Starting phenix.real_space_refine on Tue Dec 31 08:31:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a2z_15109/12_2024/8a2z_15109.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a2z_15109/12_2024/8a2z_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_15109/12_2024/8a2z_15109.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a2z_15109/12_2024/8a2z_15109.map" model { file = "/net/cci-nas-00/data/ceres_data/8a2z_15109/12_2024/8a2z_15109.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a2z_15109/12_2024/8a2z_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-5532/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: 7.98, 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: 3.78 Conformation dependent library (CDL) restraints added in 1.8 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: 2.35 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: 5.59 Time building geometry restraints manager: 4.20 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.470 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: 0.020 Extract box with map and model: 0.640 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 35.170 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.880 ------------------------------------------------------------------------------- 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= 0.250 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 *********************** 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 : 1.795 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: 1.7132 time to fit residues: 477.3881 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 : 1.832 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 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= 0.202 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 *********************** 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 : 1.658 Fit side-chains REVERT: B 286 ASP cc_start: 0.7510 (m-30) cc_final: 0.7292 (m-30) REVERT: B 299 MET cc_start: 0.8279 (mtm) cc_final: 0.8078 (mtt) REVERT: E 95 ARG cc_start: 0.7727 (OUTLIER) cc_final: 0.7414 (mtp-110) outliers start: 14 outliers final: 4 residues processed: 198 average time/residue: 1.6873 time to fit residues: 361.3556 Evaluate side-chains 178 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 173 time to evaluate : 1.826 ------------------------------------------------------------------------------- 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 90 optimal weight: 0.4980 chunk 50 optimal weight: 9.9990 chunk 136 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 163 optimal weight: 2.9990 chunk 176 optimal weight: 6.9990 chunk 145 optimal weight: 7.9990 chunk 162 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 131 optimal weight: 2.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 14805 Z= 0.297 Angle : 0.651 8.757 20090 Z= 0.322 Chirality : 0.048 0.207 2230 Planarity : 0.004 0.038 2565 Dihedral : 9.872 129.480 2055 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.61 % Allowed : 8.00 % 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: 0.96 (0.20), residues: 1795 helix: 0.32 (0.19), residues: 790 sheet: -0.29 (0.27), residues: 320 loop : 1.92 (0.26), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP B 340 HIS 0.004 0.001 HIS B 161 PHE 0.012 0.002 PHE B 262 TYR 0.012 0.001 TYR A 143 ARG 0.004 0.001 ARG E 62 *********************** 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 209 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 184 time to evaluate : 1.793 Fit side-chains REVERT: C 125 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.6962 (mp0) REVERT: B 215 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.8216 (mptm) REVERT: B 355 MET cc_start: 0.7837 (OUTLIER) cc_final: 0.7326 (mtm) REVERT: D 95 ARG cc_start: 0.7828 (OUTLIER) cc_final: 0.7285 (mpp-170) REVERT: E 57 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7493 (pt0) REVERT: E 95 ARG cc_start: 0.7719 (OUTLIER) cc_final: 0.7356 (mtp-110) outliers start: 25 outliers final: 8 residues processed: 199 average time/residue: 1.6581 time to fit residues: 357.1847 Evaluate side-chains 182 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 168 time to evaluate : 1.772 ------------------------------------------------------------------------------- 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 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 351 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 8.9990 chunk 123 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 109 optimal weight: 6.9990 chunk 164 optimal weight: 3.9990 chunk 173 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1848 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= 0.265 Angle : 0.631 8.321 20090 Z= 0.311 Chirality : 0.047 0.204 2230 Planarity : 0.004 0.033 2565 Dihedral : 9.914 129.939 