Starting phenix.real_space_refine on Fri Jun 13 16:56:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a2z_15109/06_2025/8a2z_15109.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a2z_15109/06_2025/8a2z_15109.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8a2z_15109/06_2025/8a2z_15109.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a2z_15109/06_2025/8a2z_15109.map" model { file = "/net/cci-nas-00/data/ceres_data/8a2z_15109/06_2025/8a2z_15109.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a2z_15109/06_2025/8a2z_15109.cif" } resolution = 2.15 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= 0.007 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 Ca 5 9.91 5 P 10 5.49 5 S 100 5.16 5 C 9145 2.51 5 N 2445 2.21 5 O 3355 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15060 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2870 Classifications: {'peptide': 366} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 346} 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: {' CA': 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: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 91 Classifications: {'water': 91} Link IDs: {None: 90} Chain: "B" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 123 Classifications: {'water': 123} Link IDs: {None: 122} Chain: "D" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 121 Classifications: {'water': 121} Link IDs: {None: 120} Chain: "E" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 96 Classifications: {'water': 96} Link IDs: {None: 95} Restraints were copied for chains: C, B, E, D Time building chain proxies: 8.00, per 1000 atoms: 0.53 Number of scatterers: 15060 At special positions: 0 Unit cell: (95.215, 91.74, 191.82, 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) Ca 5 19.99 S 100 16.00 P 10 15.00 O 3355 8.00 N 2445 7.00 C 9145 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: 3.76 Conformation dependent library (CDL) restraints added in 1.9 seconds 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3400 Finding SS restraints... Secondary structure from input PDB file: 115 helices and 30 sheets defined 51.9% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.44 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 97 through 101 removed outlier: 3.561A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.958A 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: 3.736A 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 removed outlier: 3.542A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 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 351 through 355 removed outlier: 4.038A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 367 through 371 Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.561A pdb=" N HIS A 101 " --> pdb=" O PRO A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.957A 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: 3.736A 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 removed outlier: 3.543A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 233 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 351 through 355 removed outlier: 4.038A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 367 through 371 Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.560A pdb=" N HIS B 101 " --> pdb=" O PRO B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.957A 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: 3.736A 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 removed outlier: 3.543A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 233 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 351 through 355 removed outlier: 4.038A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.560A pdb=" N HIS D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.957A 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: 3.735A 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 removed outlier: 3.544A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 233 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 351 through 355 removed outlier: 4.038A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 367 through 371 Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 92 Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.560A pdb=" N HIS E 101 " --> pdb=" O PRO E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.957A 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: 3.736A 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 removed outlier: 3.543A pdb=" N GLU E 207 " --> pdb=" O THR