Starting phenix.real_space_refine on Tue Nov 18 13:27:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5ooe_3838/11_2025/5ooe_3838.cif Found real_map, /net/cci-nas-00/data/ceres_data/5ooe_3838/11_2025/5ooe_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 { model { file = "/net/cci-nas-00/data/ceres_data/5ooe_3838/11_2025/5ooe_3838.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5ooe_3838/11_2025/5ooe_3838.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5ooe_3838/11_2025/5ooe_3838.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5ooe_3838/11_2025/5ooe_3838.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/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: 2.64, per 1000 atoms: 0.18 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: 1.46 Conformation dependent library (CDL) restraints added in 656.9 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: 0.75 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: 2.78 Time building geometry restraints manager: 1.86 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 - 18.22: 8425 18.22 - 36.44: 280 36.44 - 54.66: 80 54.66 - 72.87: 55 72.87 - 91.09: 40 Dihedral angle restraints: 8880 sinusoidal: 3640 harmonic: 5240 Sorted by residual: dihedral pdb=" C5' ANP A 401 " pdb=" C3' ANP A 401 " pdb=" C4' ANP A 401 " pdb=" O3' ANP A 401 " ideal model delta sinusoidal sigma weight residual -74.79 -165.88 91.09 1 3.00e+01 1.11e-03 1.09e+01 dihedral pdb=" C5' ANP E 401 " pdb=" C3' ANP E 401 " pdb=" C4' ANP E 401 " pdb=" O3' ANP E 401 " ideal model delta sinusoidal sigma weight residual -74.79 -165.88 91.09 1 3.00e+01 1.11e-03 1.09e+01 dihedral pdb=" C5' ANP B 401 " pdb=" C3' ANP B 401 " pdb=" C4' ANP B 401 " pdb=" O3' ANP B 401 " ideal model delta sinusoidal sigma weight residual -74.79 -165.86 91.07 1 3.00e+01 1.11e-03 1.09e+01 ... (remaining 8877 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: 0.04 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: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 14.460 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 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 : 13.638 91.091 5520 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 covalent geometry : bond 0.01609 (14620) covalent geometry : angle 1.63510 (19860) hydrogen bonds : bond 0.16496 ( 750) hydrogen bonds : angle 7.19826 ( 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 : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ASP cc_start: 0.8025 (p0) cc_final: 0.7803 (p0) REVERT: A 62 ARG cc_start: 0.8400 (ttp-110) cc_final: 0.8176 (ttm170) REVERT: A 191 LYS cc_start: 0.8780 (tttt) cc_final: 0.8204 (ttmm) REVERT: A 270 GLU cc_start: 0.5935 (pt0) cc_final: 0.5433 (mm-30) REVERT: A 355 MET cc_start: 0.8348 (mmm) cc_final: 0.7658 (mtt) REVERT: B 16 LEU cc_start: 0.9174 (mt) cc_final: 0.8900 (mp) REVERT: B 78 ASN cc_start: 0.8779 (t0) cc_final: 0.8306 (t0) REVERT: B 270 GLU cc_start: 0.7243 (pt0) cc_final: 0.6894 (tt0) REVERT: B 283 MET cc_start: 0.8595 (mmp) cc_final: 0.8333 (mmt) REVERT: B 291 LYS cc_start: 0.9014 (tmmt) cc_final: 0.8237 (mptt) REVERT: B 315 LYS cc_start: 0.8834 (tttm) cc_final: 0.8628 (tttm) REVERT: C 148 THR cc_start: 0.8416 (p) cc_final: 0.8184 (t) REVERT: C 283 MET cc_start: 0.8602 (mmp) cc_final: 0.8400 (mmm) REVERT: E 134 VAL cc_start: 0.8876 (t) cc_final: 0.8581 (m) REVERT: E 276 GLU cc_start: 0.8319 (mt-10) cc_final: 0.8006 (mp0) REVERT: E 367 PRO cc_start: 0.8851 (Cg_exo) cc_final: 0.7940 (Cg_endo) outliers start: 0 outliers final: 0 residues processed: 466 average time/residue: 0.1358 time to fit residues: 89.7406 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 : 0.593 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.102230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.091677 restraints weight = 25371.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.094634 restraints weight = 11991.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.096525 restraints weight = 6800.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.097774 restraints weight = 4352.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.098624 restraints weight = 3037.346| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 14620 Z= 0.154 Angle : 0.591 6.516 19860 Z= 0.325 Chirality : 0.047 0.174 2215 Planarity : 0.008 0.080 2525 Dihedral : 8.959 64.013 2130 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.37 % Allowed : 9.67 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.20), residues: 1775 helix: -0.08 (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 0.007 0.001 ARG B 147 TYR 0.013 0.001 TYR D 294 PHE 0.012 0.001 PHE D 124 TRP 0.012 0.001 TRP C 340 HIS 0.006 0.001 HIS C 88 Details of bonding type rmsd covalent geometry : bond 0.00356 (14620) covalent geometry : angle 0.59131 (19860) hydrogen bonds : bond 0.04063 ( 750) hydrogen bonds : angle 5.17198 ( 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 340 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 319 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 LYS cc_start: 0.8403 (tttt) cc_final: 0.7675 (ttmm) REVERT: A 270 GLU cc_start: 0.5249 (pt0) cc_final: 0.4878 (mm-30) REVERT: A 283 MET cc_start: 0.8407 (mmm) cc_final: 0.8140 (mmm) REVERT: B 76 ILE cc_start: 0.8948 (mp) cc_final: 0.8684 (mp) REVERT: B 78 ASN cc_start: 0.8702 (t0) cc_final: 0.8148 (t0) REVERT: B 149 THR