Starting phenix.real_space_refine on Sat May 17 00:46:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oi8_16888/05_2025/8oi8_16888.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oi8_16888/05_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_16888/05_2025/8oi8_16888.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oi8_16888/05_2025/8oi8_16888.map" model { file = "/net/cci-nas-00/data/ceres_data/8oi8_16888/05_2025/8oi8_16888.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oi8_16888/05_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 7.99, per 1000 atoms: 0.54 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: 3.48 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: 2.14 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: 5.29 Time building geometry restraints manager: 4.15 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: 0.11 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: 3.530 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: 0.740 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 35.480 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.180 ------------------------------------------------------------------------------- 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 : 1.749 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: 1.4942 time to fit residues: 403.2248 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 : 1.701 ------------------------------------------------------------------------------- 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 = 50)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.090794 restraints weight = 15711.394| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 1.29 r_work: 0.2903 rms_B_bonded: 1.79 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 : 1.752 Fit side-chains REVERT: C 57 GLU cc_start: 0.7810 (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: 0.9406 (OUTLIER) cc_final: 0.8772 (pp) REVERT: A 72 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8271 (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: 0.8329 (OUTLIER) cc_final: 0.7255 (mpt) REVERT: D 125 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7828 (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: 0.7366 (tm130) REVERT: E 44 MET cc_start: 0.8109 (OUTLIER) cc_final: 0.6713 (mpt) REVERT: E 64 ILE cc_start: 0.9180 (OUTLIER) cc_final: 0.8548 (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: 1.4055 time to fit residues: 332.1007 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 : 1.719 ------------------------------------------------------------------------------- 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: 0.1980 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: 10.0000 chunk 96 optimal weight: 1.9990 chunk 118 optimal weight: 0.7980 chunk 165 optimal weight: 5.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 225 GLN B 12 ASN D 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 = 0.3291 r_free = 0.3291 target = 0.107533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.086766 restraints weight = 15676.213| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 1.30 r_work: 0.2840 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14630 Z= 0.156 Angle : 0.599 7.727 19870 Z= 0.287 Chirality : 0.046 0.188 2215 Planarity : 0.004 0.036 2525 Dihedral : 9.772 137.805 2026 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 3.59 % Allowed : 6.27 % Favored : 90.13 % 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: 1.53 (0.21), residues: 1780 helix: 0.57 (0.19), residues: 745 sheet: 0.43 (0.26), residues: 330 loop : 2.22 (0.26), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 340 HIS 0.004 0.001 HIS B 88 PHE 0.010 0.001 PHE D 262 TYR 0.014 0.001 TYR A 143 ARG 0.002 0.000 ARG D 290 Details of bonding type rmsd hydrogen bonds : bond 0.04520 ( 718) hydrogen bonds : angle 4.87825 ( 1863) covalent geometry : bond 0.00356 (14630) covalent geometry : angle 0.59939 (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 230 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 175 time to evaluate : 1.834 Fit side-chains REVERT: C 44 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.6898 (mpt) REVERT: C 72 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.7644 (mp0) REVERT: C 246 GLN cc_start: 0.8558 (OUTLIER) cc_final: 0.8094 (tt0) REVERT: C 314 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.8358 (tt0) REVERT: A 72 GLU cc_start: 0.8559 (mt-10) cc_final: 0.8302 (mp0) REVERT: A 276 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8079 (mt-10) REVERT: A 326 LYS cc_start: 