Starting phenix.real_space_refine on Wed Mar 4 17:55:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a2s_15105/03_2026/8a2s_15105.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a2s_15105/03_2026/8a2s_15105.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8a2s_15105/03_2026/8a2s_15105.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a2s_15105/03_2026/8a2s_15105.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8a2s_15105/03_2026/8a2s_15105.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a2s_15105/03_2026/8a2s_15105.map" } resolution = 2.22 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 15 5.49 5 Mg 5 5.21 5 S 100 5.16 5 C 9170 2.51 5 N 2450 2.21 5 O 3401 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15141 Number of models: 1 Model: "" Number of chains: 7 Chain: "C" Number of atoms: 2877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2877 Classifications: {'peptide': 367} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 347} 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: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 145 Classifications: {'water': 145} Link IDs: {None: 144} Chain: "A" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 100 Classifications: {'water': 100} Link IDs: {None: 99} Chain: "B" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 122 Classifications: {'water': 122} Link IDs: {None: 121} Chain: "D" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 130 Classifications: {'water': 130} Link IDs: {None: 129} Chain: "E" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 94 Classifications: {'water': 94} Link IDs: {None: 93} Restraints were copied for chains: A, B, D, E Time building chain proxies: 2.45, per 1000 atoms: 0.16 Number of scatterers: 15141 At special positions: 0 Unit cell: (94.52, 87.57, 193.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 100 16.00 P 15 15.00 Mg 5 11.99 O 3401 8.00 N 2450 7.00 C 9170 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.44 Conformation dependent library (CDL) restraints added in 627.8 milliseconds 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3410 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 30 sheets defined 53.4% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 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 Processing helix chain 'C' and resid 112 through 126 removed outlier: 4.103A 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: 3.690A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 222 through 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 349 Processing helix chain 'C' and resid 350 through 355 removed outlier: 3.532A pdb=" N GLN C 353 " --> pdb=" O SER C 350 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 364 removed outlier: 3.556A pdb=" N GLU C 364 " --> pdb=" O GLN C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 368 removed outlier: 4.235A pdb=" N SER C 368 " --> pdb=" O ALA C 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 365 through 368' Processing helix chain 'C' and resid 369 through 374 Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 97 through 101 Processing helix chain 'A' and resid 112 through 126 removed outlier: 4.103A 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: 3.690A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 222 through 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 349 Processing helix chain 'A' and resid 350 through 355 removed outlier: 3.533A pdb=" N GLN A 353 " --> pdb=" O SER A 350 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 364 removed outlier: 3.557A pdb=" N GLU A 364 " --> pdb=" O GLN A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 368 removed outlier: 4.235A pdb=" N SER A 368 " --> pdb=" O ALA A 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 365 through 368' Processing helix chain 'A' and resid 369 through 374 Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 112 through 126 removed outlier: 4.102A 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: 3.690A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 222 through 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 349 Processing helix chain 'B' and resid 350 through 355 removed outlier: 3.533A pdb=" N GLN B 353 " --> pdb=" O SER B 350 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 364 removed outlier: 3.557A pdb=" N GLU B 364 " --> pdb=" O GLN B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 368 removed outlier: 4.236A pdb=" N SER B 368 " --> pdb=" O ALA B 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 365 through 368' Processing helix chain 'B' and resid 369 through 374 Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 97 through 101 Processing helix chain 'D' and resid 112 through 126 removed outlier: 4.103A 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: 3.690A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 197 No H-bonds generated for 'chain 'D' and resid 195 through 197' Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 222 through 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 349 Processing helix chain 'D' and resid 350 through 355 removed outlier: 3.533A pdb=" N GLN D 353 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 364 removed outlier: 3.557A pdb=" N GLU D 364 " --> pdb=" O GLN D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 368 removed outlier: 4.235A pdb=" N SER D 368 " --> pdb=" O ALA D 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 365 through 368' Processing helix chain 'D' and resid 369 through 374 Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 92 Processing helix chain 'E' and resid 97 through 101 Processing helix chain 'E' and resid 112 through 126 removed outlier: 4.103A 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: 3.690A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'E' and resid 202 through 217 Processing helix chain 'E' and resid 222 through 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 349 Processing helix chain 'E' and resid 350 through 355 removed outlier: 3.533A pdb=" N GLN E 353 " --> pdb=" O SER E 350 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 364 removed outlier: 3.557A pdb=" N GLU E 364 " --> pdb=" O GLN E 360 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 368 removed outlier: 4.235A pdb=" N SER E 368 " --> pdb=" O ALA E 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 365 through 368' Processing helix chain 'E' and resid 369 through 374 Processing sheet with id=AA1, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.599A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.355A 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 41 through 42 removed outlier: 3.829A pdb=" N GLN C 41 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 41 through 42 removed outlier: 3.829A pdb=" N GLN C 41 " --> pdb=" O ALA A 170 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AA6, first strand: chain 'C' and resid 176 through 178 removed outlier: 6.353A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 176 through 178 removed outlier: 3.866A pdb=" N GLN E 41 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AA9, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.599A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AB2, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AB3, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.599A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.355A 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 176 through 178 removed outlier: 6.351A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 176 through 178 removed outlier: 3.903A pdb=" N GLN D 41 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.600A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.355A 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: 6.352A 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: 6.600A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.355A 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: 6.352A 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 241 743 hydrogen bonds defined for protein. 1908 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.99 Time building geometry restraints manager: 1.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4520 1.33 - 1.45: 2105 1.45 - 1.57: 8045 1.57 - 1.69: 15 1.69 - 1.81: 175 Bond restraints: 14860 Sorted by residual: bond pdb=" O4 PO4 B 403 " pdb=" P PO4 B 403 " ideal model delta sigma weight residual 1.568 1.491 0.077 2.00e-02 2.50e+03 1.48e+01 bond pdb=" O4 PO4 C 403 " pdb=" P PO4 C 403 " ideal model delta sigma weight residual 1.568 1.491 0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" O4 PO4 A 403 " pdb=" P PO4 A 403 " ideal model delta sigma weight residual 1.568 1.491 0.077 2.00e-02 2.50e+03 1.46e+01 bond pdb=" O4 PO4 D 403 " pdb=" P PO4 D 403 " ideal model delta sigma weight residual 1.568 1.492 0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" O4 PO4 E 403 " pdb=" P PO4 E 403 " ideal model delta sigma weight residual 1.568 1.492 0.076 2.00e-02 2.50e+03 1.45e+01 ... (remaining 14855 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 19570 1.60 - 3.19: 452 3.19 - 4.79: 113 4.79 - 6.38: 20 6.38 - 7.98: 15 Bond angle restraints: 20170 Sorted by residual: angle pdb=" PA ADP E 401 " pdb=" O3A ADP E 401 " pdb=" PB ADP E 401 " ideal model delta sigma weight residual 120.50 128.48 -7.98 3.00e+00 1.11e-01 7.07e+00 angle pdb=" PA ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " ideal model delta sigma weight residual 120.50 128.46 -7.96 3.00e+00 1.11e-01 7.04e+00 angle pdb=" PA ADP A 401 " pdb=" O3A ADP A 401 " pdb=" PB ADP A 401 " ideal model delta sigma weight residual 120.50 128.43 -7.93 3.00e+00 1.11e-01 6.98e+00 angle pdb=" PA ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PB ADP B 401 " ideal model delta sigma weight residual 120.50 128.42 -7.92 3.00e+00 1.11e-01 6.97e+00 angle pdb=" PA ADP D 401 " pdb=" O3A ADP D 401 " pdb=" PB