E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 233 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 351 through 355 removed outlier: 4.037A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 367 through 371 Processing sheet with id=AA1, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.537A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N CYS 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 71 through 72 Processing sheet with id=AA4, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AA5, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.299A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.536A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AB2, first strand: chain 'A' and resid 169 through 170 removed outlier: 6.300A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) 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: 6.537A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N CYS 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 169 through 170 Processing sheet with id=AB8, first strand: chain 'B' and resid 169 through 170 removed outlier: 6.300A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (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: 6.537A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N CYS 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: 6.300A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC7, first strand: chain 'E' and resid 29 through 32 removed outlier: 6.536A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N CYS 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: 6.300A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 238 through 241 730 hydrogen bonds defined for protein. 1860 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: 5.43 Time building geometry restraints manager: 4.41 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: 4705 1.34 - 1.46: 3130 1.46 - 1.58: 6780 1.58 - 1.69: 15 1.69 - 1.81: 175 Bond restraints: 14805 Sorted by residual: bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.54e+00 bond pdb=" CE1 HIC D 73 " pdb=" NE2 HIC D 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.52e+00 bond pdb=" CE1 HIC E 73 " pdb=" NE2 HIC E 73 " ideal model delta sigma weight residual 1.347 1.401 -0.054 2.00e-02 2.50e+03 7.35e+00 bond pdb=" CE1 HIC B 73 " pdb=" NE2 HIC B 73 " ideal model delta sigma weight residual 1.347 1.401 -0.054 2.00e-02 2.50e+03 7.34e+00 bond pdb=" CE1 HIC A 73 " pdb=" NE2 HIC A 73 " ideal model delta sigma weight residual 1.347 1.401 -0.054 2.00e-02 2.50e+03 7.34e+00 ... (remaining 14800 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 19565 1.40 - 2.81: 357 2.81 - 4.21: 122 4.21 - 5.61: 26 5.61 - 7.01: 20 Bond angle restraints: 20090 Sorted by residual: angle pdb=" NE ARG A 39 " pdb=" CZ ARG A 39 " pdb=" NH2 ARG A 39 " ideal model delta sigma weight residual 119.20 121.54 -2.34 9.00e-01 1.23e+00 6.78e+00 angle pdb=" NE ARG D 95 " pdb=" CZ ARG D 95 " pdb=" NH2 ARG D 95 " ideal model delta sigma weight residual 119.20 121.52 -2.32 9.00e-01 1.23e+00 6.66e+00 angle pdb=" NE ARG D 39 " pdb=" CZ ARG D 39 " pdb=" NH2 ARG D 39 " ideal model delta sigma weight residual 119.20 121.52 -2.32 9.00e-01 1.23e+00 6.62e+00 angle pdb=" NE ARG E 256 " pdb=" CZ ARG E 256 " pdb=" NH2 ARG E 256 " ideal model delta sigma weight residual 119.20 121.51 -2.31 9.00e-01 1.23e+00 6.58e+00 angle pdb=" NE ARG A 37 " pdb=" CZ ARG A 37 " pdb=" NH2 ARG A 37 " ideal model delta sigma weight residual 119.20 121.51 -2.31 9.00e-01 1.23e+00 6.58e+00 ... (remaining 20085 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.67: 8665 23.67 - 47.34: 195 47.34 - 71.00: 15 71.00 - 94.67: 30 94.67 - 118.34: 5 Dihedral angle restraints: 8910 sinusoidal: 3610 harmonic: 5300 Sorted by residual: dihedral pdb=" O1B ADP D 401 " pdb=" O3A ADP D 401 " pdb=" PB ADP D 401 " pdb=" PA ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 -178.34 118.34 1 2.00e+01 2.50e-03 3.54e+01 dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 -178.30 118.29 1 2.00e+01 2.50e-03 3.54e+01 dihedral pdb=" O1B ADP A 401 " pdb=" O3A ADP A 401 " pdb=" PB ADP A 401 " pdb=" PA ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 -178.29 118.29 1 2.00e+01 2.50e-03 3.54e+01 ... (remaining 8907 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1292 0.031 - 0.063: 625 0.063 - 0.094: 198 0.094 - 0.126: 109 0.126 - 0.157: 6 Chirality restraints: 2230 Sorted by residual: 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 -2.67 0.16 2.00e-01 2.50e+01 6.18e-01 chirality pdb=" C3' ADP D 401 " pdb=" C2' ADP D 401 " pdb=" C4' ADP D 401 " pdb=" O3' ADP