0.8557 (mptp) cc_final: 0.8264 (mmmt) REVERT: B 95 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.7883 (mtp180) REVERT: B 125 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.7303 (mp0) REVERT: B 314 GLN cc_start: 0.8972 (OUTLIER) cc_final: 0.8555 (tt0) REVERT: D 44 MET cc_start: 0.8334 (OUTLIER) cc_final: 0.7064 (mpt) REVERT: D 334 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7389 (pp20) REVERT: E 44 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.6586 (mpt) REVERT: E 64 ILE cc_start: 0.9203 (OUTLIER) cc_final: 0.8591 (pp) REVERT: E 167 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.7965 (mp0) REVERT: E 314 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8386 (tt0) REVERT: E 328 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8648 (tttt) outliers start: 55 outliers final: 15 residues processed: 205 average time/residue: 1.4292 time to fit residues: 319.6881 Evaluate side-chains 202 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 172 time to evaluate : 1.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 MET 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 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 D residue 44 MET 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: 5.9990 chunk 101 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 161 HIS A 225 GLN B 12 ASN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 161 HIS 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 = 0.3271 r_free = 0.3271 target = 0.106205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.085160 restraints weight = 15539.239| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 1.32 r_work: 0.2810 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14630 Z= 0.178 Angle : 0.616 8.081 19870 Z= 0.296 Chirality : 0.046 0.199 2215 Planarity : 0.004 0.036 2525 Dihedral : 9.913 139.040 2026 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 3.40 % Allowed : 6.86 % Favored : 89.74 % 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: 1.70 (0.20), residues: 1780 helix: 0.88 (0.19), residues: 745 sheet: 0.47 (0.26), residues: 330 loop : 2.13 (0.25), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 340 HIS 0.005 0.001 HIS B 161 PHE 0.012 0.001 PHE D 262 TYR 0.014 0.001 TYR A 143 ARG 0.003 0.000 ARG B 290 Details of bonding type rmsd hydrogen bonds : bond 0.04228 ( 718) hydrogen bonds : angle 4.82753 ( 1863) covalent geometry : bond 0.00417 (14630) covalent geometry : angle 0.61608 (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 228 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 176 time to evaluate : 1.814 Fit side-chains REVERT: C 57 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7701 (pt0) REVERT: C 72 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.7631 (mp0) REVERT: C 246 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.8122 (tt0) REVERT: C 314 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.8374 (tt0) REVERT: A 72 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8269 (mp0) REVERT: A 276 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8125 (mt-10) REVERT: A 326 LYS cc_start: 0.8601 (mptp) cc_final: 0.8066 (tttt) REVERT: B 95 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.7810 (mtp180) REVERT: B 125 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.7235 (mp0) REVERT: B 227 MET cc_start: 0.8801 (mmm) cc_final: 0.8451 (mmm) REVERT: B 314 GLN cc_start: 0.8970 (OUTLIER) cc_final: 0.8537 (tt0) REVERT: D 44 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.7040 (mpt) REVERT: D 180 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8890 (tp) REVERT: D 292 ASP cc_start: 0.8747 (m-30) cc_final: 0.8441 (m-30) REVERT: D 334 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7499 (pp20) REVERT: E 41 GLN cc_start: 0.6758 (OUTLIER) cc_final: 0.6448 (pm20) REVERT: E 44 MET cc_start: 0.8073 (OUTLIER) cc_final: 0.6471 (mpt) REVERT: E 64 ILE cc_start: 0.9218 (OUTLIER) cc_final: 0.8615 (pp) REVERT: E 132 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.8501 (ttp) REVERT: E 167 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.7975 (mp0) REVERT: E 314 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.8335 (tt0) REVERT: E 328 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8633 (tttt) outliers start: 52 outliers final: 16 residues processed: 204 average time/residue: 1.3733 time to fit residues: 306.5030 Evaluate side-chains 207 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 173 time to evaluate : 1.747 ------------------------------------------------------------------------------- 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 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 351 THR 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 132 MET 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 328 LYS Chi-restraints excluded: chain E residue 351 THR 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: 0.7980 chunk 50 optimal weight: 9.9990 chunk 104 optimal weight: 0.0020 chunk 114 optimal weight: 0.3980 chunk 177 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 124 optimal weight: 0.6980 chunk 80 optimal weight: 7.