc_start: 0.8346 (mmm) cc_final: 0.7660 (mtt) REVERT: B 16 LEU cc_start: 0.9172 (mt) cc_final: 0.8898 (mp) REVERT: B 78 ASN cc_start: 0.8779 (t0) cc_final: 0.8306 (t0) REVERT: B 270 GLU cc_start: 0.7244 (pt0) cc_final: 0.6900 (tt0) REVERT: B 283 MET cc_start: 0.8593 (mmp) cc_final: 0.8331 (mmt) REVERT: B 291 LYS cc_start: 0.9012 (tmmt) cc_final: 0.8232 (mptt) REVERT: B 315 LYS cc_start: 0.8837 (tttm) cc_final: 0.8632 (tttm) REVERT: C 148 THR cc_start: 0.8410 (p) cc_final: 0.8180 (t) REVERT: C 283 MET cc_start: 0.8603 (mmp) cc_final: 0.8400 (mmm) REVERT: E 134 VAL cc_start: 0.8871 (t) cc_final: 0.8574 (m) REVERT: E 276 GLU cc_start: 0.8322 (mt-10) cc_final: 0.8008 (mp0) REVERT: E 367 PRO cc_start: 0.8849 (Cg_exo) cc_final: 0.7939 (Cg_endo) outliers start: 0 outliers final: 0 residues processed: 466 average time/residue: 0.1328 time to fit residues: 88.6660 Evaluate side-chains 210 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 161 HIS B 59 GLN B 161 HIS B 173 HIS B 371 HIS C 161 HIS C 371 HIS D 161 HIS E 161 HIS E 246 GLN ** E 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.102410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.091961 restraints weight = 25392.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.094879 restraints weight = 11875.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.096689 restraints weight = 6739.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.097957 restraints weight = 4373.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.098801 restraints weight = 3055.294| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 14620 Z= 0.151 Angle : 0.583 6.647 19860 Z= 0.323 Chirality : 0.046 0.175 2215 Planarity : 0.008 0.080 2525 Dihedral : 5.344 35.617 1990 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.50 % Allowed : 9.41 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.20), residues: 1775 helix: -0.09 (0.18), residues: 755 sheet: -0.17 (0.31), residues: 270 loop : 0.39 (0.26), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 147 TYR 0.013 0.001 TYR D 294 PHE 0.012 0.001 PHE D 124 TRP 0.012 0.002 TRP C 340 HIS 0.006 0.001 HIS C 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (14620) covalent geometry : angle 0.58302 / 0.32 (19860) hydrogen bonds : bond 0.04107 / 2.83 ( 750) hydrogen bonds : angle 5.17053 / 3.66 ( 1935) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 314 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.9063 (mt) cc_final: 0.8824 (mt) REVERT: A 176 MET cc_start: 0.8168 (mmm) cc_final: 0.7896 (mmt) REVERT: A 191 LYS cc_start: 0.8404 (tttt) cc_final: 0.7704 (ttmm) REVERT: A 270 GLU cc_start: 0.5227 (pt0) cc_final: 0.4876 (mm-30) REVERT: A 283 MET cc_start: 0.8431 (mmm) cc_final: 0.8147 (mmm) REVERT: B 76 ILE cc_start: 0.8947 (mp) cc_final: 0.8705 (mp) REVERT: B 149 THR cc_start: 0.8808 (m) cc_final: 0.8525 (p) REVERT: B 291 LYS cc_start: 0.8865 (tmmt) cc_final: 0.8128 (mptt) REVERT: B 313 MET cc_start: 0.8234 (tpt) cc_final: 0.7962 (tpt) REVERT: C 64 ILE cc_start: 0.9334 (mm) cc_final: 0.8958 (pt) REVERT: C 248 ILE cc_start: 0.9060 (OUTLIER) cc_final: 0.8711 (pt) REVERT: C 283 MET cc_start: 0.8069 (mmp) cc_final: 0.7683 (mmm) REVERT: D 12 ASN cc_start: 0.8299 (t0) cc_final: 0.7995 (t0) REVERT: D 249 THR cc_start: 0.8773 (m) cc_final: 0.8461 (p) REVERT: D 276 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7442 (mm-30) REVERT: D 283 MET cc_start: 0.7969 (mmp) cc_final: 0.7135 (mmm) REVERT: E 10 CYS cc_start: 0.8644 (t) cc_final: 0.8376 (t) REVERT: E 157 ASP cc_start: 0.7442 (t0) cc_final: 0.7212 (t0) REVERT: E 249 THR cc_start: 0.8448 (m) cc_final: 0.7978 (p) outliers start: 23 outliers final: 10 residues processed: 328 average time/residue: 0.0971 time to fit residues: 50.0899 Evaluate side-chains 227 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 216 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 329 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 137 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 chunk 98 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 132 optimal weight: 0.0370 chunk 9 optimal weight: 8.9990 chunk 151 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 59 optimal weight: 7.9990 overall best weight: 1.3862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 GLN ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 HIS C 371 HIS ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.098975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.088375 restraints weight = 25746.