Starting phenix.real_space_refine on Tue Nov 18 14:29:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6fhl_4259/11_2025/6fhl_4259.cif Found real_map, /net/cci-nas-00/data/ceres_data/6fhl_4259/11_2025/6fhl_4259.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6fhl_4259/11_2025/6fhl_4259.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6fhl_4259/11_2025/6fhl_4259.map" model { file = "/net/cci-nas-00/data/ceres_data/6fhl_4259/11_2025/6fhl_4259.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6fhl_4259/11_2025/6fhl_4259.cif" } resolution = 3.3 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= 0.015 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 105 5.16 5 C 9235 2.51 5 N 2470 2.21 5 O 2835 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 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: 14665 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} 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: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Restraints were copied for chains: B, C, D, E Time building chain proxies: 2.72, per 1000 atoms: 0.19 Number of scatterers: 14665 At special positions: 0 Unit cell: (96.8, 92.4, 187, 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 105 16.00 P 15 15.00 Mg 5 11.99 O 2835 8.00 N 2470 7.00 C 9235 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: 1.26 Conformation dependent library (CDL) restraints added in 693.0 milliseconds 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3430 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 30 sheets defined 52.8% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 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: 3.905A 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 197 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 261 through 262 No H-bonds generated for 'chain 'A' and resid 261 through 262' Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 273 through 285 Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 289 through 295 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 Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.735A pdb=" N LYS A 373 " --> pdb=" O ILE A 369 " (cutoff:3.500A) 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: 3.905A 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 197 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 261 through 262 No H-bonds generated for 'chain 'B' and resid 261 through 262' Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 273 through 285 Processing helix chain 'B' and resid 286 through 288 No H-bonds generated for 'chain 'B' and resid 286 through 288' Processing helix chain 'B' and resid 289 through 295 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 Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 368 through 373 removed outlier: 3.735A pdb=" N LYS B 373 " --> pdb=" O ILE B 369 " (cutoff:3.500A) 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: 3.906A 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 197 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 261 through 262 No H-bonds generated for 'chain 'C' and resid 261 through 262' Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 285 Processing helix chain 'C' and resid 286 through 288 No H-bonds generated for 'chain 'C' and resid 286 through 288' Processing helix chain 'C' and resid 289 through 295 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 Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.735A pdb=" N LYS C 373 " --> pdb=" O ILE C 369 " (cutoff:3.500A) 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: 3.905A 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 197 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 261 through 262 No H-bonds generated for 'chain 'D' and resid 261 through 262' Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 273 through 285 Processing helix chain 'D' and resid 286 through 288 No H-bonds generated for 'chain 'D' and resid 286 through 288' Processing helix chain 'D' and resid 289 through 295 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 Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 368 through 373 removed outlier: 3.736A pdb=" N LYS D 373 " --> pdb=" O ILE D 369 " (cutoff:3.500A) 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: 3.906A 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 197 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 261 through 262 No H-bonds generated for 'chain 'E' and resid 261 through 262' Processing helix chain 'E' and resid 263 through 268 Processing helix chain 'E' and resid 273 through 285 Processing helix chain 'E' and resid 286 through 288 No H-bonds generated for 'chain 'E' and resid 286 through 288' Processing helix chain 'E' and resid 289 through 295 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 Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 368 through 373 removed outlier: 3.734A pdb=" N LYS E 373 " --> pdb=" O ILE E 369 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 4.148A pdb=" N THR A 106 " --> pdb=" O CYS A 10 " (cutoff:3.500A) removed outlier: 5.329A 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 Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 240 Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 32 removed outlier: 4.148A pdb=" N THR B 106 " --> pdb=" O CYS B 10 " (cutoff:3.500A) removed outlier: 5.329A 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 Processing sheet with id=AB3, first strand: chain 'B' and resid 238 through 240 Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 32 removed outlier: 4.148A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 5.329A 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 Processing sheet with id=AB9, first strand: chain 'C' and resid 238 through 240 Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 32 removed outlier: 4.148A pdb=" N THR D 106 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 5.330A 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 Processing sheet with id=AC6, first strand: chain 'D' and resid 238 through 240 Processing sheet with id=AC7, first strand: chain 'E' and resid 29 through 32 removed outlier: 4.148A pdb=" N THR E 106 " --> pdb=" O CYS E 10 " (cutoff:3.500A) removed outlier: 5.329A 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 Processing sheet with id=AD3, first strand: chain 'E' and resid 238 through 240 805 hydrogen bonds defined for protein. 