Starting phenix.real_space_refine on Fri Jun 13 13:37:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oi8_16888/06_2025/8oi8_16888.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oi8_16888/06_2025/8oi8_16888.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8oi8_16888/06_2025/8oi8_16888.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oi8_16888/06_2025/8oi8_16888.map" model { file = "/net/cci-nas-00/data/ceres_data/8oi8_16888/06_2025/8oi8_16888.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oi8_16888/06_2025/8oi8_16888.cif" } resolution = 2.28 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 10 5.49 5 Mg 5 5.21 5 S 95 5.16 5 C 9050 2.51 5 N 2390 2.21 5 O 3345 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 14895 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2834 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 19, 'TRANS': 343} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 139 Classifications: {'water': 139} Link IDs: {None: 138} Chain: "A" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 105 Classifications: {'water': 105} Link IDs: {None: 104} Chain: "B" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 131 Classifications: {'water': 131} Link IDs: {None: 130} Chain: "D" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 129 Classifications: {'water': 129} Link IDs: {None: 128} Chain: "E" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 81 Classifications: {'water': 81} Link IDs: {None: 80} Restraints were copied for chains: C, B, E, D Time building chain proxies: 7.57, per 1000 atoms: 0.51 Number of scatterers: 14895 At special positions: 0 Unit cell: (92.435, 93.13, 193.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 95 16.00 P 10 15.00 Mg 5 11.99 O 3345 8.00 N 2390 7.00 C 9050 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.57 Conformation dependent library (CDL) restraints added in 2.2 seconds 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3370 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 30 sheets defined 50.7% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.20 Creating SS restraints... Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.945A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 194 removed outlier: 3.730A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 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 284 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 305 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 347 Processing helix chain 'C' and resid 348 through 353 removed outlier: 6.279A pdb=" N THR C 351 " --> pdb=" O SER C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 367 through 371 Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.946A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 181 through 194 removed outlier: 3.729A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 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 284 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 305 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 347 Processing helix chain 'A' and resid 348 through 353 removed outlier: 6.279A pdb=" N THR A 351 " --> pdb=" O SER A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 367 through 371 Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.946A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 181 through 194 removed outlier: 3.730A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 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 284 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 305 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 347 Processing helix chain 'B' and resid 348 through 353 removed outlier: 6.279A pdb=" N THR B 351 " --> pdb=" O SER B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.945A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 Processing helix chain 'D' and resid 172 through 175 Processing helix chain 'D' and resid 181 through 194 removed outlier: 3.730A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 197 No H-bonds generated for 'chain 'D' and resid 195 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 284 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 305 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 347 Processing helix chain 'D' and resid 348 through 353 removed outlier: 6.279A pdb=" N THR D 351 " --> pdb=" O SER D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 367 through 371 Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 92 Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.946A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 145 Processing helix chain 'E' and resid 172 through 175 Processing helix chain 'E' and resid 181 through 194 removed outlier: 3.730A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 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 284 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 305 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 347 Processing helix chain 'E' and resid 348 through 353 removed outlier: 6.279A pdb=" N THR E 351 " --> pdb=" O SER E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 367 through 371 Processing sheet with id=AA1, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.589A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N VAL C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'C' and resid 41 through 42 removed outlier: 4.274A pdb=" N GLN C 41 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 41 through 42 removed outlier: 4.274A pdb=" N GLN C 41 " --> pdb=" O ALA A 170 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N THR A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AA6, first strand: chain 'C' and resid 176 through 178 