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- 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 = 0.3321 r_free = 0.3321 target = 0.109527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.088829 restraints weight = 15851.722| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 1.33 r_work: 0.2875 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14630 Z= 0.093 Angle : 0.539 6.898 19870 Z= 0.254 Chirality : 0.043 0.170 2215 Planarity : 0.003 0.036 2525 Dihedral : 9.376 134.074 2026 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 2.68 % Allowed : 8.17 % 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: 1.18 (0.19), residues: 740 sheet: 0.60 (0.26), residues: 330 loop : 2.32 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 79 HIS 0.003 0.001 HIS B 161 PHE 0.008 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 0.02989 ( 718) hydrogen bonds : angle 4.48742 ( 1863) covalent geometry : bond 0.00200 (14630) covalent geometry : angle 0.53907 (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 224 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 183 time to evaluate : 1.702 Fit side-chains REVERT: C 57 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7676 (pt0) REVERT: C 72 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.7662 (mp0) REVERT: C 171 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8515 (mp) REVERT: C 314 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.8402 (tt0) REVERT: A 72 GLU cc_start: 0.8474 (mt-10) cc_final: 0.8233 (mp0) REVERT: A 276 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8117 (mt-10) REVERT: A 326 LYS cc_start: 0.8578 (mptp) cc_final: 0.8095 (tttt) REVERT: B 57 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7738 (pt0) REVERT: B 314 GLN cc_start: 0.8949 (OUTLIER) cc_final: 0.8514 (tt0) REVERT: B 326 LYS cc_start: 0.8450 (mmtt) cc_final: 0.7831 (pttm) REVERT: D 44 MET cc_start: 0.8297 (OUTLIER) cc_final: 0.7265 (mpt) REVERT: D 51 ASP cc_start: 0.7829 (t0) cc_final: 0.7508 (p0) REVERT: D 180 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8794 (tp) REVERT: E 41 GLN cc_start: 0.6720 (OUTLIER) cc_final: 0.6476 (pm20) REVERT: E 44 MET cc_start: 0.8097 (OUTLIER) cc_final: 0.6667 (mpt) REVERT: E 51 ASP cc_start: 0.8049 (t0) cc_final: 0.7795 (t70) REVERT: E 64 ILE cc_start: 0.9183 (OUTLIER) cc_final: 0.8543 (pp) REVERT: E 99 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8169 (mp0) REVERT: E 167 GLU cc_start: 0.8468 (mp0) cc_final: 0.7954 (mp0) REVERT: E 314 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.8316 (tt0) outliers start: 41 outliers final: 6 residues processed: 206 average time/residue: 1.4215 time to fit residues: 320.1278 Evaluate side-chains 194 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 174 time to evaluate : 1.651 ------------------------------------------------------------------------------- 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 171 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain A residue 44 MET 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 30 optimal weight: 0.7980 chunk 178 optimal weight: 0.2980 chunk 165 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 168 optimal weight: 0.6980 chunk 80 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.3297 r_free = 0.3297 target = 0.107903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.087042 restraints weight = 15737.273| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 1.32 r_work: 0.2846 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14630 Z= 0.123 Angle : 0.563 7.170 19870 Z= 0.266 Chirality : 0.044 0.175 2215 Planarity : 0.003 0.036 2525 Dihedral : 9.512 132.393 2026 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.42 % Allowed : 8.50 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.15 (0.20), residues: 1780 helix: 1.28 (0.20), residues: 740 sheet: 0.65 (0.26), residues: 330 loop : 2.36 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 340 HIS 0.004 0.001 HIS B 161 PHE 0.008 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 0.03441 ( 