cc_start: 0.8815 (m) cc_final: 0.8547 (p) REVERT: B 291 LYS cc_start: 0.8858 (tmmt) cc_final: 0.8128 (mptt) REVERT: B 313 MET cc_start: 0.8225 (tpt) cc_final: 0.7963 (tpt) REVERT: C 64 ILE cc_start: 0.9330 (mm) cc_final: 0.8958 (pt) REVERT: C 248 ILE cc_start: 0.9053 (OUTLIER) cc_final: 0.8700 (pt) REVERT: C 283 MET cc_start: 0.8076 (mmp) cc_final: 0.7697 (mmm) REVERT: D 12 ASN cc_start: 0.8296 (t0) cc_final: 0.7963 (t0) REVERT: D 249 THR cc_start: 0.8764 (m) cc_final: 0.8461 (p) REVERT: D 276 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7451 (mm-30) REVERT: D 283 MET cc_start: 0.7993 (mmp) cc_final: 0.7170 (mmm) REVERT: D 355 MET cc_start: 0.8548 (mmm) cc_final: 0.7723 (mmm) REVERT: E 10 CYS cc_start: 0.8629 (t) cc_final: 0.8360 (t) REVERT: E 157 ASP cc_start: 0.7413 (t0) cc_final: 0.7103 (t0) REVERT: E 249 THR cc_start: 0.8455 (m) cc_final: 0.7992 (p) outliers start: 21 outliers final: 9 residues processed: 332 average time/residue: 0.1002 time to fit residues: 52.0959 Evaluate side-chains 227 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 217 time to evaluate : 0.551 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 102 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 132 optimal weight: 0.8980 chunk 9 optimal weight: 8.9990 chunk 151 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 59 optimal weight: 7.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 GLN A 275 HIS B 12 ASN B 371 HIS C 371 HIS ** E 12 ASN ** 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 = 0.3144 r_free = 0.3144 target = 0.096658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.086105 restraints weight = 25928.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.088923 restraints weight = 12699.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.090767 restraints weight = 7381.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.091984 restraints weight = 4787.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.092836 restraints weight = 3380.098| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.4272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 14620 Z= 0.187 Angle : 0.574 6.375 19860 Z= 0.303 Chirality : 0.046 0.149 2215 Planarity : 0.006 0.048 2525 Dihedral : 8.058 65.974 2130 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.59 % Allowed : 11.57 % Favored : 84.84 % 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: 0.56 (0.20), residues: 1775 helix: 0.47 (0.19), residues: 755 sheet: -0.19 (0.29), residues: 300 loop : 0.80 (0.25), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 147 TYR 0.016 0.001 TYR B 294 PHE 0.012 0.001 PHE E 124 TRP 0.018 0.002 TRP B 79 HIS 0.009 0.002 HIS C 88 Details of bonding type rmsd covalent geometry : bond 0.00439 (14620) covalent geometry : angle 0.57352 (19860) hydrogen bonds : bond 0.03802 ( 750) hydrogen bonds : angle 4.79300 ( 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 304 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 249 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 THR cc_start: 0.8768 (OUTLIER) cc_final: 0.8400 (p) REVERT: A 191 LYS cc_start: 0.8535 (tttt) cc_final: 0.7908 (ttmm) REVERT: A 305 MET cc_start: 0.8882 (mmm) cc_final: 0.8343 (mpp) REVERT: B 76 ILE cc_start: 0.9026 (mp) cc_final: 0.8600 (mp) REVERT: B 82 MET cc_start: 0.8595 (tpp) cc_final: 0.8359 (tpt) REVERT: B 157 ASP cc_start: 0.7733 (t0) cc_final: 0.7469 (m-30) REVERT: B 215 LYS cc_start: 0.8556 (mttm) cc_final: 0.8234 (mtpp) REVERT: B 291 LYS cc_start: 0.8912 (tmmt) cc_final: 0.8157 (mttt) REVERT: B 313 MET cc_start: 0.8330 (tpt) cc_final: 0.8020 (tpt) REVERT: C 9 VAL cc_start: 0.9417 (t) cc_final: 0.9186 (m) REVERT: C 24 ASP cc_start: 0.7829 (OUTLIER) cc_final: 0.7211 (m-30) REVERT: C 64 ILE cc_start: 0.9343 (mm) cc_final: 0.8913 (pt) REVERT: C 72 GLU cc_start: 0.7928 (pm20) cc_final: 0.7582 (pm20) REVERT: C 305 MET cc_start: 0.8718 (mmm) cc_final: 0.8001 (mpp) REVERT: C 328 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8309 (tttm) REVERT: D 249 THR cc_start: 0.8692 (m) cc_final: 0.8449 (p) REVERT: D 276 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7622 (mm-30) REVERT: D 283 MET cc_start: 0.7948 (mmp) cc_final: 0.7462 (mmm) REVERT: D 353 GLN cc_start: 0.7548 (mm-40) cc_final: 0.7314 (mm110) REVERT: D 355 MET cc_start: 0.8572 (mmm) cc_final: 0.8062 (mmt) REVERT: E 12 ASN cc_start: 0.8300 (p0) cc_final: 0.8052 (p0) REVERT: E 118 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8465 (mttp) REVERT: E 125 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7857 (mm-30) REVERT: E 249 THR cc_start: 0.8814 (m) cc_final: 0.8409 (p) REVERT: E 314 GLN cc_start: 0.8360 (tm-30) cc_final: 0.7698 (tm-30) outliers start: 55 outliers final: 36 residues processed: 289 average time/residue: 0.1021 time to fit residues: 46.5628 Evaluate side-chains 247 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 206 time to evaluate : 0.553 ------------------------------------------------------------------------------- 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 143 TYR Chi-restraints excluded: chain A residue 277 THR 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 B residue 274 ILE 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 159 VAL Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 328 LYS 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 224 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 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 159 VAL Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 260 THR 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: 0.9980 chunk 175 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 163 optimal weight: 1.9990 chunk 179 optimal weight: 7.9990 chunk 122 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 146 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN ** B 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN C 371 HIS ** 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 = 0.3141 r_free = 0.3141 target = 0.096378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.085951 restraints weight = 25873.