2025 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: 2.88 Time building geometry restraints manager: 1.65 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: 3476 1.32 - 1.44: 3303 1.44 - 1.56: 8006 1.56 - 1.68: 10 1.68 - 1.80: 185 Bond restraints: 14980 Sorted by residual: bond pdb=" CA ILE C 151 " pdb=" C ILE C 151 " ideal model delta sigma weight residual 1.523 1.466 0.057 1.26e-02 6.30e+03 2.07e+01 bond pdb=" CA ILE E 151 " pdb=" C ILE E 151 " ideal model delta sigma weight residual 1.523 1.466 0.057 1.26e-02 6.30e+03 2.05e+01 bond pdb=" CA ILE A 151 " pdb=" C ILE A 151 " ideal model delta sigma weight residual 1.523 1.467 0.056 1.26e-02 6.30e+03 1.99e+01 bond pdb=" CA ILE D 151 " pdb=" C ILE D 151 " ideal model delta sigma weight residual 1.523 1.467 0.056 1.26e-02 6.30e+03 1.99e+01 bond pdb=" CA ILE B 151 " pdb=" C ILE B 151 " ideal model delta sigma weight residual 1.523 1.467 0.056 1.26e-02 6.30e+03 1.97e+01 ... (remaining 14975 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 17331 2.01 - 4.02: 2401 4.02 - 6.03: 448 6.03 - 8.04: 101 8.04 - 10.05: 54 Bond angle restraints: 20335 Sorted by residual: angle pdb=" C ALA D 331 " pdb=" N PRO D 332 " pdb=" CA PRO D 332 " ideal model delta sigma weight residual 119.66 126.92 -7.26 7.20e-01 1.93e+00 1.02e+02 angle pdb=" C ALA B 331 " pdb=" N PRO B 332 " pdb=" CA PRO B 332 " ideal model delta sigma weight residual 119.66 126.91 -7.25 7.20e-01 1.93e+00 1.01e+02 angle pdb=" C ALA A 331 " pdb=" N PRO A 332 " pdb=" CA PRO A 332 " ideal model delta sigma weight residual 119.66 126.89 -7.23 7.20e-01 1.93e+00 1.01e+02 angle pdb=" C ALA C 331 " pdb=" N PRO C 332 " pdb=" CA PRO C 332 " ideal model delta sigma weight residual 119.66 126.88 -7.22 7.20e-01 1.93e+00 1.01e+02 angle pdb=" C ALA E 331 " pdb=" N PRO E 332 " pdb=" CA PRO E 332 " ideal model delta sigma weight residual 119.66 126.88 -7.22 7.20e-01 1.93e+00 1.01e+02 ... (remaining 20330 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.17: 8805 30.17 - 60.34: 150 60.34 - 90.51: 30 90.51 - 120.68: 0 120.68 - 150.85: 10 Dihedral angle restraints: 8995 sinusoidal: 3635 harmonic: 5360 Sorted by residual: dihedral pdb=" O1B ADP D 401 " pdb=" O3A ADP D 401 " pdb=" PB ADP D 401 " pdb=" PA ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 90.85 -150.85 1 2.00e+01 2.50e-03 4.50e+01 dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 90.82 -150.82 1 2.00e+01 2.50e-03 4.50e+01 dihedral pdb=" O1B ADP E 401 " pdb=" O3A ADP E 401 " pdb=" PB ADP E 401 " pdb=" PA ADP E 401 " ideal model delta sinusoidal sigma weight residual -60.00 90.82 -150.82 1 2.00e+01 2.50e-03 4.50e+01 ... (remaining 8992 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 946 0.051 - 0.101: 821 0.101 - 0.152: 368 0.152 - 0.203: 90 0.203 - 0.253: 30 Chirality restraints: 2255 Sorted by residual: chirality pdb=" CA PRO D 32 " pdb=" N PRO D 32 " pdb=" C PRO D 32 " pdb=" CB PRO D 32 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA PRO E 32 " pdb=" N PRO E 32 " pdb=" C PRO E 32 " pdb=" CB PRO E 32 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CA PRO C 32 " pdb=" N PRO C 32 " pdb=" C PRO C 32 " pdb=" CB PRO C 32 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 2252 not shown) Planarity restraints: 2595 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 163 " -0.085 5.00e-02 4.00e+02 1.30e-01 2.70e+01 pdb=" N PRO A 164 " 0.225 5.00e-02 4.00e+02 pdb=" CA PRO A 164 " -0.073 5.00e-02 4.00e+02 pdb=" CD PRO A 164 " -0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 163 " 0.085 5.00e-02 4.00e+02 1.30e-01 2.69e+01 pdb=" N PRO B 164 " -0.224 5.00e-02 4.00e+02 pdb=" CA PRO B 164 " 0.073 5.00e-02 4.00e+02 pdb=" CD PRO B 164 " 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 163 " -0.085 5.00e-02 4.00e+02 1.30e-01 2.69e+01 pdb=" N PRO C 164 " 0.224 5.00e-02 4.00e+02 pdb=" CA PRO C 164 " -0.073 5.00e-02 4.00e+02 pdb=" CD PRO C 164 " -0.066 5.00e-02 4.00e+02 ... (remaining 2592 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 43 2.57 - 3.15: 13758 3.15 - 3.73: 23332 3.73 - 4.32: 35478 4.32 - 4.90: 55562 Nonbonded interactions: 128173 Sorted by model distance: nonbonded pdb="MG MG C 402 " pdb=" O3 PO4 C 403 " model vdw 1.986 2.170 nonbonded pdb="MG MG B 402 " pdb=" O3 PO4 B 403 " model vdw 1.986 2.170 nonbonded pdb="MG MG A 402 " pdb=" O3 PO4 A 403 " model vdw 1.986 2.170 nonbonded pdb="MG MG E 402 " pdb=" O3 PO4 E 403 " model vdw 1.986 2.170 nonbonded pdb="MG MG D 402 " pdb=" O3 PO4 D 403 " model vdw 1.987 2.170 ... (remaining 128168 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: 0.05 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.740 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 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 : 0.018 0.083 14980 Z= 1.135 Angle : 1.586 10.050 20335 Z= 1.024 Chirality : 0.083 0.253 2255 Planarity : 0.017 0.130 2595 Dihedral : 13.072 150.851 5565 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 2.19 % Allowed : 5.46 % Favored : 92.35 % 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: -1.84 (0.18), residues: 1830 helix: -1.41 (0.14), residues: 780 sheet: -1.14 (0.31), residues: 225 loop : -0.85 (0.24), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 256 TYR 0.020 0.004 TYR B 198 PHE 0.013 0.002 PHE E 375 TRP 0.034 0.008 TRP E 340 HIS 0.005 0.002 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.01777 (14980) covalent geometry : angle 1.58645 (20335) hydrogen bonds : bond 0.16539 ( 795) hydrogen bonds : angle 7.74440 ( 2025) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 502 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.6253 (tpt) cc_final: 0.5784 (tpt) REVERT: A 68 LYS cc_start: 0.8783 (mmtt) cc_final: 0.8467 (mmtm) REVERT: A 132 MET cc_start: 0.8124 (tmm) cc_final: 0.7855 (ttt) REVERT: A 165 ILE cc_start: 0.9379 (mt) cc_final: 0.9135 (mt) REVERT: A 206 ARG cc_start: 0.8222 (ttm170) cc_final: 0.7635 (ttp80) REVERT: A 328 LYS cc_start: 0.8514 (tttt) cc_final: 0.8254 (tptt) REVERT: B 47 MET cc_start: 0.2763 (tpt) cc_final: 0.2269 (tpt) REVERT: B 184 ASP cc_start: 0.7650 (m-30) cc_final: 0.7290 (m-30) REVERT: B 191 LYS cc_start: 0.8486 (tttm) cc_final: 0.8141 (ttmm) REVERT: B 205 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7551 (mt-10) REVERT: B 325 MET cc_start: 0.7776 (mmp) cc_final: 0.7575 (mmt) REVERT: C 118 LYS cc_start: 0.8656 (tppt) cc_final: 0.8368 (mttt) REVERT: C 132 MET cc_start: 0.8404 (tmm) cc_final: 0.8190 (ttp) REVERT: C 191 LYS cc_start: 0.8199 (tttm) cc_final: 0.7881 (tttp) REVERT: C 206 ARG cc_start: 0.8036 (ttm170) cc_final: 0.7833 (ttp80) REVERT: C 214 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7869 (mt-10) REVERT: C 344 SER cc_start: 0.8766 (t) cc_final: 0.8338 (p) REVERT: D 113 LYS cc_start: 0.8746 (mttt) cc_final: 0.8474 (mmtt) REVERT: D 123 MET cc_start: 0.8611 (mmp) cc_final: 0.8361 (mmm) REVERT: D 132 MET cc_start: 0.8488 (tmm) cc_final: 0.8240 (ttp) REVERT: D 171 LEU cc_start: 0.9320 (mt) cc_final: 0.9072 (mt) REVERT: D 291 LYS cc_start: 0.8842 (tttt) cc_final: 0.8571 (ttpt) REVERT: E 66 THR cc_start: 0.8894 (m) cc_final: 0.8521 (p) REVERT: E 82 MET cc_start: 0.8315 (tpt) cc_final: 0.8079 (tpt) REVERT: E 132 MET cc_start: 0.8215 (tmm) cc_final: 0.8004 (ttp) REVERT: E 328 LYS cc_start: 0.8747 (tttt) cc_final: 0.8504 (ttpp) outliers start: 0 outliers final: 0 residues processed: 502 average time/residue: 0.1366 time to fit residues: 97.4902 Evaluate side-chains 254 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.123790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.108122 