718) hydrogen bonds : angle 4.53882 ( 1863) covalent geometry : bond 0.00279 (14630) covalent geometry : angle 0.56254 (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 212 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 175 time to evaluate : 1.687 Fit side-chains REVERT: C 57 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7708 (pt0) REVERT: C 72 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.7641 (mp0) REVERT: C 314 GLN cc_start: 0.8835 (OUTLIER) cc_final: 0.8387 (tt0) REVERT: A 72 GLU cc_start: 0.8481 (mt-10) cc_final: 0.8244 (mp0) REVERT: A 276 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8142 (mt-10) REVERT: A 326 LYS cc_start: 0.8620 (mptp) cc_final: 0.8124 (tttt) REVERT: B 57 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7823 (pt0) REVERT: B 125 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7173 (mp0) REVERT: B 314 GLN cc_start: 0.8962 (OUTLIER) cc_final: 0.8522 (tt0) REVERT: B 326 LYS cc_start: 0.8463 (mmtt) cc_final: 0.7875 (pttm) REVERT: D 44 MET cc_start: 0.8305 (OUTLIER) cc_final: 0.7210 (mpt) REVERT: D 51 ASP cc_start: 0.7833 (t0) cc_final: 0.7508 (p0) REVERT: D 180 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8797 (tp) REVERT: D 334 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7519 (pp20) REVERT: E 41 GLN cc_start: 0.6750 (OUTLIER) cc_final: 0.6439 (pm20) REVERT: E 44 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.6566 (mpt) REVERT: E 51 ASP cc_start: 0.8064 (t0) cc_final: 0.7819 (t70) REVERT: E 64 ILE cc_start: 0.9195 (OUTLIER) cc_final: 0.8575 (pp) REVERT: E 99 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8156 (mp0) REVERT: E 167 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.7971 (mp0) REVERT: E 314 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.8316 (tt0) outliers start: 37 outliers final: 11 residues processed: 197 average time/residue: 1.3752 time to fit residues: 295.7504 Evaluate side-chains 200 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 173 time to evaluate : 1.642 ------------------------------------------------------------------------------- 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 171 LEU 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 57 GLU 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 171 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 334 GLU 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 174 optimal weight: 0.8980 chunk 108 optimal weight: 10.0000 chunk 141 optimal weight: 0.9990 chunk 170 optimal weight: 8.9990 chunk 95 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 chunk 20 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 178 optimal weight: 0.9990 chunk 101 optimal weight: 4.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 = 0.3309 r_free = 0.3309 target = 0.108727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.087911 restraints weight = 15805.046| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 1.33 r_work: 0.2860 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14630 Z= 0.107 Angle : 0.550 6.996 19870 Z= 0.260 Chirality : 0.043 0.170 2215 Planarity : 0.003 0.036 2525 Dihedral : 9.402 132.156 2026 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 2.88 % Allowed : 8.56 % Favored : 88.56 % 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: 2.21 (0.20), residues: 1780 helix: 1.33 (0.20), residues: 740 sheet: 0.66 (0.26), residues: 330 loop : 2.41 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 340 HIS 0.004 0.001 HIS B 161 PHE 0.008 0.001 PHE D 262 TYR 0.011 0.001 TYR A 143 ARG 0.002 0.000 ARG E 28 Details of bonding type rmsd hydrogen bonds : bond 0.03179 ( 718) hydrogen bonds : angle 4.46103 ( 1863) covalent geometry : bond 0.00240 (14630) covalent geometry : angle 0.55039 (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 222 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 178 time to evaluate : 1.867 Fit side-chains REVERT: C 72 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.7658 (mp0) REVERT: C 95 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.7968 (mtm-85) REVERT: C 246 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.8115 (tt0) REVERT: C 314 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.8384 (tt0) REVERT: A 57 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7577 (pt0) REVERT: A 72 GLU cc_start: 0.8477 (mt-10) cc_final: 0.8235 (mp0) REVERT: A 276 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8153 (mt-10) REVERT: A 326 LYS cc_start: 0.8635 (mptp) cc_final: 0.8149 (tttt) REVERT: B 57 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7848 (pt0) REVERT: B 125 