removed outlier: 6.380A pdb=" N THR C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 176 through 178 removed outlier: 4.418A pdb=" N GLN E 41 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AA9, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.589A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N VAL A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AB2, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AB3, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.588A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N VAL B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'B' and resid 176 through 178 removed outlier: 6.380A pdb=" N THR B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 176 through 178 removed outlier: 4.499A pdb=" N GLN D 41 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.588A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N VAL D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AC5, first strand: chain 'D' and resid 169 through 170 removed outlier: 6.379A pdb=" N THR D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC7, first strand: chain 'E' and resid 29 through 32 removed outlier: 6.589A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N VAL E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC9, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AD1, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AD2, first strand: chain 'E' and resid 169 through 170 removed outlier: 6.379A pdb=" N THR E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 238 through 241 733 hydrogen bonds defined for protein. 1863 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.87 Time building geometry restraints manager: 4.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4643 1.34 - 1.46: 2873 1.46 - 1.57: 6929 1.57 - 1.69: 15 1.69 - 1.81: 170 Bond restraints: 14630 Sorted by residual: bond pdb=" CG HIC C 73 " pdb=" ND1 HIC C 73 " ideal model delta sigma weight residual 1.370 1.312 0.058 2.00e-02 2.50e+03 8.30e+00 bond pdb=" CG HIC E 73 " pdb=" ND1 HIC E 73 " ideal model delta sigma weight residual 1.370 1.313 0.057 2.00e-02 2.50e+03 8.23e+00 bond pdb=" CG HIC B 73 " pdb=" ND1 HIC B 73 " ideal model delta sigma weight residual 1.370 1.313 0.057 2.00e-02 2.50e+03 8.14e+00 bond pdb=" CG HIC D 73 " pdb=" ND1 HIC D 73 " ideal model delta sigma weight residual 1.370 1.313 0.057 2.00e-02 2.50e+03 8.05e+00 bond pdb=" CG HIC A 73 " pdb=" ND1 HIC A 73 " ideal model delta sigma weight residual 1.370 1.313 0.057 2.00e-02 2.50e+03 8.05e+00 ... (remaining 14625 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 19444 1.42 - 2.85: 235 2.85 - 4.27: 141 4.27 - 5.69: 20 5.69 - 7.11: 30 Bond angle restraints: 19870 Sorted by residual: angle pdb=" N VAL B 43 " pdb=" CA VAL B 43 " pdb=" C VAL B 43 " ideal model delta sigma weight residual 113.47 109.91 3.56 1.01e+00 9.80e-01 1.24e+01 angle pdb=" N VAL C 43 " pdb=" CA VAL C 43 " pdb=" C VAL C 43 " ideal model delta sigma weight residual 113.47 109.98 3.49 1.01e+00 9.80e-01 1.20e+01 angle pdb=" N VAL D 43 " pdb=" CA VAL D 43 " pdb=" C VAL D 43 " ideal model delta sigma weight residual 113.47 109.98 3.49 1.01e+00 9.80e-01 1.20e+01 angle pdb=" N VAL E 43 " pdb=" CA VAL E 43 " pdb=" C VAL E 43 " ideal model delta sigma weight residual 113.47 109.98 3.49 1.01e+00 9.80e-01 1.20e+01 angle pdb=" N VAL A 43 " pdb=" CA VAL A 43 " pdb=" C VAL A 43 " ideal model delta sigma weight residual 113.47 109.98 3.49 1.01e+00 9.80e-01 1.20e+01 ... (remaining 19865 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.25: 8640 32.25 - 64.50: 110 64.50 - 96.76: 10 96.76 - 129.01: 0 129.01 - 161.26: 5 Dihedral angle restraints: 8765 sinusoidal: 3515 harmonic: 5250 Sorted by residual: 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 300.00 138.74 161.26 1 2.00e+01 2.50e-03 4.67e+01 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 300.00 138.74 161.26 1 2.00e+01 2.50e-03 4.67e+01 dihedral pdb=" O1B ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PB ADP B 401 " pdb=" PA ADP B 401 " ideal model delta sinusoidal sigma weight residual 300.00 138.77 161.22 1 2.00e+01 2.50e-03 4.67e+01 ... (remaining 8762 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1261 0.031 - 0.062: 626 0.062 - 0.093: 189 0.093 - 0.124: 134 0.124 - 0.155: 5 Chirality restraints: 2215 Sorted by residual: chirality pdb=" C3' ADP C 401 " pdb=" C2' ADP C 401 " pdb=" C4' ADP C 401 " pdb=" O3' ADP C 401 " both_signs ideal model delta sigma weight residual False -2.51 -2.67 0.16 2.00e-01 2.50e+01 6.04e-01 chirality pdb=" C3' ADP E 401 " pdb=" C2' ADP E 401 " pdb=" C4' ADP E 401 " pdb=" O3' ADP E 401 " both_signs ideal model delta sigma weight residual False -2.51 -2.66 0.15 2.00e-01 2.50e+01 5.88e-01 chirality pdb=" C3' ADP A 401 " pdb=" C2' ADP A 401 " pdb=" C4' ADP A 401 " pdb=" O3' ADP A 401 " both_signs ideal model delta sigma weight residual False -2.51 -2.66 0.15 2.00e-01 2.50e+01 5.77e-01 ... (remaining 2212 not shown) Planarity restraints: 2525 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 242 " 0.020 5.00e-02 4.00e+02 2.99e-02 1.43e+00 pdb=" N PRO B 243 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO B 243 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 243 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 242 " -0.020 5.00e-02 4.00e+02 2.98e-02 1.42e+00 pdb=" N PRO C 243 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO C 243 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 243 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 242 " -0.020 5.00e-02 4.00e+02 2.97e-02 1.41e+00 pdb=" N PRO A 243 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 243 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 243 " -0.017 