restraints weight = 19303.018| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.99 r_work: 0.3092 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14980 Z= 0.167 Angle : 0.700 8.351 20335 Z= 0.355 Chirality : 0.047 0.222 2255 Planarity : 0.008 0.066 2595 Dihedral : 12.603 169.189 2085 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.27 % Allowed : 1.97 % Favored : 97.76 % Rotamer: Outliers : 1.02 % Allowed : 9.52 % Favored : 89.46 % 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: -0.44 (0.20), residues: 1830 helix: 0.16 (0.18), residues: 785 sheet: -1.01 (0.30), residues: 295 loop : -0.26 (0.24), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 206 TYR 0.017 0.001 TYR A 306 PHE 0.009 0.001 PHE D 352 TRP 0.012 0.002 TRP C 340 HIS 0.006 0.001 HIS D 101 Details of bonding type rmsd covalent geometry : bond 0.00376 (14980) covalent geometry : angle 0.69989 (20335) hydrogen bonds : bond 0.04375 ( 795) hydrogen bonds : angle 5.51729 ( 2025) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 320 time to evaluate : 0.681 Fit side-chains REVERT: A 47 MET cc_start: 0.6238 (tpt) cc_final: 0.5688 (tpt) REVERT: A 50 LYS cc_start: 0.8117 (mttt) cc_final: 0.7508 (mmtt) REVERT: A 68 LYS cc_start: 0.8894 (mmtt) cc_final: 0.8575 (mmtp) REVERT: A 118 LYS cc_start: 0.8131 (tppt) cc_final: 0.7795 (mtmt) REVERT: A 151 ILE cc_start: 0.9062 (OUTLIER) cc_final: 0.8733 (tp) REVERT: A 221 LEU cc_start: 0.8490 (tt) cc_final: 0.8253 (tp) REVERT: A 296 ASN cc_start: 0.9003 (m-40) cc_final: 0.8451 (m-40) REVERT: A 315 LYS cc_start: 0.8461 (tttm) cc_final: 0.8182 (tttm) REVERT: A 325 MET cc_start: 0.7967 (mmp) cc_final: 0.7733 (mmt) REVERT: A 328 LYS cc_start: 0.8298 (tttt) cc_final: 0.7831 (tptt) REVERT: A 334 GLU cc_start: 0.6851 (tp30) cc_final: 0.6560 (tp30) REVERT: A 355 MET cc_start: 0.7986 (mmm) cc_final: 0.7159 (mtt) REVERT: A 360 GLN cc_start: 0.8493 (tp40) cc_final: 0.8119 (mm-40) REVERT: B 143 TYR cc_start: 0.8875 (m-80) cc_final: 0.8636 (m-80) REVERT: B 184 ASP cc_start: 0.8039 (m-30) cc_final: 0.7579 (m-30) REVERT: B 334 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7777 (mm-30) REVERT: B 353 GLN cc_start: 0.7644 (mm-40) cc_final: 0.7345 (mp10) REVERT: C 83 GLU cc_start: 0.8359 (tm-30) cc_final: 0.8080 (tm-30) REVERT: C 118 LYS cc_start: 0.8362 (tppt) cc_final: 0.7947 (mttt) REVERT: C 225 ASN cc_start: 0.8392 (m-40) cc_final: 0.8143 (m-40) REVERT: C 325 MET cc_start: 0.8510 (mmp) cc_final: 0.8268 (mmm) REVERT: D 80 ASP cc_start: 0.8142 (m-30) cc_final: 0.7729 (t0) REVERT: D 113 LYS cc_start: 0.8418 (mttt) cc_final: 0.8094 (mmtt) REVERT: D 123 MET cc_start: 0.8961 (mmp) cc_final: 0.8628 (mmm) REVERT: D 291 LYS cc_start: 0.8582 (tttt) cc_final: 0.8351 (ttpt) REVERT: D 328 LYS cc_start: 0.8853 (tttt) cc_final: 0.8507 (ttpp) REVERT: D 355 MET cc_start: 0.8130 (mmm) cc_final: 0.7787 (mmt) REVERT: E 66 THR cc_start: 0.8740 (m) cc_final: 0.8423 (p) REVERT: E 82 MET cc_start: 0.8419 (tpt) cc_final: 0.8052 (tpt) REVERT: E 132 MET cc_start: 0.8821 (tmm) cc_final: 0.8560 (ttp) REVERT: E 169 TYR cc_start: 0.9157 (m-80) cc_final: 0.8924 (m-80) REVERT: E 191 LYS cc_start: 0.8521 (tttm) cc_final: 0.8192 (ttmm) REVERT: E 192 ILE cc_start: 0.8989 (mm) cc_final: 0.8570 (pt) REVERT: E 207 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7852 (tt0) REVERT: E 259 GLU cc_start: 0.8274 (tp30) cc_final: 0.7931 (tt0) REVERT: E 311 ASP cc_start: 0.8515 (m-30) cc_final: 0.8301 (m-30) REVERT: E 315 LYS cc_start: 0.8443 (tttm) cc_final: 0.8177 (ttmm) REVERT: E 328 LYS cc_start: 0.8877 (tttt) cc_final: 0.8411 (ttpt) outliers start: 16 outliers final: 9 residues processed: 330 average time/residue: 0.1214 time to fit residues: 60.1527 Evaluate side-chains 263 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 252 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 207 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 0 optimal weight: 8.9990 chunk 36 optimal weight: 8.9990 chunk 87 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 chunk 175 optimal weight: 2.9990 chunk 111 optimal weight: 7.9990 chunk 84 optimal weight: 1.9990 chunk 176 optimal weight: 0.8980 chunk 164 optimal weight: 0.7980 chunk 116 optimal weight: 4.9990 chunk 83 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 HIS B 296 ASN C 12 ASN C 161 HIS D 12 ASN D 87 HIS D 161 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.120626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.104827 restraints weight = 19773.833| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.01 r_work: 0.3056 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14980 Z= 0.160 Angle : 0.637 9.120 20335 Z= 0.311 Chirality : 0.046 0.230 2255 Planarity : 0.005 0.051 2595 Dihedral : 12.077 179.957 2085 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.27 % Allowed : 1.91 % Favored : 97.81 % Rotamer: Outliers : 1.73 % Allowed : 11.37 % Favored : 86.90 % 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: 0.22 (0.20), residues: 1830 helix: 0.61 (0.18), residues: 790 sheet: -0.79 (0.31), residues: 285 loop : 0.26 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 28 TYR 0.015 0.001 TYR A 306 PHE 0.027 0.001 PHE A 352 TRP 0.011 0.002 TRP C 340 HIS 0.005 0.001 HIS C 88 Details of bonding type rmsd covalent geometry : bond 0.00364 (14980) covalent geometry : angle 0.63717 (20335) hydrogen bonds : bond 0.03740 ( 795) hydrogen bonds : angle 5.10103 ( 2025) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 266 time to evaluate : 0.597 Fit side-chains REVERT: A 47 MET cc_start: 0.6268 (tpt) cc_final: 0.5847 (tpt) REVERT: A 50 LYS cc_start: 0.8190 (mttt) cc_final: 0.7646 (mmmt) REVERT: A 68 LYS cc_start: 0.8853 (mmtt) cc_final: 0.8429 (mmtm) REVERT: A 118 LYS cc_start: 0.8121 (tppt) cc_final: 0.7747 (mtmt) REVERT: A 206 ARG cc_start: 0.8197 (ttm170) cc_final: 0.7851 (ttp80) REVERT: A 221 LEU cc_start: 0.8575 (tt) cc_final: 0.8350 (tp) REVERT: A 296 ASN cc_start: 0.8987 (m-40) cc_final: 0.8422 (m-40) REVERT: A 315 LYS cc_start: 0.8452 (tttm) cc_final: 0.8201 (tttm) REVERT: A 328 LYS cc_start: 0.8358 (tttt) cc_final: 0.7866 (tptt) REVERT: A 334 GLU cc_start: 0.7039 (tp30) cc_final: 0.6676 (tp30) REVERT: A 355 MET cc_start: 0.8273 (mmm) cc_final: 0.7476 (mtt) REVERT: B 78 ASN cc_start: 0.8336 (t0) cc_final: 0.8078 (t0) REVERT: B 259 GLU cc_start: 0.8175 (tp30) cc_final: 0.7872 (tp30) REVERT: B 318 THR cc_start: 0.8948 (m) cc_final: 0.8670 (m) REVERT: B 334 GLU cc_start: 0.8327 (mt-10) cc_final: 0.7766 (mm-30) REVERT: C 6 THR cc_start: 0.8849 (OUTLIER) cc_final: 0.8639 (p) REVERT: C 83 GLU cc_start: 0.8395 (tm-30) cc_final: 0.8055 (tm-30) REVERT: C 118 LYS cc_start: 0.8350 (tppt) cc_final: 0.7886 (mttt) REVERT: C 123 MET cc_start: 0.9088 (mmm) cc_final: 0.8696 (mmt) REVERT: C 132 MET cc_start: 0.8596 (ttp) cc_final: 0.8196 (ttp) REVERT: C 225 ASN cc_start: 0.8478 (m-40) cc_final: 0.8197 (m-40) REVERT: C 325 MET cc_start: 0.8514 (mmp) cc_final: 0.8231 (mmm) REVERT: D 80 ASP cc_start: 