ADP D 401 " ideal model delta sigma weight residual 120.50 128.42 -7.92 3.00e+00 1.11e-01 6.96e+00 ... (remaining 20165 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 8780 35.96 - 71.92: 130 71.92 - 107.88: 10 107.88 - 143.85: 5 143.85 - 179.81: 5 Dihedral angle restraints: 8930 sinusoidal: 3615 harmonic: 5315 Sorted by residual: dihedral pdb=" O2A ADP A 401 " pdb=" O3A ADP A 401 " pdb=" PA ADP A 401 " pdb=" PB ADP A 401 " ideal model delta sinusoidal sigma weight residual 300.00 120.19 179.81 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2A ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PA ADP C 401 " pdb=" PB ADP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 120.21 179.79 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2A ADP E 401 " pdb=" O3A ADP E 401 " pdb=" PA ADP E 401 " pdb=" PB ADP E 401 " ideal model delta sinusoidal sigma weight residual 300.00 120.21 179.79 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 8927 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1187 0.040 - 0.080: 750 0.080 - 0.120: 269 0.120 - 0.161: 29 0.161 - 0.201: 5 Chirality restraints: 2240 Sorted by residual: chirality pdb=" CB ILE B 151 " pdb=" CA ILE B 151 " pdb=" CG1 ILE B 151 " pdb=" CG2 ILE B 151 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CB ILE C 151 " pdb=" CA ILE C 151 " pdb=" CG1 ILE C 151 " pdb=" CG2 ILE C 151 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CB ILE A 151 " pdb=" CA ILE A 151 " pdb=" CG1 ILE A 151 " pdb=" CG2 ILE A 151 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 9.98e-01 ... (remaining 2237 not shown) Planarity restraints: 2570 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 340 " 0.021 2.00e-02 2.50e+03 1.04e-02 2.70e+00 pdb=" CG TRP B 340 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TRP B 340 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP B 340 " -0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP B 340 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 340 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 340 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 340 " 0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 340 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 340 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 340 " 0.021 2.00e-02 2.50e+03 1.04e-02 2.68e+00 pdb=" CG TRP D 340 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TRP D 340 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP D 340 " -0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP D 340 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP D 340 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 340 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 340 " 0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 340 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP D 340 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 340 " 0.021 2.00e-02 2.50e+03 1.03e-02 2.68e+00 pdb=" CG TRP C 340 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TRP C 340 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP C 340 " -0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP C 340 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 340 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 340 " -0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 340 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 340 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 340 " 0.004 2.00e-02 2.50e+03 ... (remaining 2567 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 92 2.39 - 3.01: 8360 3.01 - 3.64: 24359 3.64 - 4.27: 41727 4.27 - 4.90: 64186 Nonbonded interactions: 138724 Sorted by model distance: nonbonded pdb="MG MG E 402 " pdb=" O HOH E 506 " model vdw 1.758 2.170 nonbonded pdb="MG MG A 402 " pdb=" O HOH A 515 " model vdw 1.780 2.170 nonbonded pdb="MG MG D 402 " pdb=" O HOH D 559 " model vdw 1.800 2.170 nonbonded pdb="MG MG D 402 " pdb=" O HOH D 527 " model vdw 1.851 2.170 nonbonded pdb="MG MG B 402 " pdb=" O HOH B 526 " model vdw 1.860 2.170 ... (remaining 138719 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: 0.04 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'A' selection = chain 'B' 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: 3.580 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: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 13.200 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 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 : 0.009 0.077 14860 Z= 0.383 Angle : 0.677 7.978 20170 Z= 0.338 Chirality : 0.053 0.201 2240 Planarity : 0.005 0.044 2570 Dihedral : 14.102 179.806 5520 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.64 % Allowed : 3.22 % Favored : 96.