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.091243 restraints weight = 12625.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.093118 restraints weight = 7294.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.094284 restraints weight = 4709.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.095151 restraints weight = 3352.542| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.4171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 14620 Z= 0.146 Angle : 0.536 6.309 19860 Z= 0.285 Chirality : 0.045 0.163 2215 Planarity : 0.006 0.046 2525 Dihedral : 4.879 31.648 1990 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.88 % Allowed : 11.63 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.21), residues: 1775 helix: 0.55 (0.19), residues: 755 sheet: -0.14 (0.31), residues: 275 loop : 1.03 (0.25), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 210 TYR 0.016 0.001 TYR B 294 PHE 0.012 0.001 PHE E 124 TRP 0.015 0.002 TRP B 79 HIS 0.007 0.001 HIS C 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (14620) covalent geometry : angle 0.53642 / 0.28 (19860) hydrogen bonds : bond 0.03507 / 2.40 ( 750) hydrogen bonds : angle 4.70324 / 3.33 ( 1935) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 264 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ILE cc_start: 0.9112 (mm) cc_final: 0.8847 (pt) REVERT: A 65 LEU cc_start: 0.8997 (mt) cc_final: 0.8796 (mt) REVERT: A 191 LYS cc_start: 0.8422 (tttt) cc_final: 0.7792 (ttmm) REVERT: B 76 ILE cc_start: 0.9005 (mp) cc_final: 0.8567 (mp) REVERT: B 78 ASN cc_start: 0.8728 (t0) cc_final: 0.7941 (t0) REVERT: B 82 MET cc_start: 0.8595 (tpp) cc_final: 0.8361 (tpt) REVERT: B 202 THR cc_start: 0.6749 (p) cc_final: 0.6495 (p) REVERT: B 215 LYS cc_start: 0.8564 (mttm) cc_final: 0.8254 (mtpp) REVERT: B 291 LYS cc_start: 0.8898 (tmmt) cc_final: 0.8209 (mptt) REVERT: B 325 MET cc_start: 0.8563 (tpp) cc_final: 0.8015 (tpt) REVERT: C 24 ASP cc_start: 0.7736 (OUTLIER) cc_final: 0.7087 (m-30) REVERT: C 64 ILE cc_start: 0.9292 (mm) cc_final: 0.8957 (pt) REVERT: C 72 GLU cc_start: 0.7829 (pm20) cc_final: 0.7617 (pm20) REVERT: C 248 ILE cc_start: 0.9040 (OUTLIER) cc_final: 0.8610 (pt) REVERT: C 305 MET cc_start: 0.8755 (mmm) cc_final: 0.8070 (mpp) REVERT: D 12 ASN cc_start: 0.8621 (t0) cc_final: 0.8412 (t0) REVERT: D 123 MET cc_start: 0.8709 (mmp) cc_final: 0.8494 (tpp) REVERT: D 249 THR cc_start: 0.8687 (m) cc_final: 0.8449 (p) REVERT: D 283 MET cc_start: 0.7957 (mmp) cc_final: 0.7392 (mmm) REVERT: D 355 MET cc_start: 0.8529 (mmm) cc_final: 0.8069 (mtt) REVERT: E 118 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8344 (mttp) REVERT: E 125 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7773 (mm-30) REVERT: E 217 CYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7599 (m) REVERT: E 249 THR cc_start: 0.8743 (m) cc_final: 0.8314 (p) REVERT: E 314 GLN cc_start: 0.8293 (tm-30) cc_final: 0.7661 (tm-30) outliers start: 44 outliers final: 28 residues processed: 296 average time/residue: 0.0949 time to fit residues: 44.8288 Evaluate side-chains 243 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 210 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 143 TYR Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain C residue 24 ASP Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 371 HIS Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 118 LYS Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 99 optimal weight: 0.6980 chunk 175 optimal weight: 9.9990 chunk 9 optimal weight: 0.4980 chunk 163 optimal weight: 0.9990 chunk 179 optimal weight: 0.0970 chunk 122 optimal weight: 7.9990 chunk 81 optimal weight: 6.9990 chunk 146 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 GLN ** B 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN C 59 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.099049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.088395 restraints weight = 25493.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.091309 restraints weight = 12558.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.093174 restraints weight = 7230.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.094414 restraints weight = 4675.