0.8048 (m-30) cc_final: 0.7728 (t0) REVERT: D 113 LYS cc_start: 0.8474 (mttt) cc_final: 0.8140 (mmtt) REVERT: D 291 LYS cc_start: 0.8648 (tttt) cc_final: 0.8405 (ttpt) REVERT: D 328 LYS cc_start: 0.8823 (tttt) cc_final: 0.8448 (ttpp) REVERT: D 355 MET cc_start: 0.8275 (mmm) cc_final: 0.7975 (mmt) REVERT: E 66 THR cc_start: 0.8822 (m) cc_final: 0.8524 (p) REVERT: E 113 LYS cc_start: 0.8148 (mttt) cc_final: 0.7725 (mmtm) REVERT: E 132 MET cc_start: 0.8905 (tmm) cc_final: 0.8557 (ttp) REVERT: E 169 TYR cc_start: 0.9161 (m-80) cc_final: 0.8885 (m-80) REVERT: E 191 LYS cc_start: 0.8556 (tttm) cc_final: 0.8204 (ttmm) REVERT: E 207 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7759 (tt0) REVERT: E 246 GLN cc_start: 0.8278 (tt0) cc_final: 0.8003 (tt0) REVERT: E 311 ASP cc_start: 0.8552 (m-30) cc_final: 0.8323 (m-30) REVERT: E 313 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.8267 (ttm) REVERT: E 328 LYS cc_start: 0.8995 (tttt) cc_final: 0.8579 (ttpt) outliers start: 27 outliers final: 14 residues processed: 287 average time/residue: 0.1127 time to fit residues: 49.9440 Evaluate side-chains 267 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 250 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 88 HIS Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 313 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 45 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 26 optimal weight: 0.0980 chunk 150 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 44 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 353 GLN D 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.116046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.100248 restraints weight = 19950.008| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.02 r_work: 0.2992 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 14980 Z= 0.226 Angle : 0.663 10.562 20335 Z= 0.321 Chirality : 0.047 0.232 2255 Planarity : 0.005 0.045 2595 Dihedral : 10.096 156.131 2085 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.27 % Allowed : 2.24 % Favored : 97.49 % Rotamer: Outliers : 3.51 % Allowed : 11.50 % Favored : 84.98 % 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: 0.19 (0.20), residues: 1830 helix: 0.67 (0.18), residues: 790 sheet: -1.07 (0.31), residues: 295 loop : 0.29 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 28 TYR 0.011 0.001 TYR B 143 PHE 0.013 0.001 PHE E 352 TRP 0.014 0.002 TRP E 79 HIS 0.009 0.001 HIS C 88 Details of bonding type rmsd covalent geometry : bond 0.00540 (14980) covalent geometry : angle 0.66349 (20335) hydrogen bonds : bond 0.03881 ( 795) hydrogen bonds : angle 5.02404 ( 2025) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 279 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.6296 (tpt) cc_final: 0.5734 (tpt) REVERT: A 50 LYS cc_start: 0.8259 (mttt) cc_final: 0.7704 (mmmt) REVERT: A 78 ASN cc_start: 0.8783 (t0) cc_final: 0.8085 (t0) REVERT: A 206 ARG cc_start: 0.8170 (ttm170) cc_final: 0.7739 (ttp80) REVERT: A 276 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7774 (mt-10) REVERT: A 288 ASP cc_start: 0.7558 (m-30) cc_final: 0.7208 (m-30) REVERT: A 296 ASN cc_start: 0.9080 (m-40) cc_final: 0.8626 (m-40) REVERT: A 315 LYS cc_start: 0.8466 (tttm) cc_final: 0.8177 (tttm) REVERT: A 328 LYS cc_start: 0.8390 (tttt) cc_final: 0.7906 (tptt) REVERT: A 334 GLU cc_start: 0.7014 (tp30) cc_final: 0.6608 (tp30) REVERT: A 355 MET cc_start: 0.8416 (mmm) cc_final: 0.7731 (mtt) REVERT: A 360 GLN cc_start: 0.8521 (mm-40) cc_final: 0.8230 (mm110) REVERT: B 78 ASN cc_start: 0.8370 (t0) cc_final: 0.8041 (t0) REVERT: B 115 ASN cc_start: 0.8997 (t0) cc_final: 0.8728 (t0) REVERT: B 259 GLU cc_start: 0.8254 (tp30) cc_final: 0.7999 (tp30) REVERT: B 325 MET cc_start: 0.8037 (mmp) cc_final: 0.7735 (mmt) REVERT: B 334 GLU cc_start: 0.8341 (mt-10) cc_final: 0.7808 (mm-30) REVERT: C 83 GLU cc_start: 0.8501 (tm-30) cc_final: 0.8150 (tm-30) REVERT: C 118 LYS cc_start: 0.8601 (tppt) cc_final: 0.8114 (mttt) REVERT: C 225 ASN cc_start: 0.8534 (m-40) cc_final: 0.8178 (m-40) REVERT: C 325 MET cc_start: 0.8413 (mmp) cc_final: 0.8177 (mmm) REVERT: C 354 GLN cc_start: 0.8387 (mm110) cc_final: 0.7909 (mt0) REVERT: D 113 LYS cc_start: 0.8576 (mttt) cc_final: 0.8161 (mmtt) REVERT: D 132 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.8485 (ttt) REVERT: D 222 ASP cc_start: 0.7910 (p0) cc_final: 0.7317 (p0) REVERT: D 291 LYS cc_start: 0.8675 (tttt) cc_final: 0.8414 (ttpt) REVERT: D 328 LYS cc_start: 0.8869 (tttt) cc_final: 0.8425 (ttpp) REVERT: E 47 MET cc_start: 0.2170 (mmm) cc_final: 0.1956 (mmm) REVERT: E 66 THR cc_start: 0.8948 (m) cc_final: 0.8743 (p) REVERT: E 68 LYS cc_start: 0.8433 (mmtt) cc_final: 0.8082 (mmtp) REVERT: E 107 GLU cc_start: 0.8498 (tt0) cc_final: 0.8252 (tt0) REVERT: E 113 LYS cc_start: 0.8383 (mttt) cc_final: 0.7894 (mmtt) REVERT: E 132 MET cc_start: 0.8862 (tmm) cc_final: 0.8441 (ttp) REVERT: E 169 TYR cc_start: 0.9181 (m-80) cc_final: 0.8827 (m-80) REVERT: E 189 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8772 (tt) REVERT: E 191 LYS cc_start: 0.8523 (tttm) cc_final: 0.8198 (ttmm) REVERT: E 207 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7782 (tt0) REVERT: E 215 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8517 (mtpt) REVERT: E 259 GLU cc_start: 0.8447 (tp30) cc_final: 0.8194 (tp30) REVERT: E 311 ASP cc_start: 0.8588 (m-30) cc_final: 0.8364 (m-30) REVERT: E 328 LYS cc_start: 0.9076 (tttt) cc_final: 0.8619 (ttpt) REVERT: E 355 MET cc_start: 0.8901 (mmm) cc_final: 0.8543 (mpp) outliers start: 55 outliers final: 34 residues processed: 314 average time/residue: 0.1117 time to fit residues: 53.9828 Evaluate side-chains 296 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 258 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 88 HIS Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 215 LYS Chi-restraints excluded: chain E residue 236 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 153 optimal weight: 0.1980 chunk 29 optimal weight: 5.9990 chunk 18 optimal weight: 0.2980 chunk 77 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 138 optimal weight: 0.9980 chunk 139 optimal weight: 0.6980 chunk 128 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN A 162 ASN B 162 ASN B 225 ASN C 12 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.120769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.105220 restraints weight = 19699.069| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.00 r_work: 0.3043 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14980 Z= 0.113 Angle : 0.594 10.285 20335 Z= 0.278 Chirality : 0.043 0.217 2255 Planarity : 0.004 0.040 2595 Dihedral : 8.365 118.341 2085 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.27 % Allowed : 1.97 % Favored : 97.76 % Rotamer: Outliers : 2.62 % Allowed : 13.29 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.20), residues: 1830 helix: 0.93 (0.19), residues: 790 sheet: -1.07 (0.31), residues: 295 loop : 0.31 