D 401 " both_signs ideal model delta sigma weight residual False -2.51 -2.66 0.15 2.00e-01 2.50e+01 5.96e-01 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 -2.66 0.15 2.00e-01 2.50e+01 5.89e-01 ... (remaining 2227 not shown) Planarity restraints: 2565 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 242 " -0.017 5.00e-02 4.00e+02 2.58e-02 1.07e+00 pdb=" N PRO C 243 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO C 243 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO C 243 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 242 " 0.017 5.00e-02 4.00e+02 2.58e-02 1.07e+00 pdb=" N PRO D 243 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO D 243 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO D 243 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 242 " -0.017 5.00e-02 4.00e+02 2.58e-02 1.06e+00 pdb=" N PRO A 243 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 243 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 243 " -0.014 5.00e-02 4.00e+02 ... (remaining 2562 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1058 2.73 - 3.27: 15349 3.27 - 3.82: 27795 3.82 - 4.36: 35515 4.36 - 4.90: 56711 Nonbonded interactions: 136428 Sorted by model distance: nonbonded pdb="CA CA B 402 " pdb=" O HOH B 578 " model vdw 2.190 2.510 nonbonded pdb="CA CA A 402 " pdb=" O HOH A 556 " model vdw 2.206 2.510 nonbonded pdb=" O2B ADP B 401 " pdb="CA CA B 402 " model vdw 2.217 2.510 nonbonded pdb=" O2B ADP E 401 " pdb="CA CA E 402 " model vdw 2.217 2.510 nonbonded pdb=" O2B ADP A 401 " pdb="CA CA A 402 " model vdw 2.217 2.510 ... (remaining 136423 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: 2.720 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: 0.680 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 36.190 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 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 0.055 14805 Z= 0.175 Angle : 0.582 7.015 20090 Z= 0.292 Chirality : 0.043 0.157 2230 Planarity : 0.004 0.033 2565 Dihedral : 11.913 118.341 5510 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.06 % Favored : 97.66 % Rotamer: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % 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: -1.13 (0.19), residues: 1795 helix: -1.95 (0.15), residues: 785 sheet: -0.73 (0.27), residues: 320 loop : 1.21 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 340 HIS 0.003 0.001 HIS E 161 PHE 0.008 0.001 PHE E 262 TYR 0.009 0.001 TYR D 143 ARG 0.003 0.001 ARG B 210 Details of bonding type rmsd hydrogen bonds : bond 0.21348 ( 720) hydrogen bonds : angle 7.85196 ( 1860) covalent geometry : bond 0.00389 (14805) covalent geometry : angle 0.58242 (20090) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 1.807 Fit side-chains REVERT: B 225 ASN cc_start: 0.7901 (m-40) cc_final: 0.7690 (m110) REVERT: B 227 MET cc_start: 0.8770 (mmm) cc_final: 0.8533 (mmm) REVERT: B 286 ASP cc_start: 0.7554 (m-30) cc_final: 0.7347 (m-30) REVERT: D 92 ASN cc_start: 0.8523 (m-40) cc_final: 0.8307 (m110) REVERT: D 128 ASN cc_start: 0.8408 (m-40) cc_final: 0.8200 (m110) outliers start: 0 outliers final: 0 residues processed: 258 average time/residue: 1.6484 time to fit residues: 459.3264 Evaluate side-chains 185 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 1.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 0.8980 chunk 136 optimal weight: 4.9990 chunk 75 optimal weight: 0.0010 chunk 46 optimal weight: 4.9990 chunk 92 optimal weight: 0.7980 chunk 72 optimal weight: 10.0000 chunk 141 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 105 optimal weight: 0.6980 chunk 163 optimal weight: 6.9990 overall best weight: 1.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 59 GLN A 59 GLN A 225 ASN A 353 GLN B 59 GLN B 88 HIS B 360 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 GLN D 246 GLN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 GLN E 353 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.120624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.099699 restraints weight = 14449.895| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.12 r_work: 0.3024 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14805 Z= 0.144 Angle : 0.610 8.082 20090 Z= 0.299 Chirality : 0.045 0.204 2230 Planarity : 0.004 0.032 2565 Dihedral : 9.523 124.723 2055 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.90 % Allowed : 8.06 % Favored : 91.03 % 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: 0.60 (0.20), residues: 1795 helix: -0.15 (0.18), residues: 775 sheet: -0.41 (0.26), residues: 320 loop : 1.91 