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.19), residues: 1800 helix: -2.19 (0.14), residues: 775 sheet: -0.30 (0.25), residues: 330 loop : 1.26 (0.26), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 177 TYR 0.008 0.002 TYR A 143 PHE 0.016 0.002 PHE B 262 TRP 0.021 0.004 TRP B 340 HIS 0.005 0.002 HIS B 173 Details of bonding type rmsd covalent geometry : bond 0.00883 (14860) covalent geometry : angle 0.67692 (20170) hydrogen bonds : bond 0.22234 ( 728) hydrogen bonds : angle 7.80262 ( 1908) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 262 time to evaluate : 0.582 Fit side-chains REVERT: C 28 ARG cc_start: 0.8243 (ttm170) cc_final: 0.8026 (ttm170) REVERT: C 121 GLN cc_start: 0.8463 (tt0) cc_final: 0.8258 (tt0) REVERT: A 44 MET cc_start: 0.8413 (mmm) cc_final: 0.8201 (mmt) REVERT: A 191 LYS cc_start: 0.8441 (tttm) cc_final: 0.8200 (ttmm) REVERT: B 41 GLN cc_start: 0.7252 (tt0) cc_final: 0.6595 (tp-100) REVERT: B 64 ILE cc_start: 0.9145 (OUTLIER) cc_final: 0.8587 (pp) REVERT: B 121 GLN cc_start: 0.8331 (tt0) cc_final: 0.8075 (tt0) REVERT: B 125 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7467 (mt-10) REVERT: B 211 ASP cc_start: 0.7917 (t70) cc_final: 0.7637 (t70) REVERT: B 355 MET cc_start: 0.8207 (mmm) cc_final: 0.7962 (mmm) REVERT: D 41 GLN cc_start: 0.6948 (tt0) cc_final: 0.6351 (tp-100) REVERT: D 57 GLU cc_start: 0.7397 (tt0) cc_final: 0.7118 (mt-10) REVERT: D 128 ASN cc_start: 0.7942 (m110) cc_final: 0.7678 (t0) REVERT: E 50 LYS cc_start: 0.7811 (mtmm) cc_final: 0.7528 (mtpt) REVERT: E 214 GLU cc_start: 0.8210 (mt-10) cc_final: 0.8000 (mt-10) outliers start: 10 outliers final: 5 residues processed: 272 average time/residue: 0.7201 time to fit residues: 212.0793 Evaluate side-chains 202 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 196 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain E residue 45 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.6980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 92 ASN A 59 GLN A 225 ASN A 314 GLN B 246 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.120339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.101945 restraints weight = 15161.796| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.20 r_work: 0.3064 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14860 Z= 0.137 Angle : 0.608 7.646 20170 Z= 0.298 Chirality : 0.046 0.199 2240 Planarity : 0.004 0.029 2570 Dihedral : 12.076 179.652 2068 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.61 % Allowed : 8.94 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.20), residues: 1800 helix: -0.10 (0.19), residues: 740 sheet: -0.10 (0.25), residues: 330 loop : 1.88 (0.26), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 28 TYR 0.010 0.001 TYR B 143 PHE 0.012 0.001 PHE D 262 TRP 0.015 0.002 TRP D 79 HIS 0.005 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00296 (14860) covalent geometry : angle 0.60793 (20170) hydrogen bonds : bond 0.04316 ( 728) hydrogen bonds : angle 5.27307 ( 1908) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 218 time to evaluate : 0.578 Fit side-chains REVERT: C 95 ARG cc_start: 0.7889 (mtt90) cc_final: 0.7664 (mtt90) REVERT: C 225 ASN cc_start: 0.8171 (m-40) cc_final: 0.7838 (m110) REVERT: C 276 GLU cc_start: 0.8317 (mm-30) cc_final: 0.7982 (mt-10) REVERT: A 64 ILE cc_start: 0.9382 (OUTLIER) cc_final: 0.9107 (pp) REVERT: A 66 THR cc_start: 0.8891 (OUTLIER) cc_final: 0.8618 (m) REVERT: A 191 LYS cc_start: 0.8761 (tttm) cc_final: 0.8381 (ttmm) REVERT: B 41 GLN cc_start: 0.7878 (tt0) cc_final: 0.7260 (tp-100) REVERT: B 95 ARG cc_start: 0.8097 (mtt-85) cc_final: 0.7786 (mtp85) REVERT: B 121 GLN cc_start: 0.8837 (tt0) cc_final: 0.8615 (tt0) REVERT: D 41 GLN cc_start: 0.7694 (tt0) cc_final: 0.7234 (tp40) REVERT: D 57 GLU cc_start: 0.8175 (tt0) cc_final: 0.7913 (pt0) REVERT: D 128 ASN cc_start: 0.8198 (m110) cc_final: 0.7855 (t0) REVERT: E 50 LYS cc_start: 0.8052 (mtmm) cc_final: 0.7726 (mtpt) REVERT: E 57 GLU cc_start: 0.8415 (tt0) cc_final: 0.8094 (pt0) REVERT: E 118 LYS cc_start: 0.8476 (mtmt) cc_final: 0.8217 (mtpt) REVERT: E 214 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8371 (mt-10) outliers start: 25 outliers final: 11 residues processed: 228 average time/residue: 0.7188 time to fit residues: 177.2739 Evaluate side-chains 202 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 189 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain D residue 360 GLN Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 323 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 132 optimal weight: 4.9990 chunk 62 optimal weight: 8.9990 chunk 111 optimal weight: 6.9990 chunk 171 optimal weight: 3.9990 chunk 67 optimal weight: 0.4980 chunk 178 optimal weight: 7.9990 chunk 97 optimal weight: 0.8980 chunk 166 optimal weight: 9.9990 chunk 157 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN C 59 GLN A 225 ASN A 353 GLN B 246 GLN E 59 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.116424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.097840 restraints weight = 15263.819| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 1.18 r_work: 0.2993 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 14860 Z= 0.246 