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 28 TYR 0.011 0.001 TYR C 306 PHE 0.009 0.001 PHE C 223 TRP 0.010 0.001 TRP D 340 HIS 0.003 0.001 HIS D 101 Details of bonding type rmsd covalent geometry : bond 0.00259 (14980) covalent geometry : angle 0.59390 (20335) hydrogen bonds : bond 0.03146 ( 795) hydrogen bonds : angle 4.80437 ( 2025) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 272 time to evaluate : 0.542 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.6029 (tpt) cc_final: 0.5592 (tpt) REVERT: A 50 LYS cc_start: 0.8265 (mttt) cc_final: 0.7633 (mmmt) REVERT: A 107 GLU cc_start: 0.8021 (tt0) cc_final: 0.7772 (tt0) REVERT: A 222 ASP cc_start: 0.8213 (t0) cc_final: 0.8008 (t0) REVERT: A 276 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7703 (tt0) REVERT: A 288 ASP cc_start: 0.7670 (m-30) cc_final: 0.7403 (m-30) REVERT: A 292 ASP cc_start: 0.8048 (m-30) cc_final: 0.7702 (m-30) REVERT: A 296 ASN cc_start: 0.9053 (m-40) cc_final: 0.8486 (m-40) REVERT: A 315 LYS cc_start: 0.8479 (tttm) cc_final: 0.8241 (tttm) REVERT: A 328 LYS cc_start: 0.8421 (tttt) cc_final: 0.7887 (tptt) REVERT: A 334 GLU cc_start: 0.6989 (tp30) cc_final: 0.6592 (tp30) REVERT: A 355 MET cc_start: 0.8319 (mmm) cc_final: 0.7640 (mtt) REVERT: B 8 LEU cc_start: 0.9026 (mp) cc_final: 0.8758 (mt) REVERT: B 78 ASN cc_start: 0.8350 (t0) cc_final: 0.7596 (t0) REVERT: B 81 ASP cc_start: 0.8520 (m-30) cc_final: 0.7967 (m-30) REVERT: B 259 GLU cc_start: 0.8192 (tp30) cc_final: 0.7949 (tp30) REVERT: B 334 GLU cc_start: 0.8283 (mt-10) cc_final: 0.7746 (mm-30) REVERT: B 353 GLN cc_start: 0.7704 (OUTLIER) cc_final: 0.6500 (mp-120) REVERT: C 44 MET cc_start: 0.7963 (mmm) cc_final: 0.7740 (mmm) REVERT: C 83 GLU cc_start: 0.8406 (tm-30) cc_final: 0.8075 (tm-30) REVERT: C 118 LYS cc_start: 0.8442 (tppt) cc_final: 0.7923 (mttt) REVERT: C 225 ASN cc_start: 0.8422 (m-40) cc_final: 0.8106 (m-40) REVERT: C 249 THR cc_start: 0.8891 (OUTLIER) cc_final: 0.8562 (p) REVERT: C 354 GLN cc_start: 0.8305 (mm110) cc_final: 0.7878 (mt0) REVERT: D 80 ASP cc_start: 0.7962 (m-30) cc_final: 0.7738 (t0) REVERT: D 82 MET cc_start: 0.8929 (tpt) cc_final: 0.8601 (tpt) REVERT: D 113 LYS cc_start: 0.8522 (mttt) cc_final: 0.8075 (mmtt) REVERT: D 119 MET cc_start: 0.8820 (ttm) cc_final: 0.8495 (ttm) REVERT: D 132 MET cc_start: 0.8678 (OUTLIER) cc_final: 0.8434 (ttt) REVERT: D 291 LYS cc_start: 0.8587 (tttt) cc_final: 0.8337 (ttpt) REVERT: D 328 LYS cc_start: 0.8874 (tttt) cc_final: 0.8384 (ttpp) REVERT: E 68 LYS cc_start: 0.8455 (mmtt) cc_final: 0.8083 (mmtp) REVERT: E 78 ASN cc_start: 0.8014 (t0) cc_final: 0.7569 (t0) REVERT: E 113 LYS cc_start: 0.8329 (mttt) cc_final: 0.7905 (mmtp) REVERT: E 132 MET cc_start: 0.8814 (tmm) cc_final: 0.8426 (ttp) REVERT: E 169 TYR cc_start: 0.9038 (m-80) cc_final: 0.8692 (m-80) REVERT: E 191 LYS cc_start: 0.8511 (tttm) cc_final: 0.8190 (ttmm) REVERT: E 207 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7699 (tt0) REVERT: E 215 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8513 (mtpt) REVERT: E 246 GLN cc_start: 0.8353 (tt0) cc_final: 0.8030 (mm-40) REVERT: E 259 GLU cc_start: 0.8429 (tp30) cc_final: 0.8123 (tp30) REVERT: E 328 LYS cc_start: 0.8987 (tttt) cc_final: 0.8542 (ttpt) outliers start: 41 outliers final: 19 residues processed: 301 average time/residue: 0.1130 time to fit residues: 52.4297 Evaluate side-chains 264 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 240 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 353 GLN Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 215 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 138 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 184 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 24 optimal weight: 0.3980 chunk 135 optimal weight: 0.0870 chunk 165 optimal weight: 4.9990 chunk 159 optimal weight: 5.9990 overall best weight: 1.6964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 ASN D 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.118181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.102511 restraints weight = 19827.959| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.01 r_work: 0.3027 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 14980 Z= 0.192 Angle : 0.635 10.604 20335 Z= 0.298 Chirality : 0.046 0.243 2255 Planarity : 0.004 0.047 2595 Dihedral : 8.177 108.991 2085 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.27 % Allowed : 2.13 % Favored : 97.60 % Rotamer: Outliers : 3.19 % Allowed : 13.23 % Favored : 83.58 % 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: 0.50 (0.20), residues: 1830 helix: 1.12 (0.19), residues: 760 sheet: -1.02 (0.31), residues: 295 loop : 0.29 (0.23), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 206 TYR 0.008 0.001 TYR D 188 PHE 0.011 0.001 PHE C 352 TRP 0.010 0.002 TRP B 79 HIS 0.007 0.001 HIS C 88 Details of bonding type rmsd covalent geometry : bond 0.00461 (14980) covalent geometry : angle 0.63513 (20335) hydrogen bonds : bond 0.03462 ( 795) hydrogen bonds : angle 4.84340 ( 2025) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 255 time to evaluate : 0.604 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.5894 (tpt) cc_final: 0.5570 (tpt) REVERT: A 78 ASN cc_start: 0.8751 (t0) cc_final: 0.7988 (t0) REVERT: A 107 GLU cc_start: 0.8079 (tt0) cc_final: 0.7872 (tt0) REVERT: A 128 ASN cc_start: 0.8400 (t0) cc_final: 0.7885 (t0) REVERT: A 225 ASN cc_start: 0.8616 (m-40) cc_final: 0.8406 (m-40) REVERT: A 276 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7752 (tt0) REVERT: A 292 ASP cc_start: 0.8042 (m-30) cc_final: 0.7818 (m-30) REVERT: A 296 ASN cc_start: 0.9091 (m-40) cc_final: 0.8593 (m-40) REVERT: A 328 LYS cc_start: 0.8483 (tttt) cc_final: 0.7951 (tptt) REVERT: A 334 GLU cc_start: 0.7106 (tp30) cc_final: 0.6728 (tp30) REVERT: A 355 MET cc_start: 0.8399 (mmm) cc_final: 0.7734 (mtt) REVERT: A 360 GLN cc_start: 0.8597 (mm-40) cc_final: 0.8394 (mm110) REVERT: B 44 MET cc_start: 0.8305 (mtt) cc_final: 0.8078 (mtt) REVERT: B 78 ASN cc_start: 0.8448 (t0) cc_final: 0.8096 (t0) REVERT: B 259 GLU cc_start: 0.8222 (tp30) cc_final: 0.7962 (tp30) REVERT: B 305 MET cc_start: 0.8939 (mmm) cc_final: 0.8587 (mmt) REVERT: B 334 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7726 (mm-30) REVERT: B 353 GLN cc_start: 0.7925 (OUTLIER) cc_final: 0.6704 (mp-120) REVERT: C 83 GLU cc_start: 0.8430 (tm-30) cc_final: 0.8110 (tm-30) REVERT: C 118 LYS cc_start: 0.8461 (tppt) cc_final: 0.7924 (mttt) REVERT: C 123 MET cc_start: 0.9069 (mmt) cc_final: 0.8832 (mmm) REVERT: C 225 ASN cc_start: 0.8485 (m-40) cc_final: 0.8131 (m-40) REVERT: C 249 THR cc_start: 0.8986 (OUTLIER) cc_final: 0.8651 (p) REVERT: C 354 GLN cc_start: 0.8346 (mm110) cc_final: 0.7907 (mt0) REVERT: D 44 MET cc_start: 0.8382 (mmm) cc_final: 0.7987 (mmm) REVERT: D 113 LYS cc_start: 0.8606 (mttt) cc_final: 0.8082 (mmtt) REVERT: D 119 MET cc_start: 0.8853 (ttm) cc_final: 0.8567 (ttm) REVERT: D 125 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.6949 (mp0) REVERT: D 132 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.8480 (ttt) REVERT: D 291 LYS cc_start: 0.8633 (tttt) cc_final: 0.8390 (ttpt) REVERT: D 328 LYS cc_start: 0.8902 (tttt) cc_final: 0.8438 (ttpp) REVERT: E 68 LYS cc_start: 0.8517 (mmtt) cc_final: 0.8106 (mmtp) REVERT: E 78 ASN cc_start: 0.8104 (t0) cc_final: 0.7482 (t0) REVERT: E 81 ASP cc_start: 0.8161 (m-30) cc_final: 0.7394 (m-30) REVERT: E 113 LYS cc_start: 0.8410 (mttt) cc_final: 0.7995 (mmtp) REVERT: E 132 MET cc_start: 0.8832 (tmm) cc_final: 0.8472 (ttp) REVERT: E 169 TYR cc_start: 0.9127 (m-80) cc_final: 0.8273 (m-80) REVERT: E 191 LYS cc_start: 0.8528 (tttm) cc_final: 0.8210 (ttmm) REVERT: E 207 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7781 (tt0) REVERT: E 215 LYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8563 (mtpt) REVERT: E 246 GLN cc_start: 0.8421 (tt0) cc_final: 0.8172 (mm-40) REVERT: E 259 GLU cc_start: 0.8471 (tp30) cc_final: 0.8139 (tp30) REVERT: E 328 LYS cc_start: 0.8992 (tttt) cc_final: 0.8559 (ttpt) outliers start: 50 outliers final: 34 residues processed: 288 average time/residue: 0.1132 time to fit residues: 50.2995 Evaluate side-chains 280 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 240 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 353 GLN Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 88 HIS Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 215 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 4.9990 chunk 181 optimal weight: 4.9990 chunk 162 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 150 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 147 optimal weight: 5.9990 chunk 160 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN B 162 ASN D 12 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.113620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.097576 restraints weight = 19711.235| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.09 r_work: 0.2981 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 14980 Z= 0.265 Angle : 0.677 11.455 20335 Z= 0.322 Chirality : 0.048 0.246 2255 Planarity : 0.005 0.050 2595 Dihedral : 8.097 105.036 2085 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.57 % Favored : 97.27 % Rotamer: Outliers : 3.64 % Allowed : 13.35 % Favored : 83.00 % 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: 0.13 (0.20), residues: 1830 helix: 0.75 (0.19), residues: 790 sheet: -1.06 (0.31), residues: 295 loop : 0.06 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 206 TYR 0.013 0.001 TYR C 279 PHE 0.013 0.002 PHE E 352 TRP 0.012 0.002 TRP B 79 HIS 0.009 0.001 HIS C 88 Details of bonding type rmsd covalent geometry : bond 0.00634 (14980) covalent geometry : angle 0.67746 (20335) hydrogen bonds : bond 0.03815 ( 795) hydrogen bonds : angle 4.97485 ( 2025) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 255 time to evaluate : 0.539 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.5840 (tpt) cc_final: 0.5500 (tpt) REVERT: A 78 ASN cc_start: 0.8735 (t0) cc_final: 0.7929 (t0) REVERT: A 128 ASN cc_start: 0.8379 (t0) cc_final: 0.7878 (t0) REVERT: A 225 ASN cc_start: 0.8630 (m-40) cc_final: 0.8429 (m-40) REVERT: A 276 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7759 (mt-10) REVERT: A 296 ASN cc_start: 0.9029 (m-40) cc_final: 0.8604 (m-40) REVERT: A 328 LYS cc_start: 0.8500 (tttt) cc_final: 0.7891 (tptt) REVERT: A 355 MET cc_start: 0.8439 (mmm) cc_final: 0.7833 (mtt) REVERT: B 44 MET cc_start: 0.8395 (mtt) cc_final: 0.8181 (mtt) REVERT: B 78 ASN cc_start: 0.8578 (t0) cc_final: 0.8141 (t0) REVERT: B 123 MET cc_start: 0.8699 (mmt) cc_final: 0.8367 (mmt) REVERT: B 259 GLU cc_start: 0.8253 (tp30) cc_final: 0.7967 (tp30) REVERT: B 305 MET cc_start: 0.8979 (mmm) cc_final: 0.8593 (mmt) REVERT: B 334 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7741 (mm-30) REVERT: B 353 GLN cc_start: 0.7981 (OUTLIER) cc_final: 0.6754 (mp-120) REVERT: C 83 GLU cc_start: 0.8383 (tm-30) cc_final: 0.7935 (mt-10) REVERT: C 225 ASN cc_start: 0.8519 (m-40) cc_final: 0.8153 (m-40) REVERT: C 270 GLU cc_start: 0.8246 (tp30) cc_final: 0.7963 (tp30) REVERT: C 354 GLN cc_start: 0.8364 (mm110) cc_final: 0.7907 (mt0) REVERT: D 44 MET cc_start: 0.8307 (mmm) cc_final: 0.7958 (mmm) REVERT: D 80 ASP cc_start: 0.8146 (m-30) cc_final: 0.7841 (t0) REVERT: D 81 ASP cc_start: 0.8434 (m-30) cc_final: 0.8214 (m-30) REVERT: D 83 GLU cc_start: 0.8216 (tt0) cc_final: 0.7800 (tm-30) REVERT: D 125 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.7041 (mp0) REVERT: D 132 MET cc_start: 0.8725 (OUTLIER) cc_final: 0.8494 (ttt) REVERT: D 207 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7838 (tp30) REVERT: D 328 LYS cc_start: 0.8899 (tttt) cc_final: 0.8403 (ttpp) REVERT: E 68 LYS cc_start: 0.8519 (mmtt) cc_final: 0.8097 (mmtp) REVERT: E 78 ASN cc_start: 0.8188 (t0) cc_final: 0.7597 (t0) REVERT: E 107 GLU cc_start: 0.8642 (tt0) cc_final: 0.8409 (tt0) REVERT: E 113 LYS cc_start: 0.8493 (mttt) cc_final: 0.8032 (mmtp) REVERT: E 132 MET cc_start: 0.8966 (tmm) cc_final: 0.8583 (ttp) REVERT: E 169 TYR cc_start: 0.9133 (m-80) cc_final: 0.8261 (m-80) REVERT: E 191 LYS cc_start: 0.8537 (tttm) cc_final: 0.8225 (ttmm) REVERT: E 207 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7877 (tt0) REVERT: E 215 LYS cc_start: 0.8814 (OUTLIER) cc_final: 0.8550 (mtpt) REVERT: E 259 GLU cc_start: 0.8622 (tp30) cc_final: 0.8293 (tp30) REVERT: E 328 LYS cc_start: 0.8976 (tttt) cc_final: 0.8539 (ttpt) outliers start: 57 outliers final: 44 residues processed: 295 average time/residue: 0.1057 time to fit residues: 49.1547 Evaluate side-chains 292 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 242 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 353 GLN Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 88 HIS Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 215 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 43 optimal weight: 0.5980 chunk 89 optimal weight: 0.7980 chunk 172 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 166 optimal weight: 0.9980 chunk 127 optimal weight: 0.5980 chunk 128 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN A 297 ASN B 162 ASN B 225 ASN D 12 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.119522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.103646 restraints weight = 19329.125| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.07 r_work: 0.3036 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.4281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14980 Z= 0.129 Angle : 0.613 11.165 20335 Z= 0.285 Chirality : 0.044 0.217 2255 Planarity : 0.004 0.045 2595 Dihedral : 7.674 96.660 2085 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.80 % Favored : 98.09 % Rotamer: Outliers : 2.88 % Allowed : 15.40 % Favored : 81.73 % 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: 0.33 (0.20), residues: 1830 helix: 1.00 (0.19), residues: 790 sheet: -0.97 (0.32), residues: 295 loop : 0.05 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 