2055 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.48 % Allowed : 8.52 % 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: 1.13 (0.20), residues: 1795 helix: 0.50 (0.19), residues: 790 sheet: -0.25 (0.27), residues: 320 loop : 1.99 (0.26), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 340 HIS 0.005 0.001 HIS B 161 PHE 0.010 0.002 PHE B 262 TYR 0.010 0.001 TYR A 143 ARG 0.003 0.000 ARG E 62 *********************** 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 195 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 172 time to evaluate : 1.825 Fit side-chains REVERT: C 125 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.6957 (mp0) REVERT: B 215 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8164 (mptm) REVERT: B 355 MET cc_start: 0.7832 (OUTLIER) cc_final: 0.7328 (mtm) REVERT: D 95 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.7244 (mpp-170) REVERT: E 57 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7549 (pt0) REVERT: E 95 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.7355 (mtp-110) outliers start: 23 outliers final: 9 residues processed: 186 average time/residue: 1.6835 time to fit residues: 339.0043 Evaluate side-chains 182 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 167 time to evaluate : 1.772 ------------------------------------------------------------------------------- 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 10.0000 chunk 98 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 148 optimal weight: 8.9990 chunk 120 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 88 optimal weight: 0.7980 chunk 156 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 88 HIS ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1901 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= 0.262 Angle : 0.629 8.551 20090 Z= 0.309 Chirality : 0.047 0.204 2230 Planarity : 0.004 0.032 2565 Dihedral : 9.930 129.879 2055 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.55 % Allowed : 8.65 % Favored : 89.81 % 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: 1.22 (0.20), residues: 1795 helix: 0.59 (0.19), residues: 790 sheet: -0.23 (0.27), residues: 320 loop : 2.04 (0.26), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 340 HIS 0.005 0.001 HIS B 161 PHE 0.010 0.001 PHE B 262 TYR 0.009 0.001 TYR A 143 ARG 0.003 0.000 ARG B 183 *********************** 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 197 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 173 time to evaluate : 1.754 Fit side-chains REVERT: C 125 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.6922 (mp0) REVERT: B 215 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.8151 (mptm) REVERT: B 355 MET cc_start: 0.7832 (OUTLIER) cc_final: 0.7322 (mtm) REVERT: D 95 ARG cc_start: 0.7802 (OUTLIER) cc_final: 0.7250 (mpp-170) REVERT: E 57 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7520 (pt0) REVERT: E 95 ARG cc_start: 0.7696 (OUTLIER) cc_final: 0.7352 (mtp-110) outliers start: 24 outliers final: 10 residues processed: 189 average time/residue: 1.6615 time to fit residues: 340.0669 Evaluate side-chains 184 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 168 time to evaluate : 1.748 ------------------------------------------------------------------------------- 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 351 THR Chi-restraints excluded: chain B residue 178 LEU 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 57 GLU Chi-restraints excluded: chain E residue 95 ARG 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 58 optimal weight: 9.9990 chunk 156 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 174 optimal weight: 5.9990 chunk 144 optimal weight: 9.9990 chunk 80 optimal weight: 0.2980 chunk 14 optimal weight: 8.9990 chunk 57 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 GLN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1958 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= 0.209 Angle : 0.600 8.213 20090 Z= 0.292 Chirality : 0.045 0.196 2230 Planarity : 0.003 0.032 2565 Dihedral : 9.840 129.424 2055 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.35 % Allowed : 9.10 % Favored : 89.55 % 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: 1.32 (0.20), residues: 1795 helix: 0.68 (0.19), residues: 790 sheet: -0.22 (0.27), residues: 320 loop : 2.09 (0.26), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 340 HIS 0.005 0.001 HIS D 161 PHE 0.009 0.001 PHE B 262 TYR 0.009 0.001 TYR C 143 ARG 0.002 0.000 ARG B 95 *********************** 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 194 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 173 time to evaluate : 1.895 Fit side-chains REVERT: B 355 MET cc_start: 0.7828 (OUTLIER) cc_final: 0.7311 (mtm) REVERT: E 57 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7516 (pt0) REVERT: E 95 ARG cc_start: 0.7670 (OUTLIER) cc_final: 0.7328 (mtp-110) outliers start: 21 outliers final: 13 residues processed: 183 average time/residue: 1.6480 time to fit residues: 326.9504 Evaluate side-chains 184 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 168 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 57 GLU Chi-restraints excluded: chain E residue 95 ARG 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 167 optimal weight: 0.7980 chunk 19 optimal weight: 5.9990 chunk 99 optimal weight: 0.9980 chunk 127 optimal weight: 7.9990 chunk 98 optimal weight: 0.6980 chunk 146 optimal weight: 0.4980 chunk 97 optimal weight: 0.7980 chunk 173 optimal weight: 8.9990 chunk 108 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN B 360 GLN D 246 GLN E 246 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2060 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= 0.145 Angle : 0.562 7.630 20090 Z= 0.269 Chirality : 0.044 0.181 2230 Planarity : 0.003 0.033 2565 Dihedral : 9.593 127.991 2055 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.29 % Allowed : 9.29 % Favored : 89.42 % 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: 1.63 (0.21), residues: 1795 helix: 0.88 (0.19), residues: 780 sheet: -0.03 (0.26), residues: 340 loop : 2.38 (0.26), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 340 HIS 0.004 0.001 HIS D 161 PHE 0.008 0.001 PHE D 31 TYR 0.008 0.001 TYR C 143 ARG 0.003 0.000 ARG E 28 *********************** 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 195 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 175 time to evaluate : 1.769 Fit side-chains REVERT: C 125 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.6886 (mp0) REVERT: B 215 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.8098 (mptm) REVERT: B 355 MET cc_start: 0.7824 (OUTLIER) cc_final: 0.7312 (mtm) REVERT: E 95 ARG cc_start: 0.7624 (OUTLIER) cc_final: 0.7301 (mtp-110) outliers start: 20 outliers final: 8 residues processed: 187 average time/residue: 1.7013 time to fit residues: 346.3278 Evaluate side-chains 182 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 170 time to evaluate : 1.881 ------------------------------------------------------------------------------- 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 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 370 VAL Chi-restraints excluded: chain E residue 95 ARG 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 107 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 34 optimal weight: 0.0060 chunk 33 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 136 optimal weight: 0.6980 overall best weight: 1.0800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN D 246 GLN E 246 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2060 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= 0.175 Angle : 0.577 7.953 20090 Z= 0.278 Chirality : 0.044 0.183 2230 Planarity : 0.003 0.032 2565 Dihedral : 9.591 127.839 2055 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.03 % Allowed : 9.48 % Favored : 89.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.61 (0.21), residues: 1795 helix: 0.92 (0.19), residues: 780 sheet: -0.14 (0.28), residues: 310 loop : 2.23 (0.25), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 340 HIS 0.004 0.001 HIS D 161 PHE 0.007 0.001 PHE D 31 TYR 0.009 0.001 TYR C 143 ARG 0.003 0.000 ARG E 28 *********************** 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 190 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 174 time to evaluate : 1.789 Fit side-chains REVERT: C 125 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.6892 (mp0) REVERT: B 215 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8148 (mptm) REVERT: B 355 MET cc_start: 0.7824 (OUTLIER) cc_final: 0.7315 (mtm) REVERT: D 95 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.7224 (mpp-170) REVERT: E 95 ARG cc_start: 0.7634 (OUTLIER) cc_final: 0.7312 (mtp-110) outliers start: 16 outliers final: 9 residues processed: 182 average time/residue: 1.7154 time to fit residues: 337.8976 Evaluate side-chains 185 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 171 time to evaluate : 1.757 ------------------------------------------------------------------------------- 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 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 368 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 0.8980 chunk 166 optimal weight: 7.9990 chunk 151 optimal weight: 5.9990 chunk 161 optimal weight: 8.9990 chunk 97 optimal weight: 3.9990 chunk 70 optimal weight: 0.5980 chunk 126 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 146 optimal weight: 1.9990 chunk 152 optimal weight: 0.4980 chunk 106 optimal weight: 5.