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 340 HIS 0.004 0.001 HIS E 161 PHE 0.009 0.001 PHE B 262 TYR 0.010 0.001 TYR A 143 ARG 0.003 0.000 ARG B 183 Details of bonding type rmsd hydrogen bonds : bond 0.04418 ( 720) hydrogen bonds : angle 5.25076 ( 1860) covalent geometry : bond 0.00311 (14805) covalent geometry : angle 0.60953 (20090) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 192 time to evaluate : 1.683 Fit side-chains REVERT: B 286 ASP cc_start: 0.7943 (m-30) cc_final: 0.7705 (m-30) REVERT: B 328 LYS cc_start: 0.8505 (ttmt) cc_final: 0.8291 (mtmm) REVERT: D 41 GLN cc_start: 0.6968 (pm20) cc_final: 0.6527 (mm110) REVERT: D 92 ASN cc_start: 0.8736 (m-40) cc_final: 0.8523 (m110) REVERT: D 222 ASP cc_start: 0.8649 (t70) cc_final: 0.8370 (t0) REVERT: E 95 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7759 (mtp-110) outliers start: 14 outliers final: 4 residues processed: 198 average time/residue: 1.6055 time to fit residues: 344.1445 Evaluate side-chains 180 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 175 time to evaluate : 1.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 171 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 59 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 chunk 132 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 148 optimal weight: 7.9990 chunk 149 optimal weight: 0.9990 chunk 174 optimal weight: 4.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 88 HIS A 353 GLN A 360 GLN B 225 ASN ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.119728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.099266 restraints weight = 14461.707| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.08 r_work: 0.3024 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14805 Z= 0.158 Angle : 0.612 8.285 20090 Z= 0.299 Chirality : 0.046 0.196 2230 Planarity : 0.004 0.034 2565 Dihedral : 9.697 128.335 2055 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.68 % Allowed : 7.94 % Favored : 90.39 % 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: 1.01 (0.20), residues: 1795 helix: 0.37 (0.19), residues: 790 sheet: -0.30 (0.27), residues: 320 loop : 1.96 (0.26), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 340 HIS 0.004 0.001 HIS B 161 PHE 0.009 0.001 PHE B 262 TYR 0.011 0.001 TYR A 143 ARG 0.003 0.000 ARG E 62 Details of bonding type rmsd hydrogen bonds : bond 0.04309 ( 720) hydrogen bonds : angle 4.97112 ( 1860) covalent geometry : bond 0.00350 (14805) covalent geometry : angle 0.61201 (20090) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 185 time to evaluate : 1.920 Fit side-chains REVERT: C 99 GLU cc_start: 0.8068 (pm20) cc_final: 0.7798 (pm20) REVERT: C 125 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.7338 (mp0) REVERT: B 64 ILE cc_start: 0.9453 (OUTLIER) cc_final: 0.9249 (pp) REVERT: B 215 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8435 (mptm) REVERT: B 355 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.8042 (mtm) REVERT: D 41 GLN cc_start: 0.6944 (pm20) cc_final: 0.6538 (mm110) REVERT: D 92 ASN cc_start: 0.8723 (m-40) cc_final: 0.8512 (m110) REVERT: D 95 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7559 (mpp-170) REVERT: D 351 THR cc_start: 0.8775 (OUTLIER) cc_final: 0.8464 (p) REVERT: E 57 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7919 (pt0) REVERT: E 95 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7740 (mtp-110) REVERT: E 355 MET cc_start: 0.8309 (mtp) cc_final: 0.7953 (mtt) outliers start: 26 outliers final: 9 residues processed: 201 average time/residue: 1.6262 time to fit residues: 354.2922 Evaluate side-chains 186 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 169 time to evaluate : 1.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 108 optimal weight: 10.0000 chunk 87 optimal weight: 0.4980 chunk 118 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 116 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 177 optimal weight: 7.