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7161 (mp0) REVERT: B 314 GLN cc_start: 0.8958 (OUTLIER) cc_final: 0.8521 (tt0) REVERT: B 326 LYS cc_start: 0.8464 (mmtt) cc_final: 0.7892 (pttm) REVERT: D 44 MET cc_start: 0.8305 (OUTLIER) cc_final: 0.7234 (mpt) REVERT: D 51 ASP cc_start: 0.7824 (t0) cc_final: 0.7501 (p0) REVERT: D 180 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8795 (tp) REVERT: E 41 GLN cc_start: 0.6730 (OUTLIER) cc_final: 0.6404 (pm20) REVERT: E 44 MET cc_start: 0.8080 (OUTLIER) cc_final: 0.6609 (mpt) REVERT: E 51 ASP cc_start: 0.8068 (t0) cc_final: 0.7810 (t70) REVERT: E 64 ILE cc_start: 0.9190 (OUTLIER) cc_final: 0.8565 (pp) REVERT: E 99 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8126 (mp0) REVERT: E 167 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.7976 (mp0) REVERT: E 314 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.8334 (tt0) outliers start: 44 outliers final: 10 residues processed: 204 average time/residue: 1.4318 time to fit residues: 318.9660 Evaluate side-chains 203 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 176 time to evaluate : 1.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 57 GLU 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 171 LEU 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 99 GLU Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain E residue 314 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 124 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 117 optimal weight: 0.7980 chunk 135 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 132 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 126 optimal weight: 0.5980 chunk 102 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 E 92 ASN E 296 ASN E 354 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.108252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.087394 restraints weight = 15682.291| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 1.32 r_work: 0.2853 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.3101 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= 0.117 Angle : 0.558 7.115 19870 Z= 0.264 Chirality : 0.044 0.174 2215 Planarity : 0.003 0.035 2525 Dihedral : 9.451 131.852 2026 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.55 % Allowed : 8.82 % Favored : 88.63 % 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: 1.37 (0.20), residues: 740 sheet: 0.70 (0.26), residues: 330 loop : 2.40 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 340 HIS 0.004 0.001 HIS B 161 PHE 0.008 0.001 PHE D 262 TYR 0.010 0.001 TYR A 143 ARG 0.002 0.000 ARG E 28 Details of bonding type rmsd hydrogen bonds : bond 0.03331 ( 718) hydrogen bonds : angle 4.48635 ( 1863) covalent geometry : bond 0.00263 (14630) covalent geometry : angle 0.55776 (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 215 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 176 time to evaluate : 1.681 Fit side-chains REVERT: C 72 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.7624 (mp0) REVERT: C 95 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.7989 (mtm-85) REVERT: C 246 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.8105 (tt0) REVERT: C 314 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.8380 (tt0) REVERT: A 57 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7585 (pt0) REVERT: A 72 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8244 (mp0) REVERT: A 276 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8136 (mt-10) REVERT: A 326 LYS cc_start: 0.8605 (mptp) cc_final: 0.8135 (tttt) REVERT: B 57 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7858 (pt0) REVERT: B 125 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7170 (mp0) REVERT: B 314 GLN cc_start: 0.8965 (OUTLIER) cc_final: 0.8530 (tt0) REVERT: B 326 LYS cc_start: 0.8471 (mmtt) cc_final: 0.7913 (pttm) REVERT: D 44 MET cc_start: 0.8310 (OUTLIER) cc_final: 0.7205 (mpt) REVERT: D 51 ASP cc_start: 0.7837 (t0) cc_final: 0.7501 (p0) REVERT: D 180 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8788 (tp) REVERT: E 41 GLN cc_start: 0.6737 (OUTLIER) cc_final: 0.6406 (pm20) REVERT: E 44 MET cc_start: 0.8068 (OUTLIER) cc_final: 0.6598 (mpt) REVERT: E 64 ILE cc_start: 0.9195 (OUTLIER) cc_final: 0.8576 (pp) REVERT: E 99 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8131 (mp0) REVERT: E 167 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.7982 (mp0) REVERT: E 314 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.8307 (tt0) outliers start: 39 outliers final: 14 residues processed: 198 average time/residue: 1.4051 time to fit residues: 304.1293 Evaluate side-chains 204 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 173 time to evaluate : 1.