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.088712 restraints weight = 12691.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.090491 restraints weight = 7400.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.091731 restraints weight = 4839.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.092572 restraints weight = 3400.460| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.4630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 14620 Z= 0.165 Angle : 0.544 5.927 19860 Z= 0.284 Chirality : 0.045 0.141 2215 Planarity : 0.005 0.042 2525 Dihedral : 7.954 67.025 2130 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.88 % Allowed : 13.40 % Favored : 83.73 % 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: 0.86 (0.21), residues: 1775 helix: 0.70 (0.19), residues: 755 sheet: -0.14 (0.29), residues: 310 loop : 1.06 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 116 TYR 0.010 0.001 TYR B 294 PHE 0.010 0.001 PHE A 124 TRP 0.014 0.002 TRP B 79 HIS 0.014 0.002 HIS C 371 Details of bonding type rmsd covalent geometry : bond 0.00394 (14620) covalent geometry : angle 0.54401 (19860) hydrogen bonds : bond 0.03464 ( 750) hydrogen bonds : angle 4.60851 ( 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 263 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 219 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 ILE cc_start: 0.9099 (mm) cc_final: 0.8782 (pt) REVERT: A 191 LYS cc_start: 0.8490 (tttt) cc_final: 0.7828 (ttmm) REVERT: A 283 MET cc_start: 0.8369 (mmm) cc_final: 0.8069 (mmm) REVERT: A 305 MET cc_start: 0.8820 (mmm) cc_final: 0.8307 (mpp) REVERT: B 76 ILE cc_start: 0.9014 (mp) cc_final: 0.8562 (mp) REVERT: B 157 ASP cc_start: 0.7646 (t0) cc_final: 0.7399 (m-30) REVERT: B 215 LYS cc_start: 0.8383 (mttm) cc_final: 0.8063 (mtpp) REVERT: B 291 LYS cc_start: 0.8842 (tmmt) cc_final: 0.8206 (mptt) REVERT: B 313 MET cc_start: 0.8275 (tpt) cc_final: 0.8015 (tpt) REVERT: C 9 VAL cc_start: 0.9407 (t) cc_final: 0.9176 (m) REVERT: C 24 ASP cc_start: 0.7927 (OUTLIER) cc_final: 0.7396 (m-30) REVERT: C 72 GLU cc_start: 0.7873 (pm20) cc_final: 0.7619 (pm20) REVERT: C 283 MET cc_start: 0.8089 (mmm) cc_final: 0.7817 (mmm) REVERT: C 305 MET cc_start: 0.8692 (mmm) cc_final: 0.7970 (mpp) REVERT: C 371 HIS cc_start: 0.6918 (OUTLIER) cc_final: 0.6322 (m90) REVERT: D 249 THR cc_start: 0.8734 (m) cc_final: 0.8486 (p) REVERT: D 283 MET cc_start: 0.7833 (mmp) cc_final: 0.7491 (mmm) REVERT: D 355 MET cc_start: 0.8630 (mmm) cc_final: 0.8090 (mmt) REVERT: E 12 ASN cc_start: 0.8300 (p0) cc_final: 0.7985 (p0) REVERT: E 125 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7800 (mm-30) REVERT: E 217 CYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7631 (m) REVERT: E 249 THR cc_start: 0.8849 (m) cc_final: 0.8472 (p) REVERT: E 313 MET cc_start: 0.8508 (tpp) cc_final: 0.8304 (ttm) REVERT: E 314 GLN cc_start: 0.8435 (tm-30) cc_final: 0.8226 (tm-30) outliers start: 44 outliers final: 32 residues processed: 250 average time/residue: 0.0937 time to fit residues: 38.0352 Evaluate side-chains 237 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 201 time to evaluate : 0.597 ------------------------------------------------------------------------------- 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 83 GLU Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 143 TYR Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 30 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 260 THR Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain C residue 24 ASP 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 371 HIS 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 201 VAL 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 44 MET 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 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: 4.9990 chunk 138 optimal weight: 0.9980 chunk 152 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 125 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 164 optimal weight: 0.8980 chunk 159 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 108 optimal weight: 10.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN C 173 HIS C 371 HIS ** 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 = 0.3176 r_free = 0.3176 target = 0.098494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.087993 restraints weight = 25763.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.090861 restraints weight = 12719.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.092710 restraints weight = 7359.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.093969 restraints weight = 4749.