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 GLN E 353 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.121859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.101652 restraints weight = 14505.361| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.08 r_work: 0.3063 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 14805 Z= 0.107 Angle : 0.559 7.560 20090 Z= 0.268 Chirality : 0.044 0.184 2230 Planarity : 0.003 0.032 2565 Dihedral : 9.501 127.184 2055 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.29 % Allowed : 8.58 % 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: 1.42 (0.20), residues: 1795 helix: 0.64 (0.19), residues: 780 sheet: -0.08 (0.25), residues: 340 loop : 2.32 (0.26), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 340 HIS 0.003 0.001 HIS D 161 PHE 0.007 0.001 PHE B 255 TYR 0.008 0.001 TYR A 143 ARG 0.002 0.000 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.03330 ( 720) hydrogen bonds : angle 4.67856 ( 1860) covalent geometry : bond 0.00225 (14805) covalent geometry : angle 0.55871 (20090) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 178 time to evaluate : 1.659 Fit side-chains REVERT: B 299 MET cc_start: 0.8888 (mtm) cc_final: 0.8676 (mtt) REVERT: B 355 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.7995 (mtm) REVERT: D 41 GLN cc_start: 0.6896 (pm20) cc_final: 0.6553 (mm110) REVERT: D 351 THR cc_start: 0.8698 (OUTLIER) cc_final: 0.8425 (p) REVERT: E 95 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7744 (mtp-110) REVERT: E 355 MET cc_start: 0.8325 (mtp) cc_final: 0.7937 (mtt) outliers start: 20 outliers final: 10 residues processed: 192 average time/residue: 1.6109 time to fit residues: 334.9508 Evaluate side-chains 180 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 167 time to evaluate : 1.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain E residue 276 GLU 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 125 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 131 optimal weight: 0.6980 chunk 105 optimal weight: 7.9990 chunk 86 optimal weight: 10.0000 chunk 63 optimal weight: 0.2980 chunk 103 optimal weight: 0.2980 chunk 41 optimal weight: 7.9990 chunk 167 optimal weight: 1.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 88 HIS D 92 ASN D 246 GLN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.120183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.099734 restraints weight = 14568.095| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 1.08 r_work: 0.3031 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14805 Z= 0.149 Angle : 0.596 8.303 20090 Z= 0.290 Chirality : 0.045 0.188 2230 Planarity : 0.003 0.032 2565 Dihedral : 9.629 128.499 2055 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.35 % Allowed : 8.65 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.33 (0.20), residues: 1795 helix: 0.69 (0.19), residues: 790 sheet: -0.22 (0.27), residues: 320 loop : 2.11 (0.26), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 340 HIS 0.004 0.001 HIS B 161 PHE 0.009 0.001 PHE D 262 TYR 0.009 0.001 TYR A 143 ARG 0.002 0.000 ARG E 62 Details of bonding type rmsd hydrogen bonds : bond 0.03948 ( 720) hydrogen bonds : angle 4.75503 ( 1860) covalent geometry : bond 0.00327 (14805) covalent geometry : angle 0.59646 (20090) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 177 time to evaluate : 1.864 Fit side-chains REVERT: C 125 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.7326 (mp0) REVERT: B 41 GLN cc_start: 0.7681 (pm20) cc_final: 0.7338 (pm20) REVERT: B 215 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8464 (mptm) REVERT: B 355 MET cc_start: 0.8526 (OUTLIER) cc_final: 0.8039 (mtm) REVERT: D 41 GLN cc_start: 0.6911 (pm20) cc_final: 0.6544 (mm110) REVERT: D 95 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7586 (mpp-170) REVERT: E 57 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7874 (pt0) REVERT: E 95 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.7762 (mtp-110) REVERT: E 314 GLN cc_start: 0.8873 (OUTLIER) cc_final: 0.8301 (tt0) REVERT: E 355 MET cc_start: 0.8346 (mtp) cc_final: 0.7956 (mtt) outliers start: 21 outliers final: 8 residues processed: 188 average time/residue: 1.7824 time to fit residues: 362.7782 Evaluate side-chains 189 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 174 time to evaluate : 2.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 354 GLN Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 128 optimal weight: 0.0010 chunk 8 optimal weight: 0.9990 chunk 111 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 45 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 42 optimal weight: 0.0670 chunk 109 optimal weight: 7.9990 chunk 82 optimal weight: 4.9990 overall best weight: 0.8128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 GLN D 246 GLN E 246 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.122056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.101847 restraints weight = 14517.705| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.08 r_work: 0.3067 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 14805 Z= 0.106 Angle : 0.557 7.564 20090 Z= 0.267 Chirality : 0.044 0.180 2230 