Angle : 0.676 8.030 20170 Z= 0.338 Chirality : 0.051 0.191 2240 Planarity : 0.005 0.040 2570 Dihedral : 11.979 179.953 2060 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.25 % Allowed : 10.23 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.20), residues: 1800 helix: 0.06 (0.18), residues: 790 sheet: -0.14 (0.25), residues: 345 loop : 1.75 (0.27), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 28 TYR 0.009 0.002 TYR A 143 PHE 0.018 0.002 PHE D 262 TRP 0.021 0.004 TRP D 340 HIS 0.006 0.002 HIS D 173 Details of bonding type rmsd covalent geometry : bond 0.00567 (14860) covalent geometry : angle 0.67612 (20170) hydrogen bonds : bond 0.05359 ( 728) hydrogen bonds : angle 5.26455 ( 1908) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 200 time to evaluate : 0.576 Fit side-chains REVERT: C 225 ASN cc_start: 0.8152 (m-40) cc_final: 0.7900 (m110) REVERT: C 276 GLU cc_start: 0.8339 (mm-30) cc_final: 0.7965 (mt-10) REVERT: A 28 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.8225 (ttm170) REVERT: A 64 ILE cc_start: 0.9388 (OUTLIER) cc_final: 0.9115 (pp) REVERT: A 66 THR cc_start: 0.8899 (t) cc_final: 0.8663 (m) REVERT: A 84 LYS cc_start: 0.9003 (OUTLIER) cc_final: 0.8677 (mttm) REVERT: A 191 LYS cc_start: 0.8771 (tttm) cc_final: 0.8390 (ttmm) REVERT: A 292 ASP cc_start: 0.8389 (m-30) cc_final: 0.8163 (m-30) REVERT: B 41 GLN cc_start: 0.7885 (tt0) cc_final: 0.7265 (tp40) REVERT: B 95 ARG cc_start: 0.8072 (mtt-85) cc_final: 0.7654 (mtp85) REVERT: B 121 GLN cc_start: 0.8766 (tt0) cc_final: 0.8530 (tt0) REVERT: D 41 GLN cc_start: 0.7729 (tt0) cc_final: 0.7252 (tp40) REVERT: D 57 GLU cc_start: 0.8194 (tt0) cc_final: 0.7740 (mt-10) REVERT: D 64 ILE cc_start: 0.9211 (OUTLIER) cc_final: 0.8959 (pp) REVERT: D 125 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.7289 (mp0) REVERT: D 128 ASN cc_start: 0.8238 (m110) cc_final: 0.7869 (t0) REVERT: D 276 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.8015 (tt0) REVERT: D 355 MET cc_start: 0.8809 (OUTLIER) cc_final: 0.7910 (mtp) REVERT: E 50 LYS cc_start: 0.8069 (mtmm) cc_final: 0.7705 (mtpt) REVERT: E 57 GLU cc_start: 0.8463 (tt0) cc_final: 0.8066 (pt0) REVERT: E 118 LYS cc_start: 0.8444 (mtmt) cc_final: 0.8119 (mtpt) REVERT: E 214 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8419 (mt-10) REVERT: E 355 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.8239 (mtp) outliers start: 35 outliers final: 15 residues processed: 220 average time/residue: 0.7324 time to fit residues: 174.4196 Evaluate side-chains 213 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 190 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain A residue 28 ARG Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 84 LYS Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain D residue 360 GLN Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 323 SER Chi-restraints excluded: chain E residue 355 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 153 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 144 optimal weight: 7.9990 chunk 58 optimal weight: 10.0000 chunk 115 optimal weight: 0.1980 chunk 59 optimal weight: 3.9990 chunk 171 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 172 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN A 225 ASN A 353 GLN B 246 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.116772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.098176 restraints weight = 15172.099| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.19 r_work: 0.3000 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 14860 Z= 0.213 Angle : 0.650 7.881 20170 Z= 0.323 Chirality : 0.049 0.192 2240 Planarity : 0.004 0.038 2570 Dihedral : 11.820 179.555 2060 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 2.44 % Allowed : 10.55 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.20), residues: 1800 helix: 0.42 (0.19), residues: 765 sheet: 0.07 (0.26), residues: 335 loop : 1.69 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 95 TYR 0.008 0.001 TYR A 143 PHE 0.016 0.002 PHE D 262 TRP 0.020 0.003 TRP D 340 HIS 0.005 0.002 HIS D 173 Details of bonding type rmsd covalent geometry : bond 0.00491 (14860) covalent geometry : angle 0.65000 (20170) hydrogen bonds : bond 0.04821 ( 728) hydrogen bonds : angle 5.10945 ( 1908) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 199 time to evaluate : 0.581 Fit side-chains REVERT: C 125 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.7344 (mp0) REVERT: C 225 ASN cc_start: 0.8151 (m-40) cc_final: 0.7922 (m-40) REVERT: C 276 GLU cc_start: 0.8344 (mm-30) cc_final: 0.7961 (mt-10) REVERT: C 334 GLU cc_start: 0.7927 (pm20) cc_final: 0.7688 (pm20) REVERT: A 64 ILE cc_start: 0.9376 (OUTLIER) cc_final: 0.9103 (pp) REVERT: A 66 THR cc_start: 0.8881 (t) cc_final: 0.8667 (m) REVERT: A 191 LYS cc_start: 0.8785 (tttm) cc_final: 0.8400 (ttmm) REVERT: A 292 ASP cc_start: 0.8389 (m-30) cc_final: 0.8162 (m-30) REVERT: B 41 GLN cc_start: 0.7882 (tt0) cc_final: 0.7257 (tp40) REVERT: B 44 MET cc_start: 0.8899 (mtp) cc_final: 0.8335 (mtp) REVERT: B 64 ILE cc_start: 0.9455 (OUTLIER) cc_final: 0.8865 (pp) REVERT: B 95 ARG cc_start: 0.8070 (mtt-85) cc_final: 0.7742 (mtp85) REVERT: B 121 GLN cc_start: 0.8745 (tt0) cc_final: 0.8514 (tt0) REVERT: D 41 GLN cc_start: 0.7714 (tt0) cc_final: 0.7233 (tp40) REVERT: D 57 GLU cc_start: 0.8172 (tt0) cc_final: 0.7730 (mt-10) REVERT: D 64 ILE cc_start: 0.9216 (OUTLIER) cc_final: 0.8983 (pp) REVERT: D 125 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7272 (mp0) REVERT: D 128 ASN cc_start: 0.8239 (m110) cc_final: 0.7858 (t0) REVERT: D 355 MET cc_start: 0.8786 (OUTLIER) cc_final: 0.7951 (mtp) REVERT: E 50 LYS cc_start: 0.8053 (mtmm) cc_final: 0.7680 (mtpt) REVERT: E 57 GLU cc_start: 0.8466 (tt0) cc_final: 0.8087 (pt0) REVERT: E 100 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7748 (pm20) REVERT: E 118 LYS cc_start: 0.8456 (mtmt) cc_final: 0.8128 (mtpt) REVERT: E 191 LYS cc_start: 0.8658 (tttm) cc_final: 0.8405 (ttmm) REVERT: E 214 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8381 (mt-10) REVERT: E 215 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8365 (mppt) REVERT: E 355 MET cc_start: 0.8717 (OUTLIER) cc_final: 0.8273 (mtp) outliers start: 38 outliers final: 18 residues processed: 224 average time/residue: 0.7631 time to fit residues: 184.8732 Evaluate side-chains 219 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 192 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 328 LYS Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 215 LYS Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 323 SER Chi-restraints excluded: chain E residue 355 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 145 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 152 optimal weight: 6.9990 chunk 122 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 154 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN C 354 GLN A 225 ASN A 353 GLN B 246 GLN D 59 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.116660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.098095 restraints weight = 15211.862| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.18 r_work: 0.2997 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 14860 Z= 0.225 Angle : 0.657 7.884 20170 Z= 0.327 Chirality : 0.050 0.197 2240 Planarity : 0.005 0.039 2570 Dihedral : 11.740 179.814 2060 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.57 % Allowed : 10.80 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.20), residues: 1800 helix: 0.48 (0.19), residues: 765 sheet: 0.11 (0.26), residues: 335 loop : 1.69 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 95 TYR 0.008 0.001 TYR B 294 PHE 0.017 0.002 PHE D 262 TRP 0.021 0.003 TRP D 340 HIS 0.005 0.002 HIS C 173 Details of bonding type rmsd covalent geometry : bond 0.00518 (14860) covalent geometry : angle 0.65662 (20170) hydrogen bonds : bond 0.04886 ( 728) hydrogen bonds : angle 5.07481 ( 1908) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 195 time to evaluate : 0.597 Fit side-chains REVERT: C 125 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.7367 (mp0) REVERT: C 225 ASN cc_start: 0.8156 (m-40) cc_final: 0.7938 (m-40) REVERT: C 276 GLU cc_start: 0.8327 (mm-30) cc_final: 0.7953 (mt-10) REVERT: C 334 GLU cc_start: 0.7925 (pm20) cc_final: 0.7678 (pm20) REVERT: A 64 ILE cc_start: 0.9374 (OUTLIER) cc_final: 0.9125 (pp) REVERT: A 66 THR cc_start: 0.8877 (t) cc_final: 0.8672 (m) REVERT: A 84 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8664 (mttm) REVERT: A 191 LYS cc_start: 0.8793 (tttm) cc_final: 0.8410 (ttmm) REVERT: A 292 ASP cc_start: 0.8394 (m-30) cc_final: 0.8173 (m-30) REVERT: B 41 GLN cc_start: 0.7879 (tt0) cc_final: 0.7253 (tp40) REVERT: B 44 MET cc_start: 0.8882 (mtp) cc_final: 0.8450 (mtp) REVERT: B 64 ILE cc_start: 0.9457 (OUTLIER) cc_final: 0.8865 (pp) REVERT: B 95 ARG cc_start: 0.8050 (mtt-85) cc_final: 0.7729 (mtp85) REVERT: B 121 GLN cc_start: 0.8750 (tt0) cc_final: 0.8535 (tt0) REVERT: D 41 GLN cc_start: 0.7713 (tt0) cc_final: 0.7237 (tp40) REVERT: D 57 GLU cc_start: 0.8190 (tt0) cc_final: 0.7774 (mt-10) REVERT: D 64 ILE cc_start: 0.9220 (OUTLIER) cc_final: 0.8990 (pp) REVERT: D 125 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7263 (mp0) REVERT: D 128 ASN cc_start: 0.8243 (m110) cc_final: 0.7846 (t0) REVERT: D 355 MET cc_start: 0.8794 (OUTLIER) cc_final: 0.7962 (mtp) REVERT: E 50 LYS cc_start: 0.8050 (mtmm) cc_final: 0.7680 (mtpt) REVERT: E 57 GLU cc_start: 0.8466 (tt0) cc_final: 0.8086 (pt0) REVERT: E 64 ILE cc_start: 0.9016 (OUTLIER) cc_final: 0.8788 (pp) REVERT: E 100 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7743 (pm20) REVERT: E 118 LYS cc_start: 0.8447 (mtmt) cc_final: 0.8131 (mtpt) REVERT: E 191 LYS cc_start: 0.8663 (tttm) cc_final: 0.8419 (ttmm) REVERT: E 214 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8377 (mt-10) REVERT: E 215 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8373 (mppt) REVERT: E 234 SER cc_start: 0.8118 (OUTLIER) cc_final: 0.7758 (t) REVERT: E 355 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.8270 (mtp) outliers start: 40 outliers final: 20 residues processed: 224 average time/residue: 0.7451 time to fit residues: 180.2362 Evaluate side-chains 224 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 192 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 84 LYS Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 328 LYS Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 215 LYS Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 323 SER Chi-restraints excluded: chain E residue 355 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 130 optimal weight: 0.0010 chunk 19 optimal weight: 0.4980 chunk 131 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 141 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 173 optimal weight: 4.9990 chunk 122 optimal weight: 9.9990 chunk 163 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN C 354 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.120184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.101878 restraints weight = 15196.415| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.19 r_work: 0.3059 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14860 Z= 0.104 Angle : 0.564 7.078 20170 Z= 0.271 Chirality : 0.045 0.182 2240 Planarity : 0.003 0.037 2570 Dihedral : 10.990 175.876 2060 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 1.93 % Allowed : 11.64 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.21), residues: 1800 helix: 0.84 (0.20), residues: 750 sheet: 0.23 (0.26), residues: 335 loop : 1.94 (0.25), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 95 TYR 0.008 0.001 TYR B 294 PHE 0.010 0.001 PHE E 31 TRP 0.014 0.002 TRP D 340 HIS 0.003 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00220 (14860) covalent geometry : angle 0.56376 (20170) hydrogen bonds : bond 0.03298 ( 728) hydrogen bonds : angle 4.69496 ( 1908) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 196 time to evaluate : 0.625 Fit side-chains REVERT: C 125 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.7355 (mp0) REVERT: C 225 ASN cc_start: 0.8117 (m-40) cc_final: 0.7899 (m-40) REVERT: C 276 GLU cc_start: 0.8322 (mm-30) cc_final: 0.7943 (mt-10) REVERT: C 334 GLU cc_start: 0.7850 (pm20) cc_final: 0.7586 (pm20) REVERT: A 64 ILE cc_start: 0.9381 (OUTLIER) cc_final: 0.9117 (pp) REVERT: A 95 ARG cc_start: 0.8175 (mtm-85) cc_final: 0.7964 (mtm-85) REVERT: A 191 LYS cc_start: 0.8744 (tttm) cc_final: 0.8337 (ttmm) REVERT: B 41 GLN cc_start: 0.7870 (tt0) cc_final: 0.7245 (tp-100) REVERT: B 44 MET cc_start: 0.8861 (mtp) cc_final: 0.8395 (mtp) REVERT: B 64 ILE cc_start: 0.9445 (OUTLIER) cc_final: 0.8799 (pp) REVERT: B 95 ARG cc_start: 0.8057 (mtt-85) cc_final: 0.7663 (mtp85) REVERT: B 121 GLN cc_start: 0.8706 (tt0) cc_final: 0.8481 (tt0) REVERT: D 41 GLN cc_start: 0.7707 (tt0) cc_final: 0.7244 (tp40) REVERT: D 57 GLU cc_start: 0.8156 (tt0) cc_final: 0.7828 (pt0) REVERT: D 64 ILE cc_start: 0.9223 (OUTLIER) cc_final: 0.8979 (pp) REVERT: D 125 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7201 (mp0) REVERT: D 128 ASN cc_start: 0.8183 (m110) cc_final: 0.7821 (t0) REVERT: D 355 MET cc_start: 0.8743 (OUTLIER) cc_final: 0.7931 (mtp) REVERT: E 25 ASP cc_start: 0.8068 (OUTLIER) cc_final: 0.7701 (p0) REVERT: E 50 LYS cc_start: 0.8045 (mtmm) cc_final: 0.7671 (mtpt) REVERT: E 57 GLU cc_start: 0.8405 (tt0) cc_final: 0.8036 (pt0) REVERT: E 95 ARG cc_start: 0.7757 (mtt-85) cc_final: 0.7362 (mtt180) REVERT: E 100 GLU cc_start: 0.8136 (pt0) cc_final: 0.7741 (pm20) REVERT: E 117 GLU cc_start: 0.8251 (mt-10) cc_final: 0.7954 (mt-10) REVERT: E 118 LYS cc_start: 0.8465 (mtmt) cc_final: 0.8133 (mtpt) REVERT: E 355 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.8258 (mtp) outliers start: 30 outliers final: 10 residues processed: 211 average time/residue: 0.7613 time to fit residues: 173.2142 Evaluate side-chains 201 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 183 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 323 SER Chi-restraints excluded: chain E residue 326 LYS Chi-restraints excluded: chain E residue 355 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 48 optimal weight: 0.0970 chunk 151 optimal weight: 0.8980 chunk 95 optimal weight: 0.8980 chunk 177 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 14 optimal weight: 8.9990 chunk 140 optimal weight: 5.9990 chunk 131 optimal weight: 0.8980 chunk 159 optimal weight: 0.9980 chunk 168 optimal weight: 4.9990 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN C 354 GLN E 87 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.120261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.101946 restraints weight = 15118.599| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.19 r_work: 0.3063 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14860 Z= 0.108 Angle : 0.563 6.730 20170 Z= 0.270 Chirality : 