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.094793 restraints weight = 3312.363| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.4893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 14620 Z= 0.109 Angle : 0.500 5.973 19860 Z= 0.260 Chirality : 0.043 0.145 2215 Planarity : 0.005 0.040 2525 Dihedral : 7.668 69.204 2130 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.35 % Allowed : 14.25 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.21), residues: 1775 helix: 0.90 (0.19), residues: 750 sheet: -0.14 (0.29), residues: 305 loop : 1.25 (0.25), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 116 TYR 0.008 0.001 TYR C 198 PHE 0.007 0.001 PHE A 262 TRP 0.012 0.001 TRP D 340 HIS 0.011 0.001 HIS C 371 Details of bonding type rmsd covalent geometry : bond 0.00258 (14620) covalent geometry : angle 0.49986 (19860) hydrogen bonds : bond 0.03001 ( 750) hydrogen bonds : angle 4.47491 ( 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 266 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 230 time to evaluate : 0.592 Fit side-chains revert: symmetry clash REVERT: A 64 ILE cc_start: 0.9071 (mm) cc_final: 0.8836 (pt) REVERT: A 72 GLU cc_start: 0.7400 (mt-10) cc_final: 0.6926 (mm-30) REVERT: A 191 LYS cc_start: 0.8497 (tttt) cc_final: 0.7780 (ttmm) REVERT: A 283 MET cc_start: 0.8376 (mmm) cc_final: 0.7853 (tpp) REVERT: A 305 MET cc_start: 0.8793 (mmm) cc_final: 0.8372 (mpp) REVERT: B 76 ILE cc_start: 0.9001 (mp) cc_final: 0.8601 (mp) REVERT: B 157 ASP cc_start: 0.7642 (t0) cc_final: 0.7386 (m-30) REVERT: B 215 LYS cc_start: 0.8312 (mttm) cc_final: 0.8070 (mtpp) REVERT: B 291 LYS cc_start: 0.8746 (tmmt) cc_final: 0.8235 (mptt) REVERT: C 9 VAL cc_start: 0.9387 (t) cc_final: 0.9154 (m) REVERT: C 72 GLU cc_start: 0.7871 (pm20) cc_final: 0.7622 (pm20) REVERT: C 283 MET cc_start: 0.8111 (mmm) cc_final: 0.7865 (mmm) REVERT: C 305 MET cc_start: 0.8613 (mmm) cc_final: 0.7947 (mpp) REVERT: C 371 HIS cc_start: 0.7207 (OUTLIER) cc_final: 0.6920 (m-70) REVERT: D 249 THR cc_start: 0.8751 (m) cc_final: 0.8515 (p) REVERT: D 283 MET cc_start: 0.7755 (mmp) cc_final: 0.7423 (mmm) REVERT: D 325 MET cc_start: 0.8551 (mmm) cc_final: 0.8275 (mmm) REVERT: D 355 MET cc_start: 0.8621 (mmm) cc_final: 0.8056 (mmt) REVERT: E 12 ASN cc_start: 0.8366 (p0) cc_final: 0.8035 (p0) REVERT: E 217 CYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7584 (m) REVERT: E 249 THR cc_start: 0.8831 (m) cc_final: 0.8449 (p) REVERT: E 283 MET cc_start: 0.8080 (mmm) cc_final: 0.7614 (mmp) outliers start: 36 outliers final: 28 residues processed: 256 average time/residue: 0.1048 time to fit residues: 42.3315 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 : 0.559 ------------------------------------------------------------------------------- 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 83 GLU Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 30 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 260 THR 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 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 143 TYR Chi-restraints excluded: chain D residue 148 THR 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 217 CYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 172 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 120 optimal weight: 0.6980 chunk 113 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 112 optimal weight: 0.6980 chunk 155 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN B 371 HIS C 41 GLN C 88 HIS C 92 ASN C 173 HIS ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.097445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.086641 restraints weight = 25443.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.089562 restraints weight = 12649.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.091464 restraints weight = 7391.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.092752 restraints weight = 4804.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.093656 restraints weight = 3376.062| |-----------------------------------------------------------------------------| r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.5052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 14620 Z= 0.156 Angle : 0.534 7.198 19860 Z= 0.276 Chirality : 0.044 0.183 2215 Planarity : 0.005 0.038 2525 Dihedral : 7.643 67.700 2130 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.94 % Allowed : 14.58 % Favored : 82.48 % 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: 1.13 (0.20), residues: 725 sheet: 0.01 (0.29), residues: 305 loop : 1.12 (0.25), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 147 TYR 0.010 0.001 TYR E 166 PHE 0.008 0.001 PHE A 262 TRP 0.013 0.002 TRP B 79 HIS 0.008 0.002 HIS B 275 Details of bonding type rmsd covalent geometry : bond 0.00373 (14620) covalent geometry : angle 0.53425 (19860) hydrogen bonds : bond 0.03192 ( 750) hydrogen bonds : angle 4.48359 ( 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 250 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 205 time to evaluate : 0.535 Fit side-chains revert: symmetry clash REVERT: A 57 GLU cc_start: 0.8437 (mm-30) cc_final: 0.8167 (mm-30) REVERT: A 64 ILE cc_start: 0.9107 (mm) cc_final: 0.8800 (pt) REVERT: A 72 GLU cc_start: 0.7425 (mt-10) cc_final: 0.6934 (mm-30) REVERT: A 89 THR cc_start: 0.8636 (OUTLIER) cc_final: 0.8293 (p) REVERT: A 191 LYS cc_start: 0.8568 (tttt) cc_final: 0.7807 (ttmm) REVERT: A 283 MET cc_start: 0.8367 (mmm) cc_final: 0.8081 (tpp) REVERT: A 305 MET cc_start: 0.8805 (mmm) cc_final: 0.8346 (mpp) REVERT: B 76 ILE cc_start: 0.9011 (mp) cc_final: 0.8598 (mp) REVERT: B 82 MET cc_start: 0.9027 (tpt) cc_final: 0.8559 (tpt) REVERT: B 157 ASP cc_start: 0.7797 (t0) cc_final: 0.7512 (m-30) REVERT: B 215 LYS cc_start: 0.8329 (mttm) cc_final: 0.8078 (mtpp) REVERT: B 291 LYS cc_start: 0.8773 (tmmt) cc_final: 0.8263 (mptt) REVERT: B 313 MET cc_start: 0.8475 (tpt) cc_final: 0.8055 (tpt) REVERT: C 24 ASP cc_start: 0.7844 (OUTLIER) cc_final: 0.7370 (m-30) REVERT: C 283 MET cc_start: 0.8122 (mmm) cc_final: 0.7843 (mmm) REVERT: C 305 MET cc_start: 0.8665 (mmm) cc_final: 0.7948 (mpp) REVERT: D 43 VAL cc_start: 0.5011 (OUTLIER) cc_final: 0.4792 (t) REVERT: D 148 THR cc_start: 0.8381 (OUTLIER) cc_final: 0.7916 (t) REVERT: D 249 THR cc_start: 0.8747 (m) cc_final: 0.8497 (p) REVERT: D 283 MET cc_start: 0.7678 (mmp) cc_final: 0.7375 (mmm) REVERT: D 313 MET cc_start: 0.8462 (ttm) cc_final: 0.7815 (ttt) REVERT: E 142 LEU cc_start: 0.9331 (tp) cc_final: 0.9045 (mp) REVERT: E 217 CYS cc_start: 0.7935 (OUTLIER) cc_final: 0.7554 (m) REVERT: E 249 THR cc_start: 0.8881 (m) cc_final: 0.8515 (p) REVERT: E 283 MET cc_start: 0.8121 (mmm) cc_final: 0.7654 (mmp) outliers start: 45 outliers final: 32 residues processed: 244 average time/residue: 0.1048 time to fit residues: 39.9692 Evaluate side-chains 232 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 195 time to evaluate : 0.549 ------------------------------------------------------------------------------- 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 83 GLU Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 349 LEU 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 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 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 D residue 30 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 224 GLU 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 43 VAL Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 217 CYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 173 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 153 optimal weight: 0.8980 chunk 170 optimal weight: 2.9990 chunk 104 optimal weight: 0.0470 chunk 131 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 113 optimal weight: 0.9990 chunk 162 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.7882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN C 88 HIS C 92 ASN C 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 = 0.3204 r_free = 0.3204 target = 0.100316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.089517 restraints weight = 25247.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.092461 restraints weight = 12549.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.094375 restraints weight = 7329.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.095676 restraints weight = 4760.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.096590 restraints weight = 3327.119| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.5232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.121 14620 Z= 0.105 Angle : 0.501 9.192 19860 Z= 0.257 Chirality : 0.043 0.140 2215 Planarity : 0.004 0.040 2525 Dihedral : 7.394 70.226 2130 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.29 % Allowed : 15.36 % 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: 1.33 (0.21), residues: 1775 helix: 1.25 (0.20), residues: 725 sheet: -0.10 (0.31), residues: 275 loop : 1.16 (0.25), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 147 TYR 0.009 0.001 TYR D 188 PHE 0.008 0.001 PHE E 262 TRP 0.011 0.001 TRP C 340 HIS 0.005 0.001 HIS B 275 Details of bonding type rmsd covalent geometry : bond 0.00258 (14620) covalent geometry : angle 0.50143 (19860) hydrogen bonds : bond 0.02831 ( 750) hydrogen bonds : angle 4.34438 ( 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 258 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 223 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 ILE cc_start: 0.9088 (mm) cc_final: 0.8868 (pt) REVERT: A 72 GLU cc_start: 0.7428 (mt-10) cc_final: 0.6955 (mm-30) REVERT: A 191 LYS cc_start: 0.8436 (tttt) cc_final: 0.7688 (ttmm) REVERT: A 283 MET cc_start: 0.8313 (mmm) cc_final: 0.8033 (mpp) REVERT: A 305 MET cc_start: 0.8784 (mmm) cc_final: 0.8385 (mpp) REVERT: B 76 ILE cc_start: 0.8991 (mp) cc_final: 0.8573 (mp) REVERT: B 78 ASN cc_start: 0.8782 (t0) cc_final: 0.8217 (t0) REVERT: B 157 ASP cc_start: 0.7736 (t0) cc_final: 0.7473 (m-30) REVERT: B 215 LYS cc_start: 0.8252 (mttm) cc_final: 0.8030 (mtpp) REVERT: B 283 MET cc_start: 0.7528 (mmt) cc_final: 0.7314 (mmt) REVERT: B 291 LYS cc_start: 0.8718 (tmmt) cc_final: 0.8284 (mptt) REVERT: B 313 MET cc_start: 0.8423 (tpt) cc_final: 0.7984 (tpt) REVERT: B 325 MET cc_start: 0.8604 (tpt) cc_final: 0.8393 (tpt) REVERT: B 352 PHE cc_start: 0.8976 (t80) cc_final: 0.8718 (t80) REVERT: B 355 MET cc_start: 0.8026 (mtt) cc_final: 0.7776 (mtt) REVERT: C 9 VAL cc_start: 0.9382 (t) cc_final: 0.9173 (m) REVERT: C 283 MET cc_start: 0.8054 (mmm) cc_final: 0.7822 (mmm) REVERT: C 305 MET cc_start: 0.8609 (mmm) cc_final: 0.7951 (mpp) REVERT: D 43 VAL cc_start: 0.5191 (OUTLIER) cc_final: 0.4949 (t) REVERT: D 249 THR cc_start: 0.8738 (m) cc_final: 0.8494 (p) REVERT: D 283 MET cc_start: 0.7665 (mmp) cc_final: 0.7225 (mmt) REVERT: E 12 ASN cc_start: 0.8198 (p0) cc_final: 0.7907 (p0) REVERT: E 142 LEU cc_start: 0.9272 (tp) cc_final: 0.8997 (mp) REVERT: E 217 CYS cc_start: 0.7946 (OUTLIER) cc_final: 0.7619 (m) REVERT: E 249 THR cc_start: 0.8861 (m) cc_final: 0.8495 (p) REVERT: E 283 MET cc_start: 0.8116 (mmm) cc_final: 0.7671 (mmp) REVERT: E 314 GLN cc_start: 0.8321 (tm-30) cc_final: 0.7701 (tm-30) REVERT: E 325 MET cc_start: 0.8289 (tpp) cc_final: 0.7671 (tpp) outliers start: 35 outliers final: 22 residues processed: 252 average time/residue: 0.1005 time to fit residues: 40.7507 Evaluate side-chains 226 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 202 time to evaluate : 0.573 ------------------------------------------------------------------------------- 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 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 89 THR Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 89 THR 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 217 CYS Chi-restraints excluded: chain E residue 235 SER Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 174 optimal weight: 0.7980 chunk 88 optimal weight: 0.9980 chunk 137 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 129 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 31 optimal weight: 8.9990 chunk 98 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 158 optimal weight: 9.9990 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 353 GLN C 92 ASN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 173 HIS ** 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 = 0.3175 r_free = 0.3175 target = 0.098490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.087713 restraints weight = 25461.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.090635 restraints weight = 12714.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.092549 restraints weight = 7429.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.093771 restraints weight = 4821.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.094686 restraints weight = 3424.841| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.5325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.132 14620 Z= 0.145 Angle : 0.539 8.689 19860 Z= 0.275 Chirality : 0.044 0.141 2215 Planarity : 0.004 0.039 2525 Dihedral : 7.398 67.683 2130 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.16 % Allowed : 16.14 % Favored : 81.70 % 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 (0.21), residues: 1775 helix: 1.34 (0.20), residues: 725 sheet: 0.04 (0.29), residues: 305 loop : 1.14 (0.25), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 147 TYR 0.008 0.001 TYR C 166 PHE 0.008 0.001 PHE A 262 TRP 0.012 0.001 TRP B 79 HIS 0.006 0.001 HIS B 275 Details of bonding type rmsd covalent geometry : bond 0.00357 (14620) covalent geometry : angle 0.53855 (19860) hydrogen bonds : bond 0.03093 ( 750) hydrogen bonds : angle 4.41038 ( 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 248 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 215 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 ASN cc_start: 0.7950 (t0) cc_final: 0.7731 (t0) REVERT: A 64 ILE cc_start: 0.9161 (mm) cc_final: 0.8819 (pt) REVERT: A 72 GLU cc_start: 0.7427 (mt-10) cc_final: 0.6960 (mm-30) REVERT: A 191 LYS cc_start: 0.8495 (tttt) cc_final: 0.7726 (ttmm) REVERT: A 305 MET cc_start: 0.8820 (mmm) cc_final: 0.8379 (mpp) REVERT: A 325 MET cc_start: 0.7928 (tpp) cc_final: 0.7261 (tpp) REVERT: B 76 ILE cc_start: 0.8960 (mp) cc_final: 0.8523 (mp) REVERT: B 78 ASN cc_start: 0.8745 (t0) cc_final: 0.8177 (t0) REVERT: B 82 MET cc_start: 0.9054 (tpt) cc_final: 0.8643 (tpt) REVERT: B 157 ASP cc_start: 0.7799 (t0) cc_final: 0.7534 (m-30) REVERT: B 215 LYS cc_start: 0.8265 (mttm) cc_final: 0.8044 (mtpp) REVERT: B 283 MET cc_start: 0.7555 (mmt) cc_final: 0.7348 (mmt) REVERT: B 291 LYS cc_start: 0.8727 (tmmt) cc_final: 0.8248 (mptt) REVERT: B 313 MET cc_start: 0.8453 (tpt) cc_final: 0.8023 (tpt) REVERT: B 352 PHE cc_start: 0.8991 (t80) cc_final: 0.8765 (t80) REVERT: C 9 VAL cc_start: 0.9421 (t) cc_final: 0.9202 (m) REVERT: C 305 MET cc_start: 0.8673 (mmm) cc_final: 0.7966 (mpp) REVERT: D 43 VAL cc_start: 0.5391 (OUTLIER) cc_final: 0.5176 (t) REVERT: D 81 ASP cc_start: 0.6533 (m-30) cc_final: 0.6309 (m-30) REVERT: D 148 THR cc_start: 0.8553 (OUTLIER) cc_final: 0.8170 (t) REVERT: D 249 THR cc_start: 0.8750 (m) cc_final: 0.8478 (p) REVERT: D 283 MET cc_start: 0.7721 (mmp) cc_final: 0.7464 (mmt) REVERT: E 142 LEU cc_start: 0.9283 (tp) cc_final: 0.8964 (mp) REVERT: E 217 CYS cc_start: 0.7916 (m) cc_final: 0.7629 (m) REVERT: E 249 THR cc_start: 0.8905 (m) cc_final: 0.8584 (p) REVERT: E 283 MET cc_start: 0.8174 (mmm) cc_final: 0.7950 (mmm) REVERT: E 325 MET cc_start: 0.8231 (tpp) cc_final: 0.7510 (tpp) outliers start: 33 outliers final: 27 residues processed: 241 average time/residue: 0.0984 time to fit residues: 38.5845 Evaluate side-chains 228 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 199 time to evaluate : 0.541 ------------------------------------------------------------------------------- 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 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 44 MET 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 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 106 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 235 SER Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 288 ASP 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: 5.9990 chunk 120 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 179 optimal weight: 0.5980 chunk 153 optimal weight: 0.9990 chunk 165 optimal weight: 4.9990 chunk 159 optimal weight: 4.9990 chunk 176 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 162 ASN ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 HIS ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 173 HIS ** 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 = 0.3136 r_free = 0.3136 target = 0.095986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.085235 restraints weight = 25751.