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.095285 restraints weight = 3294.449| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.4527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 14620 Z= 0.122 Angle : 0.510 5.684 19860 Z= 0.267 Chirality : 0.044 0.141 2215 Planarity : 0.005 0.042 2525 Dihedral : 4.630 28.827 1990 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.16 % Allowed : 13.86 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.21), residues: 1775 helix: 0.78 (0.19), residues: 755 sheet: -0.02 (0.31), residues: 275 loop : 1.19 (0.25), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 116 TYR 0.008 0.001 TYR A 166 PHE 0.008 0.001 PHE D 262 TRP 0.011 0.001 TRP B 79 HIS 0.007 0.001 HIS B 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 (14620) covalent geometry : angle 0.51010 / 0.27 (19860) hydrogen bonds : bond 0.03186 / 2.18 ( 750) hydrogen bonds : angle 4.52576 / 3.21 ( 1935) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 232 time to evaluate : 0.588 Fit side-chains revert: symmetry clash REVERT: A 64 ILE cc_start: 0.9105 (mm) cc_final: 0.8854 (pt) REVERT: A 72 GLU cc_start: 0.7444 (mt-10) cc_final: 0.7083 (mm-30) REVERT: A 89 THR cc_start: 0.8719 (OUTLIER) cc_final: 0.8336 (p) REVERT: A 191 LYS cc_start: 0.8464 (tttt) cc_final: 0.7746 (ttmm) REVERT: B 76 ILE cc_start: 0.9004 (mp) cc_final: 0.8574 (mp) REVERT: B 215 LYS cc_start: 0.8490 (mttm) cc_final: 0.8215 (mtpp) REVERT: B 291 LYS cc_start: 0.8920 (tmmt) cc_final: 0.8162 (mttt) REVERT: B 313 MET cc_start: 0.8400 (tpt) cc_final: 0.8056 (tpt) REVERT: C 24 ASP cc_start: 0.7694 (OUTLIER) cc_final: 0.7127 (m-30) REVERT: C 64 ILE cc_start: 0.9258 (mm) cc_final: 0.9048 (pt) REVERT: C 248 ILE cc_start: 0.8998 (OUTLIER) cc_final: 0.8600 (pt) REVERT: C 259 GLU cc_start: 0.8500 (tp30) cc_final: 0.7853 (tp30) REVERT: C 283 MET cc_start: 0.7998 (mmm) cc_final: 0.7744 (mmm) REVERT: C 305 MET cc_start: 0.8712 (mmm) cc_final: 0.8014 (mpp) REVERT: D 214 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8084 (mt-10) REVERT: D 249 THR cc_start: 0.8728 (m) cc_final: 0.8505 (p) REVERT: D 283 MET cc_start: 0.7756 (mmp) cc_final: 0.7304 (mmm) REVERT: D 325 MET cc_start: 0.8631 (mmm) cc_final: 0.8430 (mmm) REVERT: D 355 MET cc_start: 0.8529 (mmm) cc_final: 0.8088 (mtt) REVERT: E 12 ASN cc_start: 0.8315 (p0) cc_final: 0.7930 (p0) REVERT: E 217 CYS cc_start: 0.8001 (m) cc_final: 0.7505 (m) REVERT: E 249 THR cc_start: 0.8807 (m) cc_final: 0.8404 (p) outliers start: 33 outliers final: 26 residues processed: 256 average time/residue: 0.0935 time to fit residues: 38.6964 Evaluate side-chains 232 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 202 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 143 TYR Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain C residue 24 ASP Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 214 GLU Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 329 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 50 optimal weight: 0.7980 chunk 138 optimal weight: 0.9980 chunk 152 optimal weight: 5.9990 chunk 153 optimal weight: 3.9990 chunk 125 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 164 optimal weight: 0.7980 chunk 159 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 HIS C 371 HIS ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.098435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.087993 restraints weight = 25821.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.090839 restraints weight = 12604.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.092690 restraints weight = 7280.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.093835 restraints weight = 4700.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.094745 restraints weight = 3376.459| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.4847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 14620 Z= 0.120 Angle : 0.503 7.038 19860 Z= 0.262 Chirality : 0.044 0.173 2215 Planarity : 0.005 0.041 2525 Dihedral : 4.491 28.545 1990 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.01 % Allowed : 13.99 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.21), residues: 1775 helix: 0.97 (0.19), residues: 755 sheet: -0.01 (0.31), residues: 275 loop : 1.26 (0.25), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 116 TYR 0.009 0.001 TYR E 294 PHE 0.009 0.001 PHE D 262 TRP 0.011 0.001 TRP B 79 HIS 0.005 0.001 HIS C 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (14620) covalent geometry : angle 0.50309 / 0.26 (19860) hydrogen bonds : bond 0.03027 / 2.06 ( 750) hydrogen bonds : angle 4.40887 / 3.13 ( 1935) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 