5.00e-02 4.00e+02 ... (remaining 2522 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 112 2.42 - 3.04: 8768 3.04 - 3.66: 23764 3.66 - 4.28: 39834 4.28 - 4.90: 61663 Nonbonded interactions: 134141 Sorted by model distance: nonbonded pdb="MG MG E 402 " pdb=" O HOH E 507 " model vdw 1.798 2.170 nonbonded pdb="MG MG D 402 " pdb=" O HOH D 512 " model vdw 1.819 2.170 nonbonded pdb="MG MG A 402 " pdb=" O HOH A 541 " model vdw 1.824 2.170 nonbonded pdb="MG MG C 402 " pdb=" O HOH C 525 " model vdw 1.827 2.170 nonbonded pdb="MG MG B 402 " pdb=" O HOH B 530 " model vdw 1.836 2.170 ... (remaining 134136 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: 0.12 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.170 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: 0.610 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 36.120 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 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 : 0.004 0.058 14630 Z= 0.188 Angle : 0.583 7.113 19870 Z= 0.280 Chirality : 0.044 0.155 2215 Planarity : 0.004 0.030 2525 Dihedral : 12.070 161.259 5395 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.65 % Allowed : 2.61 % Favored : 96.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.19), residues: 1780 helix: -2.34 (0.14), residues: 755 sheet: -0.63 (0.26), residues: 325 loop : 0.86 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 340 HIS 0.003 0.001 HIS E 88 PHE 0.009 0.001 PHE D 262 TYR 0.009 0.001 TYR D 143 ARG 0.003 0.001 ARG C 116 Details of bonding type rmsd hydrogen bonds : bond 0.23727 ( 718) hydrogen bonds : angle 8.06822 ( 1863) covalent geometry : bond 0.00426 (14630) covalent geometry : angle 0.58337 (19870) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 244 time to evaluate : 1.591 Fit side-chains REVERT: B 121 GLN cc_start: 0.8236 (tt0) cc_final: 0.8015 (tm-30) REVERT: B 211 ASP cc_start: 0.8004 (t70) cc_final: 0.7764 (t70) REVERT: D 44 MET cc_start: 0.8176 (OUTLIER) cc_final: 0.6789 (mpt) REVERT: D 276 GLU cc_start: 0.7440 (mt-10) cc_final: 0.7023 (mt-10) REVERT: E 44 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.6044 (mpt) outliers start: 10 outliers final: 0 residues processed: 249 average time/residue: 1.5927 time to fit residues: 428.8926 Evaluate side-chains 177 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 175 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain E residue 44 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 0.7980 chunk 136 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 72 optimal weight: 8.9990 chunk 141 optimal weight: 3.9990 chunk 54 optimal weight: 0.5980 chunk 85 optimal weight: 4.9990 chunk 105 optimal weight: 0.9990 chunk 163 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN A 12 ASN A 78 ASN B 12 ASN D 161 HIS D 225 GLN D 353 GLN E 12 ASN E 121 GLN E 225 GLN E 354 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.111466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.090785 restraints weight = 15711.395| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 1.29 r_work: 0.2903 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14630 Z= 0.140 Angle : 0.617 7.372 19870 Z= 0.293 Chirality : 0.045 0.185 2215 Planarity : 0.004 0.034 2525 Dihedral : 9.408 138.847 2026 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 3.14 % Allowed : 6.14 % Favored : 90.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.20), residues: 1780 helix: -0.27 (0.18), residues: 740 sheet: 0.09 (0.26), residues: 330 loop : 2.04 (0.26), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 79 HIS 0.004 0.001 HIS B 161 PHE 0.009 0.001 PHE D 262 TYR 0.014 0.001 TYR A 143 ARG 0.003 0.000 ARG A 254 Details of bonding type rmsd hydrogen bonds : bond 0.03975 ( 718) hydrogen bonds : angle 5.04834 ( 1863) covalent geometry : bond 0.00307 (14630) covalent geometry : angle 0.61656 (19870) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 192 time to evaluate : 1.708 Fit side-chains REVERT: C 57 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7506 (pt0) REVERT: C 72 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.7645 (mp0) REVERT: C 171 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8623 (mp) REVERT: C 314 GLN cc_start: 0.8852 (OUTLIER) cc_final: 0.8421 (tt0) REVERT: A 64 ILE cc_start: 0.9405 (OUTLIER) cc_final: 0.8772 (pp) REVERT: A 72 GLU cc_start: 0.8538 (mt-10) cc_final: 0.8272 (mp0) REVERT: A 276 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.8076 (mt-10) REVERT: B 171 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8572 (mp) REVERT: D 44 MET cc_start: 0.8330 (OUTLIER) cc_final: 0.7255 (mpt) REVERT: D 125 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7829 (mt-10) REVERT: D 286 ASP cc_start: 0.8248 (m-30) cc_final: 0.7893 (m-30) REVERT: D 360 GLN cc_start: 0.7612 (OUTLIER) cc_final: 0.7365 (tm130) REVERT: E 44 MET cc_start: 0.8109 (OUTLIER) cc_final: 0.6714 (mpt) REVERT: E 64 ILE cc_start: 0.9179 (OUTLIER) cc_final: 0.8547 (pp) REVERT: E 328 LYS cc_start: 0.8989 (OUTLIER) cc_final: 0.8599 (tttt) outliers start: 48 outliers final: 7 residues processed: 216 average time/residue: 1.3860 time to fit residues: 327.1322 Evaluate side-chains 187 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 167 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 360 GLN Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 328 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 15 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 chunk 88 optimal weight: 0.5980 chunk 106 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 94 optimal weight: 9.9990 chunk 96 optimal weight: 1.9990 chunk 118 optimal weight: 0.7980 chunk 165 optimal weight: 5.