Planarity : 0.003 0.032 2565 Dihedral : 9.480 127.239 2055 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.29 % Allowed : 9.10 % Favored : 89.61 % 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: 1.62 (0.21), residues: 1795 helix: 0.84 (0.19), residues: 780 sheet: 0.07 (0.26), residues: 335 loop : 2.33 (0.26), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 340 HIS 0.004 0.001 HIS D 161 PHE 0.007 0.001 PHE D 31 TYR 0.007 0.001 TYR C 143 ARG 0.003 0.000 ARG C 28 Details of bonding type rmsd hydrogen bonds : bond 0.03243 ( 720) hydrogen bonds : angle 4.56171 ( 1860) covalent geometry : bond 0.00225 (14805) covalent geometry : angle 0.55684 (20090) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 179 time to evaluate : 1.759 Fit side-chains REVERT: C 125 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.7291 (mp0) REVERT: C 269 MET cc_start: 0.8833 (mtp) cc_final: 0.8617 (mtp) REVERT: B 355 MET cc_start: 0.8514 (OUTLIER) cc_final: 0.8022 (mtm) REVERT: B 360 GLN cc_start: 0.7887 (mp10) cc_final: 0.7659 (pm20) REVERT: D 41 GLN cc_start: 0.6877 (pm20) cc_final: 0.6550 (mm110) REVERT: E 44 MET cc_start: 0.8304 (OUTLIER) cc_final: 0.7900 (mmm) REVERT: E 95 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7721 (mtp-110) REVERT: E 314 GLN cc_start: 0.8859 (OUTLIER) cc_final: 0.8306 (tt0) REVERT: E 355 MET cc_start: 0.8337 (mtp) cc_final: 0.7937 (mtm) outliers start: 20 outliers final: 8 residues processed: 188 average time/residue: 1.5855 time to fit residues: 323.8861 Evaluate side-chains 185 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 172 time to evaluate : 1.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 132 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 123 optimal weight: 7.9990 chunk 166 optimal weight: 7.9990 chunk 171 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 246 GLN E 246 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.121131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.100771 restraints weight = 14483.028| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.08 r_work: 0.3049 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14805 Z= 0.128 Angle : 0.578 8.035 20090 Z= 0.279 Chirality : 0.044 0.181 2230 Planarity : 0.003 0.031 2565 Dihedral : 9.528 127.497 2055 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.42 % Allowed : 9.29 % Favored : 89.29 % 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: 1.60 (0.20), residues: 1795 helix: 0.88 (0.19), residues: 780 sheet: -0.01 (0.28), residues: 305 loop : 2.18 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 340 HIS 0.004 0.001 HIS B 161 PHE 0.007 0.001 PHE D 262 TYR 0.008 0.001 TYR C 143 ARG 0.002 0.000 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.03593 ( 720) hydrogen bonds : angle 4.60834 ( 1860) covalent geometry : bond 0.00279 (14805) covalent geometry : angle 0.57765 (20090) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 176 time to evaluate : 1.784 Fit side-chains REVERT: C 125 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.7277 (mp0) REVERT: B 215 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8434 (mptm) REVERT: B 355 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.8027 (mtm) REVERT: B 360 GLN cc_start: 0.7874 (mp10) cc_final: 0.7636 (pm20) REVERT: D 41 GLN cc_start: 0.6887 (pm20) cc_final: 0.6529 (mm110) REVERT: D 95 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.7544 (mpp-170) REVERT: E 44 MET cc_start: 0.8283 (OUTLIER) cc_final: 0.7833 (mmm) REVERT: E 95 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7711 (mtp-110) REVERT: E 314 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.8303 (tt0) REVERT: E 355 MET cc_start: 0.8349 (mtp) cc_final: 0.7949 (mtm) outliers start: 22 outliers final: 10 residues processed: 188 average time/residue: 2.1338 time to fit residues: 432.7549 Evaluate side-chains 190 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 173 time to evaluate : 1.