228 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 ILE cc_start: 0.9062 (mm) cc_final: 0.8855 (pt) REVERT: A 72 GLU cc_start: 0.7460 (mt-10) cc_final: 0.7099 (mm-30) REVERT: A 89 THR cc_start: 0.8719 (OUTLIER) cc_final: 0.8328 (p) REVERT: A 191 LYS cc_start: 0.8463 (tttt) cc_final: 0.7802 (ttmm) REVERT: B 76 ILE cc_start: 0.9028 (mp) cc_final: 0.8562 (mp) REVERT: B 82 MET cc_start: 0.8874 (tpt) cc_final: 0.8645 (tpt) REVERT: B 215 LYS cc_start: 0.8439 (mttm) cc_final: 0.8185 (mtpp) REVERT: B 291 LYS cc_start: 0.8725 (tmmt) cc_final: 0.8307 (mptt) REVERT: B 313 MET cc_start: 0.8467 (tpt) cc_final: 0.7812 (tpt) REVERT: B 325 MET cc_start: 0.8629 (tpt) cc_final: 0.8265 (tpt) REVERT: B 352 PHE cc_start: 0.9001 (t80) cc_final: 0.8798 (t80) REVERT: B 355 MET cc_start: 0.8002 (mtt) cc_final: 0.7744 (mtt) REVERT: C 24 ASP cc_start: 0.7797 (OUTLIER) cc_final: 0.7261 (m-30) REVERT: C 64 ILE cc_start: 0.9211 (mm) cc_final: 0.8991 (pt) REVERT: C 259 GLU cc_start: 0.8514 (tp30) cc_final: 0.8082 (tp30) REVERT: C 283 MET cc_start: 0.7943 (mmm) cc_final: 0.7710 (mmm) REVERT: C 305 MET cc_start: 0.8691 (mmm) cc_final: 0.7991 (mpp) REVERT: D 249 THR cc_start: 0.8728 (m) cc_final: 0.8512 (p) REVERT: D 283 MET cc_start: 0.7676 (mmp) cc_final: 0.7446 (mmt) REVERT: D 355 MET cc_start: 0.8573 (mmm) cc_final: 0.8080 (mtt) REVERT: E 217 CYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7596 (m) REVERT: E 249 THR cc_start: 0.8834 (m) cc_final: 0.8439 (p) REVERT: E 329 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8496 (mt) outliers start: 46 outliers final: 34 residues processed: 261 average time/residue: 0.0951 time to fit residues: 39.9821 Evaluate side-chains 240 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 202 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 143 TYR Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain C residue 24 ASP Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain C residue 371 HIS Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 329 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 172 optimal weight: 0.0980 chunk 26 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 chunk 113 optimal weight: 0.6980 chunk 89 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 155 optimal weight: 7.9990 chunk 99 optimal weight: 0.4980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 GLN B 371 HIS C 59 GLN C 173 HIS C 371 HIS ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.099826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.089387 restraints weight = 25653.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.092255 restraints weight = 12623.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.094150 restraints weight = 7272.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.095411 restraints weight = 4660.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.096272 restraints weight = 3232.875| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.5043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.102 14620 Z= 0.099 Angle : 0.488 6.414 19860 Z= 0.253 Chirality : 0.043 0.145 2215 Planarity : 0.004 0.041 2525 Dihedral : 4.320 28.068 1990 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.35 % Allowed : 15.29 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.21), residues: 1775 helix: 1.13 (0.19), residues: 755 sheet: 0.03 (0.31), residues: 275 loop : 1.30 (0.25), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 147 TYR 0.007 0.001 TYR D 306 PHE 0.011 0.001 PHE E 262 TRP 0.010 0.001 TRP D 340 HIS 0.006 0.001 HIS C 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.10 (14620) covalent geometry : angle 0.48785 / 0.25 (19860) hydrogen bonds : bond 0.02786 / 1.91 ( 750) hydrogen bonds : angle 4.32715 / 3.08 ( 1935) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 223 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 THR cc_start: 0.8658 (OUTLIER) cc_final: 0.8279 (p) REVERT: A 191 LYS cc_start: 0.8462 (tttt) cc_final: 0.7647 (ttmm) REVERT: B 53 TYR cc_start: 0.8160 (m-80) cc_final: 0.7845 (m-80) REVERT: B 76 ILE cc_start: 0.8983 (mp) cc_final: 0.8557 (mp) REVERT: B 215 LYS cc_start: 0.8327 (mttm) cc_final: 0.8125 (mtpp) REVERT: B 291 LYS cc_start: 0.8703 (tmmt) cc_final: 0.8324 (mptt) REVERT: B 325 MET cc_start: 0.8643 (tpt) cc_final: 0.8427 (tpt) REVERT: B 333 PRO cc_start: 0.7913 (Cg_exo) cc_final: 0.7492 (Cg_endo) REVERT: B 352 PHE cc_start: 0.8972 (t80) cc_final: 0.8748 (t80) REVERT: B 355 MET cc_start: 0.7897 (mtt) cc_final: 0.7671 (mtt) REVERT: C 259 GLU cc_start: 0.8493 (tp30) cc_final: 0.7834 (tp30) REVERT: C 305 MET cc_start: 0.8627 (mmm) cc_final: 0.7957 (mpp) REVERT: C 371 HIS cc_start: 0.7160 (OUTLIER) cc_final: 0.6401 (m90) REVERT: D 43 VAL cc_start: 0.5044 (OUTLIER) cc_final: 0.4826 (t) REVERT: D 54 VAL cc_start: 0.9004 (t) cc_final: 0.8552 (p) REVERT: D 249 THR cc_start: 0.8771 (m) cc_final: 0.8549 (p) REVERT: D 283 MET cc_start: 0.7723 (mmp) cc_final: 0.7243 (mmt) REVERT: D 355 MET cc_start: 0.8564 (mmm) cc_final: 0.8086 (mtt) REVERT: E 217 CYS cc_start: 0.7908 (OUTLIER) cc_final: 0.7536 (m) REVERT: E 249 THR cc_start: 0.8829 (m) cc_final: 0.8440 (p) REVERT: E 283 MET cc_start: 0.8082 (mmm) cc_final: 0.7637 (mmp) REVERT: E 325 MET cc_start: 0.8474 (tpp) cc_final: 0.8243 (tpp) outliers start: 36 outliers final: 26 residues processed: 249 average time/residue: 0.0931 time to fit residues: 37.2968 Evaluate side-chains 230 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 200 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain C residue 371 HIS Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 173 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 chunk 153 optimal weight: 10.0000 chunk 170 optimal weight: 0.9980 chunk 104 optimal weight: 0.2980 chunk 131 optimal weight: 0.8980 chunk 103 optimal weight: 10.0000 chunk 37 optimal weight: 0.7980 chunk 113 optimal weight: 0.0470 chunk 162 optimal weight: 5.9990 chunk 74 optimal weight: 0.0060 overall best weight: 0.4094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 GLN ** B 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN C 173 HIS ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 HIS ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.101513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.090992 restraints weight = 25509.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.093894 restraints weight = 12614.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.095809 restraints weight = 7290.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.097061 restraints weight = 4681.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.097941 restraints weight = 3256.235| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.5231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.107 14620 Z= 0.093 Angle : 0.492 9.878 19860 Z= 0.253 Chirality : 0.042 0.141 2215 Planarity : 0.004 0.040 2525 Dihedral : 4.197 26.578 1990 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.76 % Allowed : 16.14 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.21), residues: 1775 helix: 1.23 (0.19), residues: 755 sheet: 0.16 (0.31), residues: 270 loop : 1.30 (0.25), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 147 TYR 0.010 0.001 TYR C 166 PHE 0.009 0.001 PHE E 262 TRP 0.009 0.001 TRP D 340 HIS 0.004 0.001 HIS C 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.09 (14620) covalent geometry : angle 0.49162 / 0.25 (19860) hydrogen bonds : bond 0.02680 / 1.84 ( 750) hydrogen bonds : angle 4.28687 / 3.05 ( 1935) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 234 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.8723 (OUTLIER) cc_final: 0.8446 (mmp) REVERT: A 191 LYS cc_start: 0.8506 (tttt) cc_final: 0.7705 (ttmm) REVERT: A 305 MET cc_start: 0.8868 (mtp) cc_final: 0.8527 (mtt) REVERT: B 53 TYR cc_start: 0.8116 (m-80) cc_final: 0.7703 (m-80) REVERT: B 76 ILE cc_start: 0.8948 (mp) cc_final: 0.8458 (mp) REVERT: B 78 ASN cc_start: 0.8714 (t0) cc_final: 0.7736 (t0) REVERT: B 81 ASP cc_start: 0.8346 (m-30) cc_final: 0.7584 (m-30) REVERT: B 82 MET cc_start: 0.8880 (tpt) cc_final: 0.8667 (tpt) REVERT: B 291 LYS cc_start: 0.8658 (tmmt) cc_final: 0.8277 (mptt) REVERT: B 333 PRO cc_start: 0.8120 (Cg_exo) cc_final: 0.7744 (Cg_endo) REVERT: B 352 PHE cc_start: 0.8966 (t80) cc_final: 0.8748 (t80) REVERT: B 355 MET cc_start: 0.7789 (mtt) cc_final: 0.7569 (mtt) REVERT: C 259 GLU cc_start: 0.8485 (tp30) cc_final: 0.8007 (tp30) REVERT: C 283 MET cc_start: 0.7846 (mmm) cc_final: 0.7640 (mmm) REVERT: C 305 MET cc_start: 0.8580 (mmm) cc_final: 0.7957 (mpp) REVERT: C 333 PRO cc_start: 0.8034 (Cg_exo) cc_final: 0.7831 (Cg_endo) REVERT: D 43 VAL cc_start: 0.4977 (OUTLIER) cc_final: 0.4725 (t) REVERT: D 54 VAL cc_start: 0.9020 (t) cc_final: 0.8560 (p) REVERT: D 325 MET cc_start: 0.8232 (mmm) cc_final: 0.7586 (mmm) REVERT: D 355 MET cc_start: 0.8557 (mmm) cc_final: 0.8084 (mtt) REVERT: E 191 LYS cc_start: 0.9083 (tttt) cc_final: 0.8829 (tttp) REVERT: E 217 CYS cc_start: 0.7781 (OUTLIER) cc_final: 0.7444 (m) REVERT: E 249 THR cc_start: 0.8833 (m) cc_final: 0.8452 (p) REVERT: E 283 MET cc_start: 0.8078 (mmm) cc_final: 0.7665 (mmp) outliers start: 27 outliers final: 21 residues processed: 251 average time/residue: 0.0961 time to fit residues: 38.3455 Evaluate side-chains 231 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 207 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 329 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 174 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 129 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 98 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 158 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 GLN A 275 HIS ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 HIS C 59 GLN ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 HIS ** D 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 ASN E 173 HIS E 246 GLN ** E 371 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 = 0.3104 r_free = 0.3104 target = 0.093998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.083297 restraints weight = 25993.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.086098 restraints weight = 12941.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.087954 restraints weight = 7605.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.089198 restraints weight = 4966.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.090063 restraints weight = 3505.396| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.5313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.090 14620 Z= 0.327 Angle : 0.686 9.287 19860 Z= 0.353 Chirality : 0.050 0.271 2215 Planarity : 0.005 0.043 2525 Dihedral : 5.137 35.510 1990 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.33 % Allowed : 15.16 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.20), residues: 1775 helix: 0.93 (0.19), residues: 725 sheet: -0.11 (0.30), residues: 295 loop : 0.89 (0.24), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 147 TYR 0.039 0.002 TYR C 166 PHE 0.019 0.002 PHE E 262 TRP 0.018 0.002 TRP B 79 HIS 0.013 0.002 HIS C 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00771 / 0.33 (14620) covalent geometry : angle 0.68605 / 0.35 (19860) hydrogen bonds : bond 0.04052 / 2.76 ( 750) hydrogen bonds : angle 4.85615 / 3.47 ( 1935) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 195 time to evaluate : 0.440 Fit side-chains revert: symmetry clash REVERT: A 82 MET cc_start: 0.8472 (tpp) cc_final: 0.8236 (tpp) REVERT: A 89 THR cc_start: 0.8814 (OUTLIER) cc_final: 0.8427 (p) REVERT: A 191 LYS cc_start: 0.8702 (tttt) cc_final: 0.8021 (ttmm) REVERT: A 325 MET cc_start: 0.8051 (tpp) cc_final: 0.7672 (tpp) REVERT: B 53 TYR cc_start: 0.8267 (m-80) cc_final: 0.7983 (m-80) REVERT: B 76 ILE cc_start: 0.8944 (mp) cc_final: 0.8569 (mp) REVERT: B 82 MET cc_start: 0.9064 (tpt) cc_final: 0.8726 (tpt) REVERT: B 291 LYS cc_start: 0.8849 (tmmt) cc_final: 0.8351 (mptt) REVERT: B 305 MET cc_start: 0.8978 (mmm) cc_final: 0.8691 (tpp) REVERT: B 325 MET cc_start: 0.8706 (tpt) cc_final: 0.7949 (tpt) REVERT: C 24 ASP cc_start: 0.7966 (OUTLIER) cc_final: 0.7427 (m-30) REVERT: C 259 GLU cc_start: 0.8522 (tp30) cc_final: 0.8085 (tp30) REVERT: C 305 MET cc_start: 0.8748 (mmm) cc_final: 0.7980 (mpp) REVERT: C 328 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.8248 (tttm) REVERT: D 148 THR cc_start: 0.8519 (OUTLIER) cc_final: 0.8162 (t) REVERT: D 221 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8653 (tt) REVERT: D 325 MET cc_start: 0.8545 (mmm) cc_final: 0.8230 (mmm) REVERT: D 353 GLN cc_start: 0.7770 (mm-40) cc_final: 0.7565 (mm110) REVERT: D 355 MET cc_start: 0.8624 (mmm) cc_final: 0.8194 (mtp) REVERT: E 142 LEU cc_start: 0.9337 (tp) cc_final: 0.9105 (mp) REVERT: E 217 CYS cc_start: 0.8046 (m) cc_final: 0.7771 (m) REVERT: E 249 THR cc_start: 0.8927 (m) cc_final: 0.8608 (p) REVERT: E 283 MET cc_start: 0.8236 (mmm) cc_final: 0.7732 (mmp) REVERT: E 305 MET cc_start: 0.9191 (mmm) cc_final: 0.8899 (tpp) REVERT: E 325 MET cc_start: 0.8645 (tpp) cc_final: 0.8323 (tpp) outliers start: 51 outliers final: 39 residues processed: 240 average time/residue: 0.0967 time to fit residues: 37.0267 Evaluate side-chains 220 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 176 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain C residue 24 ASP Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 173 optimal weight: 0.6980 chunk 120 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 179 optimal weight: 5.9990 chunk 153 optimal weight: 0.9980 chunk 165 optimal weight: 4.9990 chunk 159 optimal weight: 0.9980 chunk 176 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 GLN C 59 GLN C 88 HIS C 92 ASN C 173 HIS D 12 ASN D 173 HIS ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.099117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.088372 restraints weight = 25408.