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN C 161 HIS A 12 ASN A 78 ASN A 161 HIS A 225 GLN B 12 ASN B 161 HIS D 92 ASN E 161 HIS E 296 ASN E 354 GLN E 371 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.105685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.084593 restraints weight = 15635.056| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 1.32 r_work: 0.2802 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14630 Z= 0.209 Angle : 0.640 8.345 19870 Z= 0.310 Chirality : 0.048 0.195 2215 Planarity : 0.004 0.037 2525 Dihedral : 10.030 140.126 2026 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 3.79 % Allowed : 6.14 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.20), residues: 1780 helix: 0.49 (0.19), residues: 745 sheet: 0.39 (0.26), residues: 330 loop : 2.13 (0.26), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP C 340 HIS 0.005 0.001 HIS B 88 PHE 0.014 0.002 PHE D 262 TYR 0.015 0.001 TYR A 143 ARG 0.004 0.001 ARG D 290 Details of bonding type rmsd hydrogen bonds : bond 0.04937 ( 718) hydrogen bonds : angle 4.99335 ( 1863) covalent geometry : bond 0.00489 (14630) covalent geometry : angle 0.64017 (19870) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 170 time to evaluate : 1.562 Fit side-chains REVERT: C 72 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.7660 (mp0) REVERT: C 246 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.8123 (tt0) REVERT: C 314 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.8377 (tt0) REVERT: A 72 GLU cc_start: 0.8511 (mt-10) cc_final: 0.8256 (mp0) REVERT: A 95 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7678 (mtm180) REVERT: A 276 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8118 (mt-10) REVERT: A 326 LYS cc_start: 0.8541 (mptp) cc_final: 0.7953 (ttpp) REVERT: B 57 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7861 (mt-10) REVERT: B 95 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.7848 (mtp180) REVERT: B 125 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.7290 (mp0) REVERT: B 314 GLN cc_start: 0.8967 (OUTLIER) cc_final: 0.8539 (tt0) REVERT: D 44 MET cc_start: 0.8328 (OUTLIER) cc_final: 0.6960 (mpt) REVERT: D 125 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7859 (mt-10) REVERT: D 286 ASP cc_start: 0.8263 (m-30) cc_final: 0.8043 (m-30) REVERT: D 334 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7416 (pp20) REVERT: E 44 MET cc_start: 0.8084 (OUTLIER) cc_final: 0.6406 (mpt) REVERT: E 64 ILE cc_start: 0.9223 (OUTLIER) cc_final: 0.8616 (pp) REVERT: E 167 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8010 (mp0) REVERT: E 314 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.8375 (tt0) REVERT: E 328 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8609 (tttt) outliers start: 58 outliers final: 16 residues processed: 201 average time/residue: 1.4347 time to fit residues: 314.3685 Evaluate side-chains 198 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 165 time to evaluate : 1.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 328 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 48 optimal weight: 6.9990 chunk 143 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 88 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 8 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 9 optimal weight: 8.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN A 12 ASN A 225 GLN B 12 ASN B 128 ASN E 296 ASN E 354 GLN E 371 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.107462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.086783 restraints weight = 15647.021| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 1.31 r_work: 0.2843 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14630 Z= 0.119 Angle : 0.566 7.321 19870 Z= 0.269 Chirality : 0.044 0.186 2215 Planarity : 0.003 0.037 2525 Dihedral : 9.584 135.863 2026 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 2.81 % Allowed : 7.32 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.20), residues: 1780 helix: 0.93 (0.19), residues: 740 sheet: 0.51 (0.26), residues: 330 loop : 2.23 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 340 HIS 0.003 0.001 HIS B 161 PHE 0.009 0.001 PHE D 262 TYR 0.013 0.001 TYR A 143 ARG 0.002 0.000 ARG C 210 Details of bonding type rmsd hydrogen bonds : bond 0.03531 ( 718) hydrogen bonds : angle 4.65696 ( 1863) covalent geometry : bond 0.00268 (14630) covalent geometry : angle 0.56630 (19870) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 183 time to evaluate : 1.752 Fit side-chains REVERT: C 57 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7632 (pt0) REVERT: C 72 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.7620 (mp0) REVERT: C 246 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.8076 (tt0) REVERT: C 314 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.8376 (tt0) REVERT: A 72 GLU cc_start: 0.8486 (mt-10) cc_final: 0.8240 (mp0) REVERT: A 276 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8106 (mt-10) REVERT: A 326 LYS cc_start: 0.8590 (mptp) cc_final: 0.8028 (tttt) REVERT: B 171 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8635 (mp) REVERT: B 314 GLN cc_start: 0.8962 (OUTLIER) cc_final: 0.8524 (tt0) REVERT: D 44 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.7158 (mpt) REVERT: D 180 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8807 (tp) REVERT: D 286 ASP cc_start: 0.8239 (m-30) cc_final: 0.8016 (m-30) REVERT: D 292 ASP cc_start: 0.8702 (m-30) cc_final: 0.8390 (m-30) REVERT: E 41 GLN cc_start: 0.6731 (OUTLIER) cc_final: 0.6500 (pm20) REVERT: E 44 MET cc_start: 0.8088 (OUTLIER) cc_final: 0.6586 (mpt) REVERT: E 64 ILE cc_start: 0.9193 (OUTLIER) cc_final: 0.8566 (pp) REVERT: E 167 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.7980 (mp0) REVERT: E 314 GLN cc_start: 0.8868 (OUTLIER) cc_final: 0.8316 (tt0) outliers start: 43 outliers final: 8 residues processed: 207 average time/residue: 1.4146 time to fit residues: 319.5723 Evaluate side-chains 196 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 174 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 314 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 18 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 104 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 177 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 80 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 225 GLN B 12 ASN D 92 ASN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 ASN E 296 ASN E 354 GLN E 371 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.104789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.083586 restraints weight = 15746.136| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 1.32 r_work: 0.2783 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2642 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 14630 Z= 0.266 Angle : 0.675 8.732 19870 Z= 0.329 Chirality : 0.050 0.205 2215 Planarity : 0.005 0.043 2525 Dihedral : 10.250 140.702 2026 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 3.27 % Allowed : 7.06 % Favored : 89.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.20), residues: 1780 helix: 0.89 (0.19), residues: 745 sheet: 0.50 (0.26), residues: 330 loop : 2.04 (0.25), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP C 340 HIS 0.005 0.001 HIS B 88 PHE 0.016 0.002 PHE D 262 TYR 0.012 0.001 TYR A 143 ARG 0.005 0.001 ARG D 290 Details of bonding type rmsd hydrogen bonds : bond 0.04979 ( 718) hydrogen bonds : angle 4.95962 ( 1863) covalent geometry : bond 0.00630 (14630) covalent geometry : angle 0.67451 (19870) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 176 time to evaluate : 1.872 Fit side-chains REVERT: C 57 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7676 (pt0) REVERT: C 72 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.7686 (mp0) REVERT: C 95 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.7958 (mtm-85) REVERT: C 123 MET cc_start: 0.9148 (mmt) cc_final: 0.8923 (mmt) REVERT: C 246 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.8144 (tt0) REVERT: C 314 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.8381 (tt0) REVERT: A 72 GLU cc_start: 0.8534 (mt-10) cc_final: 0.8279 (mp0) REVERT: A 276 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.8099 (mt-10) REVERT: A 326 LYS cc_start: 0.8622 (mptp) cc_final: 0.8089 (tttt) REVERT: B 95 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7833 (mtp180) REVERT: B 125 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.7217 (mp0) REVERT: B 314 GLN cc_start: 0.8987 (OUTLIER) cc_final: 0.8555 (tt0) REVERT: B 326 LYS cc_start: 0.8461 (mmtm) cc_final: 0.7829 (pttm) REVERT: D 44 MET cc_start: 0.8330 (OUTLIER) cc_final: 0.6930 (mpt) REVERT: D 180 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8922 (tp) REVERT: D 286 ASP cc_start: 0.8258 (m-30) cc_final: 0.8041 (m-30) REVERT: D 334 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7538 (pp20) REVERT: E 41 GLN cc_start: 0.6716 (OUTLIER) cc_final: 0.6442 (pm20) REVERT: E 44 MET cc_start: 0.8081 (OUTLIER) cc_final: 0.6398 (mpt) REVERT: E 64 ILE cc_start: 0.9233 (OUTLIER) cc_final: 0.8646 (pp) REVERT: E 99 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8212 (mp0) REVERT: E 167 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8011 (mp0) REVERT: E 314 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.8352 (tt0) REVERT: E 355 MET cc_start: 0.8489 (mmt) cc_final: 0.8206 (mmm) outliers start: 50 outliers final: 18 residues processed: 204 average time/residue: 1.4676 time to fit residues: 326.8603 Evaluate side-chains 208 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 172 time to evaluate : 1.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 30 optimal weight: 0.9990 chunk 178 optimal weight: 1.9990 chunk 165 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 77 optimal weight: 0.0870 overall best weight: 0.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN A 12 ASN A 225 GLN B 12 ASN B 128 ASN E 92 ASN E 296 ASN E 354 GLN E 371 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.107984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.087070 restraints weight = 15714.386| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 1.33 r_work: 0.2846 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14630 Z= 0.108 Angle : 0.562 7.298 19870 Z= 0.267 Chirality : 0.044 0.184 2215 Planarity : 0.003 0.036 2525 Dihedral : 9.573 135.500 2026 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Rotamer: Outliers : 2.55 % Allowed : 8.04 % Favored : 89.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.20), residues: 1780 helix: 1.18 (0.20), residues: 740 sheet: 0.57 (0.26), residues: 330 loop : 2.23 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 79 HIS 0.003 0.001 HIS B 161 PHE 0.009 0.001 PHE D 262 TYR 0.012 0.001 TYR A 143 ARG 0.002 0.000 ARG B 28 Details of bonding type rmsd hydrogen bonds : bond 0.03304 ( 718) hydrogen bonds : angle 4.58199 ( 1863) covalent geometry : bond 0.00239 (14630) covalent geometry : angle 0.56172 (19870) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 180 time to evaluate : 1.737 Fit side-chains REVERT: C 57 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7580 (pt0) REVERT: C 72 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.7634 (mp0) REVERT: C 314 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.8391 (tt0) REVERT: A 72 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8246 (mp0) REVERT: A 276 