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 354 GLN Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 78 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 165 optimal weight: 4.9990 chunk 93 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 136 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 246 GLN E 246 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.120783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.100347 restraints weight = 14501.956| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.08 r_work: 0.3042 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 14805 Z= 0.137 Angle : 0.586 8.148 20090 Z= 0.284 Chirality : 0.045 0.185 2230 Planarity : 0.003 0.031 2565 Dihedral : 9.613 128.030 2055 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.35 % Allowed : 9.35 % Favored : 89.29 % 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: 1.49 (0.20), residues: 1795 helix: 0.84 (0.19), residues: 790 sheet: -0.07 (0.27), residues: 315 loop : 2.09 (0.26), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 340 HIS 0.004 0.001 HIS B 161 PHE 0.008 0.001 PHE D 262 TYR 0.008 0.001 TYR A 143 ARG 0.003 0.000 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.03727 ( 720) hydrogen bonds : angle 4.65220 ( 1860) covalent geometry : bond 0.00301 (14805) covalent geometry : angle 0.58648 (20090) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 179 time to evaluate : 1.774 Fit side-chains REVERT: C 125 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.7285 (mp0) REVERT: A 57 GLU cc_start: 0.8256 (tt0) cc_final: 0.8043 (pt0) REVERT: B 215 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8447 (mptm) REVERT: B 355 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.8044 (mtm) REVERT: D 28 ARG cc_start: 0.8471 (tpp-160) cc_final: 0.8236 (mtt-85) REVERT: D 41 GLN cc_start: 0.6825 (pm20) cc_final: 0.6484 (mm110) REVERT: D 354 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.7699 (pp30) REVERT: E 44 MET cc_start: 0.8258 (OUTLIER) cc_final: 0.7806 (mmm) REVERT: E 57 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7860 (pt0) REVERT: E 95 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7731 (mtp-110) REVERT: E 314 GLN cc_start: 0.8872 (OUTLIER) cc_final: 0.8302 (tt0) REVERT: E 355 MET cc_start: 0.8361 (mtp) cc_final: 0.7967 (mtm) outliers start: 21 outliers final: 9 residues processed: 189 average time/residue: 1.6802 time to fit residues: 344.3414 Evaluate side-chains 189 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 172 time to evaluate : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 354 GLN Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 354 GLN Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 69 optimal weight: 8.9990 chunk 150 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 168 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 7 optimal weight: 0.7980 chunk 17 optimal weight: 7.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 ASN D 246 GLN E 12 ASN E 246 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.119976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.098984 restraints weight = 14589.413| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.14 r_work: 0.3020 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14805 Z= 0.191 Angle : 0.631 8.528 20090 Z= 0.311 Chirality : 0.047 0.198 2230 Planarity : 0.004 0.032 2565 Dihedral : 9.852 129.895 2055 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.48 % Allowed : 9.48 % Favored : 89.03 % 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: 1.43 (0.20), residues: 1795 helix: 0.78 (0.19), residues: 790 sheet: -0.08 (0.27), residues: 315 loop : 2.08 (0.26), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 340 HIS 0.005 0.001 HIS E 161 PHE 0.010 0.002 PHE B 262 TYR 0.009 0.001 TYR A 143 ARG 0.004 0.000 ARG E 210 Details of bonding type rmsd hydrogen bonds : bond 0.04342 ( 720) hydrogen bonds : angle 4.81768 ( 1860) covalent geometry : bond 0.00429 (14805) covalent geometry : angle 0.63149 (20090) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 174 time to evaluate : 2.265 Fit side-chains REVERT: C 125 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.7284 (mp0) REVERT: B 215 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8495 (mptm) REVERT: B 241 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8334 (tt0) REVERT: B 355 MET cc_start: 0.8582 (OUTLIER) cc_final: 0.8104 (mtm) REVERT: D 28 ARG cc_start: 0.8506 (tpp-160) cc_final: 0.8282 (mtt-85) REVERT: D 95 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7555 (mpp-170) REVERT: D 354 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.7710 (pp30) REVERT: E 44 MET cc_start: 0.8282 (OUTLIER) cc_final: 0.7794 (mmm) REVERT: E 57 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7889 (pt0) REVERT: E 95 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7719 (mtp-110) REVERT: E 314 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.8289 (tt0) REVERT: E 355 MET cc_start: 0.8402 (mtp) cc_final: 0.8001 (mtm) outliers start: 23 outliers final: 10 residues processed: 186 average time/residue: 1.6512 time to fit residues: 333.8623 Evaluate side-chains 189 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 169 time to evaluate : 1.