206 TYR 0.009 0.001 TYR C 306 PHE 0.009 0.001 PHE B 31 TRP 0.011 0.002 TRP D 340 HIS 0.004 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00306 (14980) covalent geometry : angle 0.61312 (20335) hydrogen bonds : bond 0.03141 ( 795) hydrogen bonds : angle 4.80340 ( 2025) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 265 time to evaluate : 0.567 Fit side-chains REVERT: A 78 ASN cc_start: 0.8723 (t0) cc_final: 0.7938 (t0) REVERT: A 82 MET cc_start: 0.8770 (tpt) cc_final: 0.8395 (tpt) REVERT: A 128 ASN cc_start: 0.8404 (t0) cc_final: 0.7947 (t0) REVERT: A 225 ASN cc_start: 0.8620 (m-40) cc_final: 0.8414 (m-40) REVERT: A 276 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7718 (tt0) REVERT: A 296 ASN cc_start: 0.8998 (m-40) cc_final: 0.8392 (m-40) REVERT: A 328 LYS cc_start: 0.8329 (tttt) cc_final: 0.7818 (tptt) REVERT: A 334 GLU cc_start: 0.7103 (tp30) cc_final: 0.6568 (tp30) REVERT: A 355 MET cc_start: 0.8310 (mmm) cc_final: 0.7730 (mtt) REVERT: B 78 ASN cc_start: 0.8488 (t0) cc_final: 0.8114 (t0) REVERT: B 123 MET cc_start: 0.8634 (mmt) cc_final: 0.8282 (mmt) REVERT: B 259 GLU cc_start: 0.8162 (tp30) cc_final: 0.7905 (tp30) REVERT: B 305 MET cc_start: 0.8837 (mmm) cc_final: 0.8585 (mmt) REVERT: B 334 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7657 (mm-30) REVERT: B 353 GLN cc_start: 0.7819 (OUTLIER) cc_final: 0.6587 (mp-120) REVERT: C 83 GLU cc_start: 0.8340 (tm-30) cc_final: 0.7848 (mt-10) REVERT: C 123 MET cc_start: 0.9000 (mmt) cc_final: 0.8731 (mmm) REVERT: C 192 ILE cc_start: 0.8399 (tt) cc_final: 0.8030 (pt) REVERT: C 225 ASN cc_start: 0.8467 (m-40) cc_final: 0.8195 (m-40) REVERT: C 270 GLU cc_start: 0.8145 (tp30) cc_final: 0.7842 (mm-30) REVERT: C 354 GLN cc_start: 0.8353 (mm110) cc_final: 0.7974 (mt0) REVERT: D 44 MET cc_start: 0.8275 (mmm) cc_final: 0.7901 (mmm) REVERT: D 82 MET cc_start: 0.8925 (tpt) cc_final: 0.8637 (tpt) REVERT: D 113 LYS cc_start: 0.8581 (mttt) cc_final: 0.8101 (mmmt) REVERT: D 119 MET cc_start: 0.8836 (ttm) cc_final: 0.8525 (ttm) REVERT: D 132 MET cc_start: 0.8680 (OUTLIER) cc_final: 0.8439 (ttt) REVERT: D 207 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7781 (tt0) REVERT: D 328 LYS cc_start: 0.8880 (tttt) cc_final: 0.8389 (ttpp) REVERT: E 68 LYS cc_start: 0.8474 (mmtt) cc_final: 0.8062 (mmtp) REVERT: E 78 ASN cc_start: 0.8126 (t0) cc_final: 0.7278 (t0) REVERT: E 107 GLU cc_start: 0.8589 (tt0) cc_final: 0.8349 (tt0) REVERT: E 113 LYS cc_start: 0.8407 (mttt) cc_final: 0.7951 (mmtp) REVERT: E 132 MET cc_start: 0.8894 (tmm) cc_final: 0.8516 (ttp) REVERT: E 169 TYR cc_start: 0.9011 (m-80) cc_final: 0.8597 (m-80) REVERT: E 191 LYS cc_start: 0.8506 (tttm) cc_final: 0.8195 (ttmm) REVERT: E 207 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7767 (tt0) REVERT: E 215 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8463 (mtpt) REVERT: E 259 GLU cc_start: 0.8596 (tp30) cc_final: 0.8275 (tp30) REVERT: E 328 LYS cc_start: 0.8957 (tttt) cc_final: 0.8516 (ttpt) outliers start: 45 outliers final: 33 residues processed: 294 average time/residue: 0.1050 time to fit residues: 48.1829 Evaluate side-chains 288 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 250 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 353 GLN Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 88 HIS Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 215 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 13 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 90 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 138 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 137 optimal weight: 0.5980 chunk 79 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN A 246 GLN A 297 ASN B 128 ASN B 162 ASN D 12 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.117025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.100751 restraints weight = 19729.855| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.12 r_work: 0.3040 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.4385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 14980 Z= 0.129 Angle : 0.614 11.072 20335 Z= 0.285 Chirality : 0.044 0.245 2255 Planarity : 0.004 0.045 2595 Dihedral : 7.407 90.981 2085 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.86 % Favored : 98.09 % Rotamer: Outliers : 2.75 % Allowed : 15.72 % Favored : 81.53 % 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: 0.40 (0.20), residues: 1830 helix: 1.06 (0.19), residues: 790 sheet: -0.92 (0.32), residues: 295 loop : 0.08 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 206 TYR 0.009 0.001 TYR C 198 PHE 0.024 0.001 PHE A 352 TRP 0.011 0.002 TRP A 340 HIS 0.006 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00307 (14980) covalent geometry : angle 0.61384 (20335) hydrogen bonds : bond 0.03071 ( 795) hydrogen bonds : angle 4.74404 ( 2025) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 259 time to evaluate : 0.608 Fit side-chains revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8722 (t0) cc_final: 0.7957 (t0) REVERT: A 82 MET cc_start: 0.8801 (tpt) cc_final: 0.8533 (tpt) REVERT: A 128 ASN cc_start: 0.8439 (t0) cc_final: 0.8013 (t0) REVERT: A 225 ASN cc_start: 0.8629 (m-40) cc_final: 0.8390 (m-40) REVERT: A 276 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7735 (tt0) REVERT: A 296 ASN cc_start: 0.9019 (m-40) cc_final: 0.8397 (m-40) REVERT: A 305 MET cc_start: 0.8801 (mmm) cc_final: 0.8568 (mmm) REVERT: A 328 LYS cc_start: 0.8274 (tttt) cc_final: 0.7715 (tptt) REVERT: A 334 GLU cc_start: 0.7182 (tp30) cc_final: 0.6616 (tp30) REVERT: A 355 MET cc_start: 0.8298 (mmm) cc_final: 0.7770 (mtt) REVERT: B 78 ASN cc_start: 0.8505 (t0) cc_final: 0.8120 (t0) REVERT: B 259 GLU cc_start: 0.8150 (tp30) cc_final: 0.7925 (tp30) REVERT: B 305 MET cc_start: 0.8818 (mmm) cc_final: 0.8557 (mmt) REVERT: B 334 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7679 (mm-30) REVERT: B 353 GLN cc_start: 0.7843 (OUTLIER) cc_final: 0.6648 (mp-120) REVERT: C 83 GLU cc_start: 0.8335 (tm-30) cc_final: 0.7894 (mt-10) REVERT: C 192 ILE cc_start: 0.8348 (tt) cc_final: 0.7953 (pt) REVERT: C 225 ASN cc_start: 0.8393 (m-40) cc_final: 0.8088 (m-40) REVERT: C 270 GLU cc_start: 0.8097 (tp30) cc_final: 0.7774 (mm-30) REVERT: C 354 GLN cc_start: 0.8366 (mm110) cc_final: 0.7985 (mt0) REVERT: D 44 MET cc_start: 0.8294 (mmm) cc_final: 0.7919 (mmm) REVERT: D 82 MET cc_start: 0.8935 (tpt) cc_final: 0.8629 (tpt) REVERT: D 113 LYS cc_start: 0.8605 (mttt) cc_final: 0.8155 (mmmt) REVERT: D 119 MET cc_start: 0.8853 (ttm) cc_final: 0.8562 (ttm) REVERT: D 132 MET cc_start: 0.8683 (OUTLIER) cc_final: 0.8460 (ttt) REVERT: D 207 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7801 (tt0) REVERT: D 328 LYS cc_start: 0.8907 (tttt) cc_final: 0.8413 (ttpp) REVERT: E 68 LYS cc_start: 0.8496 (mmtt) cc_final: 0.8079 (mmtp) REVERT: E 78 ASN cc_start: 0.8130 (t0) cc_final: 0.7551 (t0) REVERT: E 107 GLU cc_start: 0.8606 (tt0) cc_final: 0.8365 (tt0) REVERT: E 113 LYS cc_start: 0.8463 (mttt) cc_final: 