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8112 (mt-10) REVERT: A 326 LYS cc_start: 0.8618 (mptp) cc_final: 0.8114 (tttt) REVERT: B 125 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7192 (mp0) REVERT: B 314 GLN cc_start: 0.8957 (OUTLIER) cc_final: 0.8524 (tt0) REVERT: B 326 LYS cc_start: 0.8455 (mmtm) cc_final: 0.7871 (pttm) REVERT: D 44 MET cc_start: 0.8275 (OUTLIER) cc_final: 0.7200 (mpt) REVERT: D 51 ASP cc_start: 0.7834 (t0) cc_final: 0.7523 (p0) REVERT: D 180 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8805 (tp) REVERT: D 286 ASP cc_start: 0.8206 (m-30) cc_final: 0.7988 (m-30) REVERT: E 41 GLN cc_start: 0.6751 (OUTLIER) cc_final: 0.6446 (pm20) REVERT: E 44 MET cc_start: 0.8056 (OUTLIER) cc_final: 0.6589 (mpt) REVERT: E 51 ASP cc_start: 0.8067 (t0) cc_final: 0.7829 (t70) REVERT: E 64 ILE cc_start: 0.9193 (OUTLIER) cc_final: 0.8572 (pp) REVERT: E 99 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8153 (mp0) REVERT: E 167 GLU cc_start: 0.8499 (mp0) cc_final: 0.7953 (mp0) REVERT: E 314 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8341 (tt0) outliers start: 39 outliers final: 10 residues processed: 203 average time/residue: 1.4800 time to fit residues: 327.5031 Evaluate side-chains 198 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 175 time to evaluate : 1.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 174 optimal weight: 3.9990 chunk 108 optimal weight: 10.0000 chunk 141 optimal weight: 4.9990 chunk 170 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 178 optimal weight: 0.8980 chunk 101 optimal weight: 6.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN A 12 ASN A 225 GLN B 12 ASN D 92 ASN E 92 ASN E 296 ASN E 354 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.107046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.085998 restraints weight = 15752.563| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 1.33 r_work: 0.2827 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14630 Z= 0.142 Angle : 0.583 7.644 19870 Z= 0.278 Chirality : 0.045 0.189 2215 Planarity : 0.003 0.036 2525 Dihedral : 9.707 135.435 2026 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 3.07 % Allowed : 7.78 % Favored : 89.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.20), residues: 1780 helix: 1.24 (0.20), residues: 740 sheet: 0.59 (0.26), residues: 330 loop : 2.26 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 340 HIS 0.003 0.001 HIS B 88 PHE 0.010 0.001 PHE D 262 TYR 0.011 0.001 TYR A 143 ARG 0.002 0.000 ARG B 290 Details of bonding type rmsd hydrogen bonds : bond 0.03727 ( 718) hydrogen bonds : angle 4.62686 ( 1863) covalent geometry : bond 0.00326 (14630) covalent geometry : angle 0.58327 (19870) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 173 time to evaluate : 1.725 Fit side-chains REVERT: C 57 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7684 (pt0) REVERT: C 72 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.7654 (mp0) REVERT: C 95 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.7958 (mtm-85) REVERT: C 123 MET cc_start: 0.9118 (mmt) cc_final: 0.8827 (mmt) REVERT: C 246 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.8106 (tt0) REVERT: C 314 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.8370 (tt0) REVERT: A 57 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7597 (pt0) REVERT: A 72 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8268 (mp0) REVERT: A 276 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8134 (mt-10) REVERT: A 326 LYS cc_start: 0.8623 (mptp) cc_final: 0.8121 (tttt) REVERT: B 125 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7184 (mp0) REVERT: B 314 GLN cc_start: 0.8974 (OUTLIER) cc_final: 0.8538 (tt0) REVERT: B 326 LYS cc_start: 0.8457 (mmtm) cc_final: 0.7885 (pttm) REVERT: D 44 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.7069 (mpt) REVERT: D 51 ASP cc_start: 0.7846 (t0) cc_final: 0.7578 (p0) REVERT: D 180 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8825 (tp) REVERT: D 286 ASP cc_start: 0.8218 (m-30) cc_final: 0.7996 (m-30) REVERT: D 334 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7522 (pp20) REVERT: E 41 GLN cc_start: 0.6761 (OUTLIER) cc_final: 0.6451 (pm20) REVERT: E 44 MET cc_start: 0.8034 (OUTLIER) cc_final: 0.6459 (mpt) REVERT: E 51 ASP cc_start: 0.8068 (t0) cc_final: 0.7835 (t70) REVERT: E 64 ILE cc_start: 0.9200 (OUTLIER) cc_final: 0.8586 (pp) REVERT: E 99 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8152 (mp0) REVERT: E 167 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.7984 (mp0) REVERT: E 314 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.8317 (tt0) outliers start: 47 outliers final: 16 residues processed: 199 average time/residue: 1.4604 time to fit residues: 317.3297 Evaluate side-chains 205 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 171 time to evaluate : 1.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 124 optimal weight: 0.0370 chunk 35 optimal weight: 6.9990 chunk 87 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 117 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 132 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 126 optimal weight: 0.6980 chunk 102 optimal weight: 0.7980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN A 12 ASN A 225 GLN B 12 ASN B 128 ASN D 128 ASN E 92 ASN E 296 ASN E 354 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.109043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.088297 restraints weight = 15700.378| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 1.32 r_work: 0.2868 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14630 Z= 0.098 Angle : 0.543 6.919 19870 Z= 0.257 Chirality : 0.043 0.175 2215 Planarity : 0.003 0.036 2525 Dihedral : 