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.088095 restraints weight = 12788.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.089953 restraints weight = 7490.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.091217 restraints weight = 4890.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.092080 restraints weight = 3452.205| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.5393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.120 14620 Z= 0.189 Angle : 0.575 9.942 19860 Z= 0.294 Chirality : 0.045 0.154 2215 Planarity : 0.005 0.041 2525 Dihedral : 7.482 67.748 2130 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.55 % Allowed : 16.01 % Favored : 81.44 % 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: 1.20 (0.21), residues: 1775 helix: 1.25 (0.20), residues: 725 sheet: -0.19 (0.29), residues: 300 loop : 1.02 (0.24), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 147 TYR 0.010 0.001 TYR A 279 PHE 0.012 0.001 PHE A 262 TRP 0.014 0.002 TRP B 79 HIS 0.007 0.002 HIS C 88 Details of bonding type rmsd covalent geometry : bond 0.00454 (14620) covalent geometry : angle 0.57464 (19860) hydrogen bonds : bond 0.03344 ( 750) hydrogen bonds : angle 4.52186 ( 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 252 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 213 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 THR cc_start: 0.8640 (OUTLIER) cc_final: 0.8280 (p) REVERT: A 191 LYS cc_start: 0.8536 (tttt) cc_final: 0.7805 (ttmm) REVERT: A 325 MET cc_start: 0.7925 (tpp) cc_final: 0.7468 (tpp) REVERT: B 76 ILE cc_start: 0.8975 (mp) cc_final: 0.8576 (mp) REVERT: B 78 ASN cc_start: 0.8740 (t0) cc_final: 0.8165 (t0) REVERT: B 82 MET cc_start: 0.9011 (tpt) cc_final: 0.8524 (tpt) REVERT: B 157 ASP cc_start: 0.7807 (t0) cc_final: 0.7536 (m-30) REVERT: B 215 LYS cc_start: 0.8252 (mttm) cc_final: 0.8023 (mtpp) REVERT: B 283 MET cc_start: 0.7579 (mmt) cc_final: 0.7337 (mmt) REVERT: B 291 LYS cc_start: 0.8771 (tmmt) cc_final: 0.8321 (mptt) REVERT: B 313 MET cc_start: 0.8467 (tpt) cc_final: 0.8068 (tpt) REVERT: B 325 MET cc_start: 0.8598 (tpt) cc_final: 0.7866 (tpt) REVERT: B 352 PHE cc_start: 0.8999 (t80) cc_final: 0.8778 (t80) REVERT: C 9 VAL cc_start: 0.9432 (t) cc_final: 0.9216 (m) REVERT: C 24 ASP cc_start: 0.7844 (OUTLIER) cc_final: 0.7333 (m-30) REVERT: C 143 TYR cc_start: 0.8018 (OUTLIER) cc_final: 0.7554 (t80) REVERT: C 305 MET cc_start: 0.8717 (mmm) cc_final: 0.7978 (mpp) REVERT: D 43 VAL cc_start: 0.5396 (OUTLIER) cc_final: 0.5191 (t) REVERT: D 148 THR cc_start: 0.8588 (OUTLIER) cc_final: 0.8254 (t) REVERT: D 162 ASN cc_start: 0.8303 (m-40) cc_final: 0.8094 (m-40) REVERT: D 249 THR cc_start: 0.8711 (m) cc_final: 0.8444 (p) REVERT: D 283 MET cc_start: 0.7786 (mmp) cc_final: 0.7431 (mmm) REVERT: E 12 ASN cc_start: 0.8184 (p0) cc_final: 0.7980 (p0) REVERT: E 142 LEU cc_start: 0.9313 (tp) cc_final: 0.8999 (mp) REVERT: E 217 CYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7608 (m) REVERT: E 249 THR cc_start: 0.8944 (m) cc_final: 0.8668 (p) REVERT: E 283 MET cc_start: 0.8208 (mmm) cc_final: 0.7729 (mmp) REVERT: E 325 MET cc_start: 0.8200 (tpp) cc_final: 0.7962 (mmm) outliers start: 39 outliers final: 30 residues processed: 245 average time/residue: 0.0962 time to fit residues: 38.4537 Evaluate side-chains 235 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 199 time to evaluate : 0.580 ------------------------------------------------------------------------------- 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 44 MET 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 323 SER 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 88 HIS Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 143 TYR Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 224 GLU 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 148 THR Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 235 SER Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 106 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 103 optimal weight: 0.5980 chunk 141 optimal weight: 4.9990 chunk 163 optimal weight: 3.9990 chunk 174 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 chunk 144 optimal weight: 10.0000 chunk 42 optimal weight: 0.0670 chunk 154 optimal weight: 6.9990 overall best weight: 0.6922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN C 59 GLN C 173 HIS D 12 ASN D 296 ASN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 173 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.100154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.089507 restraints weight = 25327.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.092408 restraints weight = 12405.