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.091336 restraints weight = 12555.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.093162 restraints weight = 7285.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.094484 restraints weight = 4773.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.095297 restraints weight = 3326.025| |-----------------------------------------------------------------------------| r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.5473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.132 14620 Z= 0.111 Angle : 0.541 9.467 19860 Z= 0.279 Chirality : 0.044 0.220 2215 Planarity : 0.004 0.039 2525 Dihedral : 4.580 31.135 1990 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.37 % Allowed : 17.91 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.21), residues: 1775 helix: 1.00 (0.19), residues: 755 sheet: -0.09 (0.29), residues: 305 loop : 1.14 (0.25), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 116 TYR 0.033 0.001 TYR C 166 PHE 0.012 0.001 PHE E 262 TRP 0.013 0.002 TRP D 340 HIS 0.006 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.11 (14620) covalent geometry : angle 0.54078 / 0.28 (19860) hydrogen bonds : bond 0.02893 / 1.98 ( 750) hydrogen bonds : angle 4.47879 / 3.20 ( 1935) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 214 time to evaluate : 0.541 Fit side-chains revert: symmetry clash REVERT: A 89 THR cc_start: 0.8647 (OUTLIER) cc_final: 0.8244 (p) REVERT: A 191 LYS cc_start: 0.8550 (tttt) cc_final: 0.7804 (ttmm) REVERT: A 325 MET cc_start: 0.7813 (tpp) cc_final: 0.7198 (tpp) REVERT: B 53 TYR cc_start: 0.8214 (m-80) cc_final: 0.7809 (m-80) REVERT: B 76 ILE cc_start: 0.8904 (mp) cc_final: 0.8527 (mp) REVERT: B 78 ASN cc_start: 0.8520 (t0) cc_final: 0.8307 (t0) REVERT: B 291 LYS cc_start: 0.8713 (tmmt) cc_final: 0.8293 (mptt) REVERT: B 305 MET cc_start: 0.8870 (mmm) cc_final: 0.8566 (tpp) REVERT: B 325 MET cc_start: 0.8680 (tpt) cc_final: 0.7943 (tpt) REVERT: B 352 PHE cc_start: 0.8976 (t80) cc_final: 0.8748 (t80) REVERT: C 305 MET cc_start: 0.8577 (mmm) cc_final: 0.7877 (mpp) REVERT: D 148 THR cc_start: 0.8454 (OUTLIER) cc_final: 0.8068 (t) REVERT: D 227 MET cc_start: 0.8432 (tpp) cc_final: 0.7823 (mmt) REVERT: D 355 MET cc_start: 0.8594 (mmm) cc_final: 0.8173 (mtp) REVERT: E 12 ASN cc_start: 0.8185 (p0) cc_final: 0.7977 (p0) REVERT: E 155 SER cc_start: 0.8698 (t) cc_final: 0.8251 (p) REVERT: E 217 CYS cc_start: 0.7950 (m) cc_final: 0.7596 (m) REVERT: E 249 THR cc_start: 0.8943 (m) cc_final: 0.8620 (p) REVERT: E 283 MET cc_start: 0.8135 (mmm) cc_final: 0.7636 (mmp) REVERT: E 305 MET cc_start: 0.9059 (mmm) cc_final: 0.8739 (tpp) REVERT: E 325 MET cc_start: 0.8529 (tpp) cc_final: 0.8309 (tpp) outliers start: 21 outliers final: 18 residues processed: 229 average time/residue: 0.0919 time to fit residues: 33.9748 Evaluate side-chains 217 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 197 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 329 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 106 optimal weight: 7.9990 chunk 107 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 163 optimal weight: 8.9990 chunk 174 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 144 optimal weight: 10.0000 chunk 42 optimal weight: 0.2980 chunk 154 optimal weight: 0.7980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 GLN C 59 GLN C 173 HIS D 173 HIS E 115 ASN ** E 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.096192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.085403 restraints weight = 25712.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.088306 restraints weight = 12805.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.090194 restraints weight = 7489.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.091459 restraints weight = 4873.