9.396 132.552 2026 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 2.48 % Allowed : 8.63 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.20), residues: 1780 helix: 1.35 (0.20), residues: 740 sheet: 0.63 (0.26), residues: 330 loop : 2.36 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 340 HIS 0.003 0.001 HIS B 161 PHE 0.007 0.001 PHE D 262 TYR 0.012 0.001 TYR A 143 ARG 0.002 0.000 ARG B 28 Details of bonding type rmsd hydrogen bonds : bond 0.03024 ( 718) hydrogen bonds : angle 4.44571 ( 1863) covalent geometry : bond 0.00217 (14630) covalent geometry : angle 0.54342 (19870) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 175 time to evaluate : 1.636 Fit side-chains REVERT: C 57 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7656 (pt0) REVERT: C 72 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.7636 (mp0) REVERT: C 95 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.8001 (mtm-85) REVERT: C 246 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.8090 (tt0) REVERT: C 314 GLN cc_start: 0.8827 (OUTLIER) cc_final: 0.8383 (tt0) REVERT: A 57 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7596 (pt0) REVERT: A 72 GLU cc_start: 0.8475 (mt-10) cc_final: 0.8231 (mp0) REVERT: A 276 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8142 (mt-10) REVERT: A 326 LYS cc_start: 0.8620 (mptp) cc_final: 0.8152 (tttt) REVERT: B 125 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7138 (mp0) REVERT: B 314 GLN cc_start: 0.8957 (OUTLIER) cc_final: 0.8521 (tt0) REVERT: B 326 LYS cc_start: 0.8440 (mmtm) cc_final: 0.7921 (pttm) REVERT: D 44 MET cc_start: 0.8272 (OUTLIER) cc_final: 0.7190 (mpt) REVERT: D 51 ASP cc_start: 0.7829 (t0) cc_final: 0.7507 (p0) REVERT: D 180 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8793 (tp) REVERT: D 286 ASP cc_start: 0.8226 (m-30) cc_final: 0.7990 (m-30) REVERT: E 41 GLN cc_start: 0.6752 (OUTLIER) cc_final: 0.6503 (pm20) REVERT: E 44 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.6601 (mpt) REVERT: E 51 ASP cc_start: 0.8039 (t0) cc_final: 0.7810 (t70) REVERT: E 64 ILE cc_start: 0.9181 (OUTLIER) cc_final: 0.8553 (pp) REVERT: E 99 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8128 (mp0) REVERT: E 167 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.7951 (mp0) REVERT: E 314 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.8324 (tt0) REVERT: E 355 MET cc_start: 0.8448 (mmt) cc_final: 0.8153 (mmm) outliers start: 38 outliers final: 9 residues processed: 197 average time/residue: 1.5510 time to fit residues: 333.9668 Evaluate side-chains 201 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 175 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain E residue 314 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 177 optimal weight: 8.9990 chunk 117 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 10 optimal weight: 0.5980 chunk 129 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 50 optimal weight: 9.9990 chunk 111 optimal weight: 7.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN A 12 ASN A 225 GLN B 12 ASN D 128 ASN E 92 ASN E 296 ASN E 354 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.106353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.085296 restraints weight = 15627.495| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 1.32 r_work: 0.2814 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14630 Z= 0.177 Angle : 0.610 7.987 19870 Z= 0.293 Chirality : 0.046 0.191 2215 Planarity : 0.004 0.035 2525 Dihedral : 9.861 135.974 2026 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 2.61 % Allowed : 8.50 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.20), residues: 1780 helix: 1.20 (0.20), residues: 745 sheet: 0.65 (0.26), residues: 330 loop : 2.24 (0.25), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 340 HIS 0.004 0.001 HIS B 88 PHE 0.012 0.001 PHE D 262 TYR 0.010 0.001 TYR A 143 ARG 0.003 0.000 ARG B 290 Details of bonding type rmsd hydrogen bonds : bond 0.04097 ( 718) hydrogen bonds : angle 4.68913 ( 1863) covalent geometry : bond 0.00414 (14630) covalent geometry : angle 0.60992 (19870) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 173 time to evaluate : 1.614 Fit side-chains REVERT: C 57 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7702 (pt0) REVERT: C 72 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.7645 (mp0) REVERT: C 95 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.7957 (mtm-85) REVERT: C 123 MET cc_start: 0.9118 (mmt) cc_final: 0.8822 (mmt) REVERT: C 246 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.8128 (tt0) REVERT: C 314 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.8388 (tt0) REVERT: A 57 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7611 (pt0) REVERT: A 72 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8258 (mp0) REVERT: A 276 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8116 (mt-10) REVERT: A 326 LYS cc_start: 0.8620 (mptp) cc_final: 0.8139 (tttt) REVERT: B 125 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7227 (mp0) REVERT: B 314 GLN cc_start: 0.8978 (OUTLIER) cc_final: 0.8543 (tt0) REVERT: B 326 LYS cc_start: 0.8466 (mmtm) cc_final: 0.7967 (pttm) REVERT: D 44 MET cc_start: 0.8296 (OUTLIER) cc_final: 0.7029 (mpt) REVERT: D 180 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8835 (tp) REVERT: D 286 ASP cc_start: 0.8236 (m-30) cc_final: 0.8012 (m-30) REVERT: D 314 GLN cc_start: 0.8906 (OUTLIER) cc_final: 0.8384 (tt0) REVERT: E 41 GLN cc_start: 0.6757 (OUTLIER) cc_final: 0.6456 (pm20) REVERT: E 44 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.6422 (mpt) REVERT: E 51 ASP cc_start: 0.8097 (t0) cc_final: 0.7843 (t70) REVERT: E 57 GLU cc_start: 0.8337 (tp30) cc_final: 0.8108 (pt0) REVERT: E 64 ILE cc_start: 0.9209 (OUTLIER) cc_final: 0.8610 (pp) REVERT: E 99 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8108 (mp0) REVERT: E 167 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.7989 (mp0) REVERT: E 314 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.8327 (tt0) REVERT: E 355 MET cc_start: 0.8465 (mmt) cc_final: 0.8177 (mmm) outliers start: 40 outliers final: 14 residues processed: 196 average time/residue: 1.4357 time to fit residues: 307.3737 Evaluate side-chains 203 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 171 time to evaluate : 1.