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.094292 restraints weight = 7199.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.095519 restraints weight = 4664.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.096415 restraints weight = 3295.195| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.5545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.139 14620 Z= 0.107 Angle : 0.522 9.891 19860 Z= 0.268 Chirality : 0.043 0.145 2215 Planarity : 0.004 0.040 2525 Dihedral : 7.256 71.117 2130 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.96 % Allowed : 16.93 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.35 (0.21), residues: 1775 helix: 1.34 (0.20), residues: 725 sheet: -0.14 (0.29), residues: 310 loop : 1.18 (0.25), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 210 TYR 0.015 0.001 TYR A 279 PHE 0.016 0.001 PHE C 223 TRP 0.013 0.001 TRP E 356 HIS 0.005 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00268 (14620) covalent geometry : angle 0.52229 (19860) hydrogen bonds : bond 0.02820 ( 750) hydrogen bonds : angle 4.38265 ( 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 253 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 223 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 GLU cc_start: 0.7471 (mt-10) cc_final: 0.6952 (mm-30) REVERT: A 191 LYS cc_start: 0.8466 (tttt) cc_final: 0.7656 (ttmm) REVERT: A 325 MET cc_start: 0.7864 (tpp) cc_final: 0.7234 (tpp) REVERT: B 51 ASP cc_start: 0.7366 (p0) cc_final: 0.7062 (p0) REVERT: B 76 ILE cc_start: 0.8932 (mp) cc_final: 0.8515 (mp) REVERT: B 78 ASN cc_start: 0.8718 (t0) cc_final: 0.8188 (t0) REVERT: B 157 ASP cc_start: 0.7773 (t0) cc_final: 0.7515 (m-30) REVERT: B 291 LYS cc_start: 0.8705 (tmmt) cc_final: 0.8258 (mptt) REVERT: B 313 MET cc_start: 0.8470 (tpt) cc_final: 0.8055 (tpt) REVERT: B 325 MET cc_start: 0.8540 (tpt) cc_final: 0.7872 (tpt) REVERT: B 352 PHE cc_start: 0.8931 (t80) cc_final: 0.8695 (t80) REVERT: C 9 VAL cc_start: 0.9387 (t) cc_final: 0.9174 (m) REVERT: C 305 MET cc_start: 0.8593 (mmm) cc_final: 0.7917 (mpp) REVERT: C 333 PRO cc_start: 0.8337 (Cg_exo) cc_final: 0.8131 (Cg_endo) REVERT: D 43 VAL cc_start: 0.5367 (OUTLIER) cc_final: 0.5163 (t) REVERT: D 148 THR cc_start: 0.8561 (OUTLIER) cc_final: 0.8237 (t) REVERT: D 221 LEU cc_start: 0.8876 (tp) cc_final: 0.8659 (tt) REVERT: D 227 MET cc_start: 0.8447 (tpp) cc_final: 0.7856 (mmt) REVERT: D 249 THR cc_start: 0.8712 (m) cc_final: 0.8458 (p) REVERT: D 283 MET cc_start: 0.7795 (mmp) cc_final: 0.7315 (mmm) REVERT: E 12 ASN cc_start: 0.8140 (p0) cc_final: 0.7916 (p0) REVERT: E 82 MET cc_start: 0.8937 (tpt) cc_final: 0.8473 (tpt) REVERT: E 191 LYS cc_start: 0.9035 (tttt) cc_final: 0.8767 (tttp) REVERT: E 217 CYS cc_start: 0.7942 (OUTLIER) cc_final: 0.7609 (m) REVERT: E 249 THR cc_start: 0.8923 (m) cc_final: 0.8637 (p) REVERT: E 283 MET cc_start: 0.8194 (mmm) cc_final: 0.7984 (mmm) REVERT: E 325 MET cc_start: 0.8192 (tpp) cc_final: 0.7977 (mmm) outliers start: 30 outliers final: 26 residues processed: 244 average time/residue: 0.0981 time to fit residues: 38.4840 Evaluate side-chains 237 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 208 time to evaluate : 0.570 ------------------------------------------------------------------------------- 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 298 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain C residue 30 VAL 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 D residue 30 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 235 SER Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 154 optimal weight: 0.9980 chunk 122 optimal weight: 7.9990 chunk 102 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 144 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN C 59 GLN ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 HIS ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 173 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.098583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.087905 restraints weight = 25353.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.090823 restraints weight = 12533.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.092656 restraints weight = 7273.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.093946 restraints weight = 4754.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.094794 restraints weight = 3326.655| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.5565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.131 14620 Z= 0.132 Angle : 0.541 9.516 19860 Z= 0.278 Chirality : 0.044 0.159 2215 Planarity : 0.004 0.040 2525 Dihedral : 7.251 70.633 2130 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.09 % Allowed : 17.12 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.21), residues: 1775 helix: 1.37 (0.20), residues: 720 sheet: -0.01 (0.30), residues: 305 loop : 1.10 (0.25), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 147 TYR 0.012 0.001 TYR A 279 PHE 0.019 0.001 PHE C 223 TRP 0.012 0.001 TRP C 340 HIS 0.005 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00326 (14620) covalent geometry : angle 0.54106 (19860) hydrogen bonds : bond 0.02975 ( 750) hydrogen bonds : angle 4.40736 ( 1935) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2071.35 seconds wall clock time: 37 minutes 0.12 seconds (2220.12 seconds total)