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.092316 restraints weight = 3435.275| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.5509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.130 14620 Z= 0.159 Angle : 0.573 11.008 19860 Z= 0.295 Chirality : 0.045 0.196 2215 Planarity : 0.004 0.041 2525 Dihedral : 4.646 33.223 1990 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.96 % Allowed : 17.84 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.21), residues: 1775 helix: 1.02 (0.19), residues: 755 sheet: -0.14 (0.30), residues: 305 loop : 1.13 (0.25), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 183 TYR 0.036 0.001 TYR C 166 PHE 0.015 0.001 PHE E 262 TRP 0.015 0.002 TRP B 79 HIS 0.006 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.16 (14620) covalent geometry : angle 0.57333 / 0.29 (19860) hydrogen bonds : bond 0.03148 / 2.16 ( 750) hydrogen bonds : angle 4.53547 / 3.24 ( 1935) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 201 time to evaluate : 0.560 Fit side-chains revert: symmetry clash REVERT: A 89 THR cc_start: 0.8706 (OUTLIER) cc_final: 0.8302 (p) REVERT: A 191 LYS cc_start: 0.8534 (tttt) cc_final: 0.7787 (ttmm) REVERT: A 206 ARG cc_start: 0.7870 (ttm110) cc_final: 0.7588 (ttm170) REVERT: A 305 MET cc_start: 0.8876 (mtp) cc_final: 0.8649 (mtt) REVERT: A 325 MET cc_start: 0.7924 (tpp) cc_final: 0.7466 (tpp) REVERT: B 53 TYR cc_start: 0.8237 (m-80) cc_final: 0.7849 (m-80) REVERT: B 76 ILE cc_start: 0.8984 (mp) cc_final: 0.8671 (mp) REVERT: B 291 LYS cc_start: 0.8741 (tmmt) cc_final: 0.8318 (mptt) REVERT: B 305 MET cc_start: 0.8931 (mmm) cc_final: 0.8627 (tpp) REVERT: B 325 MET cc_start: 0.8677 (tpt) cc_final: 0.8025 (tpt) REVERT: B 352 PHE cc_start: 0.9038 (t80) cc_final: 0.8821 (t80) REVERT: C 305 MET cc_start: 0.8646 (mmm) cc_final: 0.7917 (mpp) REVERT: D 81 ASP cc_start: 0.6603 (m-30) cc_final: 0.6381 (m-30) REVERT: D 148 THR cc_start: 0.8523 (OUTLIER) cc_final: 0.8197 (t) REVERT: D 353 GLN cc_start: 0.7689 (mm-40) cc_final: 0.7419 (mm110) REVERT: D 355 MET cc_start: 0.8644 (mmm) cc_final: 0.8187 (mtp) REVERT: E 155 SER cc_start: 0.8636 (t) cc_final: 0.8166 (p) REVERT: E 217 CYS cc_start: 0.7941 (m) cc_final: 0.7575 (m) REVERT: E 249 THR cc_start: 0.8932 (m) cc_final: 0.8616 (p) REVERT: E 283 MET cc_start: 0.8151 (mmm) cc_final: 0.7664 (mmp) REVERT: E 305 MET cc_start: 0.9097 (mmm) cc_final: 0.8787 (tpp) REVERT: E 325 MET cc_start: 0.8601 (tpp) cc_final: 0.8400 (tpp) outliers start: 30 outliers final: 25 residues processed: 224 average time/residue: 0.0975 time to fit residues: 35.0523 Evaluate side-chains 219 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 192 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 329 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 154 optimal weight: 0.7980 chunk 122 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 144 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 118 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 GLN C 173 HIS D 173 HIS ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 ASN ** E 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.097085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.086459 restraints weight = 25594.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.089322 restraints weight = 12657.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.091190 restraints weight = 7385.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.092418 restraints weight = 4797.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.093311 restraints weight = 3387.095| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.5573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.128 14620 Z= 0.152 Angle : 0.564 9.416 19860 Z= 0.292 Chirality : 0.045 0.190 2215 Planarity : 0.004 0.039 2525 Dihedral : 4.624 33.595 1990 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.16 % Allowed : 17.97 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.21), residues: 1775 helix: 1.00 (0.19), residues: 755 sheet: -0.16 (0.30), residues: 305 loop : 1.12 (0.25), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 183 TYR 0.033 0.001 TYR C 166 PHE 0.014 0.001 PHE E 262 TRP 0.012 0.002 TRP E 79 HIS 0.006 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.15 (14620) covalent geometry : angle 0.56438 / 0.29 (19860) hydrogen bonds : bond 0.03116 / 2.14 ( 750) hydrogen bonds : angle 4.53392 / 3.24 ( 1935) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2043.27 seconds wall clock time: 36 minutes 27.48 seconds (2187.48 seconds total)