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 37 optimal weight: 2.9990 chunk 108 optimal weight: 10.0000 chunk 143 optimal weight: 0.9990 chunk 165 optimal weight: 5.9990 chunk 60 optimal weight: 0.0030 chunk 77 optimal weight: 0.8980 chunk 172 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 68 optimal weight: 0.0030 chunk 131 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 overall best weight: 0.5804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN A 12 ASN A 225 GLN B 12 ASN B 128 ASN D 92 ASN E 92 ASN E 296 ASN E 354 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.109325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.088574 restraints weight = 15797.873| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 1.33 r_work: 0.2873 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14630 Z= 0.097 Angle : 0.545 6.901 19870 Z= 0.258 Chirality : 0.043 0.176 2215 Planarity : 0.003 0.036 2525 Dihedral : 9.380 133.188 2026 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 2.29 % Allowed : 9.02 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.20), residues: 1780 helix: 1.38 (0.20), residues: 740 sheet: 0.66 (0.26), residues: 330 loop : 2.36 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 79 HIS 0.003 0.001 HIS D 275 PHE 0.007 0.001 PHE D 262 TYR 0.012 0.001 TYR A 143 ARG 0.002 0.000 ARG B 28 Details of bonding type rmsd hydrogen bonds : bond 0.02975 ( 718) hydrogen bonds : angle 4.42503 ( 1863) covalent geometry : bond 0.00214 (14630) covalent geometry : angle 0.54508 (19870) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 174 time to evaluate : 1.806 Fit side-chains REVERT: C 57 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7663 (pt0) REVERT: C 72 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.7648 (mp0) REVERT: C 314 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.8384 (tt0) REVERT: A 57 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7545 (pt0) REVERT: A 72 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8235 (mp0) REVERT: A 276 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8139 (mt-10) REVERT: A 326 LYS cc_start: 0.8615 (mptp) cc_final: 0.8154 (tttt) REVERT: B 314 GLN cc_start: 0.8965 (OUTLIER) cc_final: 0.8532 (tt0) REVERT: B 326 LYS cc_start: 0.8462 (mmtm) cc_final: 0.7976 (pttm) REVERT: D 44 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.7253 (mpt) REVERT: D 51 ASP cc_start: 0.7832 (t0) cc_final: 0.7500 (p0) REVERT: D 180 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8796 (tp) REVERT: D 286 ASP cc_start: 0.8217 (m-30) cc_final: 0.7980 (m-30) REVERT: D 314 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.8366 (tt0) REVERT: E 41 GLN cc_start: 0.6746 (OUTLIER) cc_final: 0.6407 (pm20) REVERT: E 44 MET cc_start: 0.8049 (OUTLIER) cc_final: 0.6585 (mpt) REVERT: E 51 ASP cc_start: 0.8050 (t0) cc_final: 0.7795 (t70) REVERT: E 64 ILE cc_start: 0.9180 (OUTLIER) cc_final: 0.8556 (pp) REVERT: E 99 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8096 (mp0) REVERT: E 167 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.7944 (mp0) REVERT: E 314 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.8337 (tt0) REVERT: E 355 MET cc_start: 0.8455 (mmt) cc_final: 0.8167 (mmm) outliers start: 35 outliers final: 11 residues processed: 194 average time/residue: 1.4801 time to fit residues: 312.9999 Evaluate side-chains 198 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 172 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 370 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 155 optimal weight: 5.9990 chunk 167 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 31 optimal weight: 0.0670 chunk 76 optimal weight: 7.9990 chunk 40 optimal weight: 10.0000 chunk 63 optimal weight: 0.1980 chunk 21 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 29 optimal weight: 0.7980 overall best weight: 1.0122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN A 12 ASN A 225 GLN B 12 ASN D 128 ASN E 92 ASN E 296 ASN E 354 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.108198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.087312 restraints weight = 15687.476| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 1.32 r_work: 0.2852 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14630 Z= 0.118 Angle : 0.562 7.132 19870 Z= 0.267 Chirality : 0.044 0.175 2215 Planarity : 0.003 0.036 2525 Dihedral : 9.459 131.460 2026 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 2.16 % Allowed : 9.02 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.20), residues: 1780 helix: 1.39 (0.20), residues: 740 sheet: 0.68 (0.26), residues: 330 loop : 2.39 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 340 HIS 0.003 0.001 HIS B 161 PHE 0.009 0.001 PHE D 262 TYR 0.010 0.001 TYR A 143 ARG 0.003 0.000 ARG E 28 Details of bonding type rmsd hydrogen bonds : bond 0.03325 ( 718) hydrogen bonds : angle 4.47390 ( 1863) covalent geometry : bond 0.00268 (14630) covalent geometry : angle 0.56202 (19870) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12205.76 seconds wall clock time: 208 minutes 46.75 seconds (12526.75 seconds total)