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN B 41 GLN D 246 GLN E 246 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 14805 Z= 0.166 Angle : 0.573 7.817 20090 Z= 0.276 Chirality : 0.044 0.181 2230 Planarity : 0.003 0.032 2565 Dihedral : 9.569 127.387 2055 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.03 % Allowed : 9.42 % Favored : 89.55 % 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: 1.63 (0.21), residues: 1795 helix: 0.95 (0.19), residues: 780 sheet: -0.15 (0.27), residues: 310 loop : 2.22 (0.25), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 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 0.004 0.000 ARG D 28 *********************** 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 187 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 171 time to evaluate : 1.797 Fit side-chains REVERT: C 125 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.6869 (mp0) REVERT: B 215 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.8142 (mptm) REVERT: D 95 ARG cc_start: 0.7784 (OUTLIER) cc_final: 0.7219 (mpp-170) REVERT: E 95 ARG cc_start: 0.7607 (OUTLIER) cc_final: 0.7282 (mtp-110) REVERT: E 176 MET cc_start: 0.8034 (mtt) cc_final: 0.7833 (mtt) outliers start: 16 outliers final: 10 residues processed: 181 average time/residue: 1.7066 time to fit residues: 334.0159 Evaluate side-chains 185 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 171 time to evaluate : 1.788 ------------------------------------------------------------------------------- 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 215 LYS Chi-restraints excluded: chain B residue 350 SER 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 368 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 118 optimal weight: 3.9990 chunk 179 optimal weight: 2.9990 chunk 165 optimal weight: 0.9990 chunk 142 optimal weight: 0.0070 chunk 14 optimal weight: 6.9990 chunk 110 optimal weight: 0.0980 chunk 87 optimal weight: 7.9990 chunk 113 optimal weight: 1.9990 overall best weight: 0.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN B 41 GLN D 246 GLN E 246 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2131 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= 0.148 Angle : 0.562 7.630 20090 Z= 0.270 Chirality : 0.044 0.178 2230 Planarity : 0.003 0.033 2565 Dihedral : 9.466 126.801 2055 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.16 % Allowed : 9.35 % Favored : 89.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.71 (0.21), residues: 1795 helix: 1.00 (0.19), residues: 780 sheet: -0.05 (0.26), residues: 340 loop : 2.38 (0.26), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 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 0.004 0.000 ARG D 28 ********************** 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 191 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 173 time to evaluate : 1.667 Fit side-chains REVERT: C 125 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.6824 (mp0) REVERT: B 215 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.8129 (mptm) REVERT: B 355 MET cc_start: 0.7810 (OUTLIER) cc_final: 0.7302 (mtm) REVERT: D 95 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.7221 (mpp-170) REVERT: E 95 ARG cc_start: 0.7577 (OUTLIER) cc_final: 0.7256 (mtp-110) REVERT: E 176 MET cc_start: 0.8048 (mtt) cc_final: 0.7826 (mtt) outliers start: 18 outliers final: 8 residues processed: 185 average time/residue: 1.7283 time to fit residues: 345.6212 Evaluate side-chains 183 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 170 time to evaluate : 1.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain A residue 323 SER 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 368 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 131 optimal weight: 0.0980 chunk 21 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 143 optimal weight: 3.9990 chunk 59 optimal weight: 0.0470 chunk 146 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 125 optimal weight: 7.9990 overall best weight: 0.9680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN B 41 GLN D 246 GLN E 246 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.122039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.101328 restraints weight = 14610.530| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.14 r_work: 0.3062 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 14805 Z= 0.164 Angle : 0.571 7.829 20090 Z= 0.275 Chirality : 0.044 0.179 2230 Planarity : 0.003 0.032 2565 Dihedral : 9.494 126.982 2055 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.90 % Allowed : 9.74 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1795 helix: 1.02 (0.19), residues: 780 sheet: -0.02 (0.27), residues: 305 loop : 2.18 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 340 HIS 0.005 0.001 HIS D 161 PHE 0.008 0.001 PHE D 31 TYR 0.008 0.001 TYR C 143 ARG 0.004 0.000 ARG D 28 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6150.80 seconds wall clock time: 110 minutes 56.20 seconds (6656.20 seconds total)