0.7998 (mmtp) REVERT: E 132 MET cc_start: 0.8872 (tmm) cc_final: 0.8526 (ttp) REVERT: E 169 TYR cc_start: 0.9014 (m-80) cc_final: 0.8291 (m-80) REVERT: E 191 LYS cc_start: 0.8503 (tttm) cc_final: 0.8194 (ttmm) REVERT: E 207 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7796 (tt0) REVERT: E 215 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8452 (mtpt) REVERT: E 236 LEU cc_start: 0.8560 (tp) cc_final: 0.8166 (tt) REVERT: E 259 GLU cc_start: 0.8548 (tp30) cc_final: 0.8212 (tp30) REVERT: E 328 LYS cc_start: 0.8978 (tttt) cc_final: 0.8512 (ttpt) outliers start: 43 outliers final: 31 residues processed: 287 average time/residue: 0.1098 time to fit residues: 49.3757 Evaluate side-chains 287 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 251 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 353 GLN Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 88 HIS Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 215 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 97 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 135 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 115 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN A 246 GLN A 297 ASN B 162 ASN D 12 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.119805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.103863 restraints weight = 19437.554| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 2.06 r_work: 0.3005 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.4423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 14980 Z= 0.166 Angle : 0.638 11.275 20335 Z= 0.296 Chirality : 0.045 0.240 2255 Planarity : 0.004 0.044 2595 Dihedral : 7.265 89.071 2085 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.35 % Favored : 97.60 % Rotamer: Outliers : 2.62 % Allowed : 16.04 % Favored : 81.34 % 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: 0.34 (0.20), residues: 1830 helix: 0.99 (0.19), residues: 790 sheet: -0.92 (0.32), residues: 295 loop : 0.06 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 206 TYR 0.009 0.001 TYR E 53 PHE 0.020 0.001 PHE A 352 TRP 0.010 0.002 TRP C 79 HIS 0.007 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00400 (14980) covalent geometry : angle 0.63763 (20335) hydrogen bonds : bond 0.03235 ( 795) hydrogen bonds : angle 4.77036 ( 2025) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 249 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.5797 (tpt) cc_final: 0.5060 (tpt) REVERT: A 78 ASN cc_start: 0.8706 (t0) cc_final: 0.7894 (t0) REVERT: A 82 MET cc_start: 0.8793 (tpt) cc_final: 0.8450 (tpt) REVERT: A 128 ASN cc_start: 0.8427 (t0) cc_final: 0.7809 (t0) REVERT: A 225 ASN cc_start: 0.8661 (m-40) cc_final: 0.8417 (m-40) REVERT: A 276 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7793 (mt-10) REVERT: A 296 ASN cc_start: 0.9008 (m-40) cc_final: 0.8425 (m-40) REVERT: A 305 MET cc_start: 0.8799 (mmm) cc_final: 0.8551 (mmm) REVERT: A 325 MET cc_start: 0.5045 (mtt) cc_final: 0.3216 (ttm) REVERT: A 328 LYS cc_start: 0.8373 (tttt) cc_final: 0.7836 (tptt) REVERT: A 334 GLU cc_start: 0.7256 (tp30) cc_final: 0.6694 (tp30) REVERT: A 355 MET cc_start: 0.8328 (mmm) cc_final: 0.7804 (mtt) REVERT: B 78 ASN cc_start: 0.8526 (t0) cc_final: 0.8115 (t0) REVERT: B 305 MET cc_start: 0.8840 (mmm) cc_final: 0.8558 (mmt) REVERT: B 334 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7688 (mm-30) REVERT: B 353 GLN cc_start: 0.7826 (OUTLIER) cc_final: 0.6640 (mp-120) REVERT: C 83 GLU cc_start: 0.8326 (tm-30) cc_final: 0.7919 (mt-10) REVERT: C 225 ASN cc_start: 0.8344 (m-40) cc_final: 0.8042 (m-40) REVERT: C 270 GLU cc_start: 0.8081 (tp30) cc_final: 0.7752 (mm-30) REVERT: C 354 GLN cc_start: 0.8355 (mm110) cc_final: 0.7949 (mt0) REVERT: D 44 MET cc_start: 0.8324 (mmm) cc_final: 0.7962 (mmm) REVERT: D 119 MET cc_start: 0.8846 (ttm) cc_final: 0.8566 (ttm) REVERT: D 125 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.6700 (mp0) REVERT: D 132 MET cc_start: 0.8675 (OUTLIER) cc_final: 0.8439 (ttt) REVERT: D 207 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7813 (tp30) REVERT: D 227 MET cc_start: 0.8503 (mmm) cc_final: 0.8263 (mmm) REVERT: D 328 LYS cc_start: 0.8861 (tttt) cc_final: 0.8358 (ttpp) REVERT: E 68 LYS cc_start: 0.8528 (mmtt) cc_final: 0.8084 (mmtp) REVERT: E 78 ASN cc_start: 0.8142 (t0) cc_final: 0.7551 (t0) REVERT: E 107 GLU cc_start: 0.8611 (tt0) cc_final: 0.8372 (tt0) REVERT: E 113 LYS cc_start: 0.8452 (mttt) cc_final: 0.7957 (mmtp) REVERT: E 132 MET cc_start: 0.8893 (tmm) cc_final: 0.8565 (ttp) REVERT: E 169 TYR cc_start: 0.9045 (m-80) cc_final: 0.8219 (m-80) REVERT: E 191 LYS cc_start: 0.8489 (tttm) cc_final: 0.8185 (ttmm) REVERT: E 207 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7843 (tt0) REVERT: E 215 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8470 (mtpt) REVERT: E 236 LEU cc_start: 0.8584 (tp) cc_final: 0.8188 (tt) REVERT: E 259 GLU cc_start: 0.8541 (tp30) cc_final: 0.8185 (tp30) REVERT: E 328 LYS cc_start: 0.8972 (tttt) cc_final: 0.8496 (ttpt) outliers start: 41 outliers final: 32 residues processed: 277 average time/residue: 0.1068 time to fit residues: 46.2839 Evaluate side-chains 282 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 244 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 353 GLN Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 88 HIS Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 215 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 62 optimal weight: 0.9980 chunk 138 optimal weight: 0.9990 chunk 17 optimal weight: 8.9990 chunk 100 optimal weight: 4.9990 chunk 183 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 154 optimal weight: 0.6980 chunk 150 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN A 297 ASN B 162 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.119419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.103388 restraints weight = 19347.529| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.07 r_work: 0.3042 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.4477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14980 Z= 0.135 Angle : 0.620 11.081 20335 Z= 0.287 Chirality : 0.044 0.232 2255 Planarity : 0.004 0.041 2595 Dihedral : 7.057 85.464 2085 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.08 % Favored : 97.87 % Rotamer: Outliers : 2.49 % Allowed : 15.85 % Favored : 81.66 % 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: 0.40 (0.20), residues: 1830 helix: 1.05 (0.19), residues: 790 sheet: -0.87 (0.32), residues: 295 loop : 0.08 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 206 TYR 0.008 0.001 TYR C 198 PHE 0.018 0.001 PHE A 352 TRP 0.011 0.002 TRP C 79 HIS 0.006 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00323 (14980) covalent geometry : angle 0.62005 (20335) hydrogen bonds : bond 0.03082 ( 795) hydrogen bonds : angle 4.74781 ( 2025) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3394.05 seconds wall clock time: 59 minutes 14.18 seconds (3554.18 seconds total)