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 57 GLU 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 235 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 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 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: 0.7980 chunk 54 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 129 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 50 optimal weight: 10.0000 chunk 111 optimal weight: 8.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 E 92 ASN E 296 ASN E 354 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.107267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.086292 restraints weight = 15655.250| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 1.32 r_work: 0.2836 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.3091 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 : 0.582 7.549 19870 Z= 0.278 Chirality : 0.045 0.184 2215 Planarity : 0.003 0.035 2525 Dihedral : 9.648 134.010 2026 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 2.42 % Allowed : 9.22 % Favored : 88.37 % 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: 2.14 (0.20), residues: 1780 helix: 1.27 (0.20), residues: 745 sheet: 0.72 (0.26), residues: 330 loop : 2.32 (0.25), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 340 HIS 0.004 0.001 HIS B 161 PHE 0.009 0.001 PHE D 262 TYR 0.010 0.001 TYR A 143 ARG 0.002 0.000 ARG E 28 Details of bonding type rmsd hydrogen bonds : bond 0.03683 ( 718) hydrogen bonds : angle 4.57597 ( 1863) covalent geometry : bond 0.00326 (14630) covalent geometry : angle 0.58205 (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 211 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 174 time to evaluate : 1.735 Fit side-chains REVERT: C 72 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.7647 (mp0) REVERT: C 95 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.7939 (mtm-85) REVERT: C 246 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.8090 (tt0) REVERT: C 314 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.8389 (tt0) REVERT: A 57 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7610 (pt0) REVERT: A 72 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8236 (mp0) REVERT: A 276 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8126 (mt-10) REVERT: A 326 LYS cc_start: 0.8599 (mptp) cc_final: 0.8146 (tttt) REVERT: B 57 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7847 (pt0) REVERT: B 125 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7191 (mp0) REVERT: B 314 GLN cc_start: 0.8976 (OUTLIER) cc_final: 0.8542 (tt0) REVERT: B 326 LYS cc_start: 0.8485 (mmtt) cc_final: 0.7927 (pttm) REVERT: D 44 MET cc_start: 0.8308 (OUTLIER) cc_final: 0.7177 (mpt) REVERT: D 180 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8797 (tp) REVERT: D 354 GLN cc_start: 0.8544 (pm20) cc_final: 0.8274 (pm20) REVERT: E 41 GLN cc_start: 0.6740 (OUTLIER) cc_final: 0.6427 (pm20) REVERT: E 44 MET cc_start: 0.8046 (OUTLIER) cc_final: 0.6513 (mpt) REVERT: E 64 ILE cc_start: 0.9209 (OUTLIER) cc_final: 0.8598 (pp) REVERT: E 99 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.8093 (mp0) REVERT: E 167 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.7982 (mp0) REVERT: E 180 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8954 (tp) REVERT: E 314 GLN cc_start: 0.8908 (OUTLIER) cc_final: 0.8347 (tt0) REVERT: E 355 MET cc_start: 0.8454 (mmt) cc_final: 0.8151 (mmm) outliers start: 37 outliers final: 14 residues processed: 195 average time/residue: 1.4309 time to fit residues: 304.9195 Evaluate side-chains 204 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 172 time to evaluate : 2.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 57 GLU 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 235 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 99 GLU Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 314 GLN 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: 0.0170 chunk 165 optimal weight: 5.9990 chunk 60 optimal weight: 0.4980 chunk 77 optimal weight: 0.0870 chunk 172 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- 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 = 0.3333 r_free = 0.3333 target = 0.110350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.089725 restraints weight = 15847.757| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 1.33 r_work: 0.2893 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.3214 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= 