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 354 GLN Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 354 GLN Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 95 ARG 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 25 optimal weight: 1.9990 chunk 127 optimal weight: 0.7980 chunk 23 optimal weight: 5.9990 chunk 150 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 120 optimal weight: 7.9990 chunk 76 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 GLN B 92 ASN D 246 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.119906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.098931 restraints weight = 14649.217| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 1.14 r_work: 0.3017 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14805 Z= 0.191 Angle : 0.635 8.589 20090 Z= 0.313 Chirality : 0.047 0.199 2230 Planarity : 0.004 0.033 2565 Dihedral : 9.921 130.678 2055 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.23 % Allowed : 9.55 % Favored : 89.23 % 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: 1.40 (0.20), residues: 1795 helix: 0.75 (0.19), residues: 790 sheet: -0.10 (0.27), residues: 315 loop : 2.07 (0.26), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 340 HIS 0.005 0.001 HIS E 161 PHE 0.010 0.002 PHE B 262 TYR 0.009 0.001 TYR A 143 ARG 0.004 0.001 ARG E 210 Details of bonding type rmsd hydrogen bonds : bond 0.04340 ( 720) hydrogen bonds : angle 4.84253 ( 1860) covalent geometry : bond 0.00431 (14805) covalent geometry : angle 0.63485 (20090) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 173 time to evaluate : 1.696 Fit side-chains REVERT: C 125 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.7283 (mp0) REVERT: B 215 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8502 (mptm) REVERT: B 241 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8354 (tt0) REVERT: B 286 ASP cc_start: 0.7968 (m-30) cc_final: 0.7714 (m-30) REVERT: D 28 ARG cc_start: 0.8500 (tpp-160) cc_final: 0.8296 (mtt-85) REVERT: D 64 ILE cc_start: 0.9181 (OUTLIER) cc_final: 0.8829 (pp) REVERT: D 95 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7551 (mpp-170) REVERT: D 354 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.7718 (pp30) REVERT: E 44 MET cc_start: 0.8281 (OUTLIER) cc_final: 0.7789 (mmm) REVERT: E 57 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7886 (pt0) REVERT: E 95 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7692 (mtp-110) REVERT: E 314 GLN cc_start: 0.8872 (OUTLIER) cc_final: 0.8284 (tt0) REVERT: E 355 MET cc_start: 0.8404 (mtp) cc_final: 0.7981 (mtm) outliers start: 19 outliers final: 9 residues processed: 182 average time/residue: 1.5836 time to fit residues: 312.9104 Evaluate side-chains 190 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 171 time to evaluate : 1.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 354 GLN Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 354 GLN Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 95 ARG 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 64 optimal weight: 0.9980 chunk 151 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 167 optimal weight: 0.6980 chunk 146 optimal weight: 0.6980 chunk 160 optimal weight: 0.5980 chunk 23 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 178 optimal weight: 7.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN B 41 GLN B 92 ASN D 246 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.122445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.101718 restraints weight = 14650.741| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.14 r_work: 0.3067 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 14805 Z= 0.108 Angle : 0.564 7.554 20090 Z= 0.271 Chirality : 0.044 0.182 2230 Planarity : 0.003 0.033 2565 Dihedral : 9.634 129.834 2055 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.84 % Allowed : 10.06 % Favored : 89.10 % 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: 1.69 (0.20), residues: 1795 helix: 0.93 (0.19), residues: 780 sheet: 0.08 (0.26), residues: 335 loop : 2.34 (0.26), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 340 HIS 0.005 0.001 HIS D 161 PHE 0.007 0.001 PHE D 31 TYR 0.007 0.001 TYR C 143 ARG 0.003 0.000 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.03255 ( 720) hydrogen bonds : angle 4.55850 ( 1860) covalent geometry : bond 0.00229 (14805) covalent geometry : angle 0.56409 (20090) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15228.62 seconds wall clock time: 266 minutes 10.26 seconds (15970.26 seconds total)