0.089 Angle : 0.530 6.840 19870 Z= 0.250 Chirality : 0.043 0.163 2215 Planarity : 0.003 0.036 2525 Dihedral : 9.237 132.320 2026 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.16 % Allowed : 9.48 % Favored : 88.37 % 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: 2.33 (0.20), residues: 1780 helix: 1.45 (0.20), residues: 740 sheet: 0.73 (0.25), residues: 330 loop : 2.43 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 79 HIS 0.003 0.001 HIS B 161 PHE 0.006 0.001 PHE C 255 TYR 0.012 0.001 TYR A 143 ARG 0.002 0.000 ARG B 28 Details of bonding type rmsd hydrogen bonds : bond 0.02780 ( 718) hydrogen bonds : angle 4.33490 ( 1863) covalent geometry : bond 0.00193 (14630) covalent geometry : angle 0.53007 (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 213 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 180 time to evaluate : 1.687 Fit side-chains REVERT: C 72 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.7678 (mp0) REVERT: C 171 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8497 (mp) REVERT: C 246 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.8085 (tt0) REVERT: A 57 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7512 (pt0) REVERT: A 72 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8243 (mp0) REVERT: A 276 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.8154 (mt-10) REVERT: A 326 LYS cc_start: 0.8582 (mptp) cc_final: 0.8170 (tttt) REVERT: B 57 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7861 (pt0) REVERT: B 125 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7092 (mp0) REVERT: B 314 GLN cc_start: 0.8961 (OUTLIER) cc_final: 0.8525 (tt0) REVERT: B 326 LYS cc_start: 0.8484 (mmtt) cc_final: 0.7961 (pttm) REVERT: D 44 MET cc_start: 0.8296 (OUTLIER) cc_final: 0.7314 (mpt) REVERT: D 51 ASP cc_start: 0.7822 (t0) cc_final: 0.7488 (p0) REVERT: D 354 GLN cc_start: 0.8571 (pm20) cc_final: 0.8313 (pm20) REVERT: E 41 GLN cc_start: 0.6727 (OUTLIER) cc_final: 0.6396 (pm20) REVERT: E 44 MET cc_start: 0.8051 (OUTLIER) cc_final: 0.6620 (mpt) REVERT: E 64 ILE cc_start: 0.9181 (OUTLIER) cc_final: 0.8554 (pp) REVERT: E 99 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8086 (mp0) REVERT: E 167 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.7945 (mp0) REVERT: E 180 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8917 (tp) REVERT: E 314 GLN cc_start: 0.8901 (OUTLIER) cc_final: 0.8324 (tt0) REVERT: E 355 MET cc_start: 0.8460 (mmt) cc_final: 0.8153 (mmm) outliers start: 33 outliers final: 11 residues processed: 201 average time/residue: 1.4276 time to fit residues: 313.4123 Evaluate side-chains 203 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 176 time to evaluate : 1.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 246 GLN 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 57 GLU 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 171 LEU Chi-restraints excluded: chain D residue 235 SER 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 180 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 155 optimal weight: 5.9990 chunk 167 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 76 optimal weight: 8.9990 chunk 40 optimal weight: 9.9990 chunk 63 optimal weight: 0.3980 chunk 21 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 14 optimal weight: 9.9990 chunk 29 optimal weight: 0.9980 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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 = 0.3282 r_free = 0.3282 target = 0.106862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.085834 restraints weight = 15681.339| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 1.32 r_work: 0.2827 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14630 Z= 0.161 Angle : 0.599 7.700 19870 Z= 0.287 Chirality : 0.046 0.184 2215 Planarity : 0.004 0.034 2525 Dihedral : 9.719 133.817 2026 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 2.42 % Allowed : 9.22 % Favored : 88.37 % 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: 2.19 (0.20), residues: 1780 helix: 1.30 (0.20), residues: 745 sheet: 0.74 (0.26), residues: 330 loop : 2.36 (0.25), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 340 HIS 0.005 0.001 HIS B 161 PHE 0.010 0.001 PHE D 262 TYR 0.009 0.001 TYR C 143 ARG 0.004 0.000 ARG E 28 Details of bonding type rmsd hydrogen bonds : bond 0.03869 ( 718) hydrogen bonds : angle 4.59100 ( 1863) covalent geometry : bond 0.00373 (14630) covalent geometry : angle 0.59944 (19870) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11897.71 seconds wall clock time: 205 minutes 21.27 seconds (12321.27 seconds total)