0.045 0.176 2240 Planarity : 0.004 0.035 2570 Dihedral : 10.537 178.226 2060 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.67 % Allowed : 12.22 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.21), residues: 1800 helix: 0.95 (0.20), residues: 750 sheet: 0.32 (0.26), residues: 335 loop : 1.98 (0.25), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 95 TYR 0.008 0.001 TYR C 143 PHE 0.009 0.001 PHE E 31 TRP 0.014 0.002 TRP D 340 HIS 0.007 0.001 HIS E 87 Details of bonding type rmsd covalent geometry : bond 0.00235 (14860) covalent geometry : angle 0.56299 (20170) hydrogen bonds : bond 0.03319 ( 728) hydrogen bonds : angle 4.62151 ( 1908) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 190 time to evaluate : 0.635 Fit side-chains REVERT: C 125 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.7366 (mp0) REVERT: C 225 ASN cc_start: 0.8085 (m-40) cc_final: 0.7872 (m-40) REVERT: C 276 GLU cc_start: 0.8308 (mm-30) cc_final: 0.7931 (mt-10) REVERT: C 334 GLU cc_start: 0.7847 (pm20) cc_final: 0.7572 (pm20) REVERT: A 64 ILE cc_start: 0.9380 (OUTLIER) cc_final: 0.9115 (pp) REVERT: A 191 LYS cc_start: 0.8736 (tttm) cc_final: 0.8329 (ttmm) REVERT: B 41 GLN cc_start: 0.7874 (tt0) cc_final: 0.7262 (tp-100) REVERT: B 44 MET cc_start: 0.8847 (mtp) cc_final: 0.8423 (mtp) REVERT: B 121 GLN cc_start: 0.8691 (tt0) cc_final: 0.8469 (tt0) REVERT: D 41 GLN cc_start: 0.7721 (tt0) cc_final: 0.7257 (tp40) REVERT: D 57 GLU cc_start: 0.8149 (tt0) cc_final: 0.7866 (pt0) REVERT: D 64 ILE cc_start: 0.9223 (OUTLIER) cc_final: 0.8985 (pp) REVERT: D 128 ASN cc_start: 0.8145 (m110) cc_final: 0.7794 (t0) REVERT: D 355 MET cc_start: 0.8739 (OUTLIER) cc_final: 0.7948 (mtp) REVERT: E 25 ASP cc_start: 0.8027 (OUTLIER) cc_final: 0.7662 (p0) REVERT: E 50 LYS cc_start: 0.8043 (mtmm) cc_final: 0.7666 (mtpt) REVERT: E 57 GLU cc_start: 0.8410 (tt0) cc_final: 0.8037 (pt0) REVERT: E 100 GLU cc_start: 0.8157 (pt0) cc_final: 0.7765 (pm20) REVERT: E 117 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7956 (mt-10) REVERT: E 118 LYS cc_start: 0.8487 (mtmt) cc_final: 0.8201 (mtpt) REVERT: E 191 LYS cc_start: 0.8642 (tttm) cc_final: 0.8389 (ttmm) REVERT: E 215 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8248 (mppt) REVERT: E 234 SER cc_start: 0.8037 (OUTLIER) cc_final: 0.7767 (t) REVERT: E 355 MET cc_start: 0.8656 (OUTLIER) cc_final: 0.8251 (mtp) outliers start: 26 outliers final: 12 residues processed: 206 average time/residue: 0.7787 time to fit residues: 173.1461 Evaluate side-chains 206 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 186 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 215 LYS Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 323 SER Chi-restraints excluded: chain E residue 326 LYS Chi-restraints excluded: chain E residue 355 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 136 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 125 optimal weight: 8.9990 chunk 95 optimal weight: 3.9990 chunk 147 optimal weight: 0.6980 chunk 173 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN C 354 GLN A 246 GLN B 40 HIS B 246 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.118105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.099489 restraints weight = 15197.467| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 1.20 r_work: 0.3025 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14860 Z= 0.167 Angle : 0.610 6.901 20170 Z= 0.298 Chirality : 0.047 0.190 2240 Planarity : 0.004 0.043 2570 Dihedral : 10.712 173.164 2060 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.74 % Allowed : 12.48 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.20), residues: 1800 helix: 0.84 (0.20), residues: 750 sheet: 0.29 (0.26), residues: 335 loop : 1.98 (0.25), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 95 TYR 0.007 0.001 TYR D 69 PHE 0.012 0.001 PHE D 262 TRP 0.017 0.003 TRP D 340 HIS 0.004 0.001 HIS D 173 Details of bonding type rmsd covalent geometry : bond 0.00379 (14860) covalent geometry : angle 0.60967 (20170) hydrogen bonds : bond 0.04136 ( 728) hydrogen bonds : angle 4.80666 ( 1908) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 191 time to evaluate : 0.677 Fit side-chains REVERT: C 125 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.7362 (mp0) REVERT: C 225 ASN cc_start: 0.8127 (m-40) cc_final: 0.7914 (m-40) REVERT: C 276 GLU cc_start: 0.8335 (mm-30) cc_final: 0.7950 (mt-10) REVERT: C 334 GLU cc_start: 0.7904 (pm20) cc_final: 0.7622 (pm20) REVERT: A 64 ILE cc_start: 0.9373 (OUTLIER) cc_final: 0.9102 (pp) REVERT: A 191 LYS cc_start: 0.8771 (tttm) cc_final: 0.8374 (ttmm) REVERT: B 41 GLN cc_start: 0.7870 (tt0) cc_final: 0.7251 (tp-100) REVERT: B 44 MET cc_start: 0.8849 (mtp) cc_final: 0.8435 (mtp) REVERT: B 64 ILE cc_start: 0.9439 (OUTLIER) cc_final: 0.8810 (pp) REVERT: B 121 GLN cc_start: 0.8714 (tt0) cc_final: 0.8514 (tt0) REVERT: D 41 GLN cc_start: 0.7723 (tt0) cc_final: 0.7250 (tp40) REVERT: D 57 GLU cc_start: 0.8185 (tt0) cc_final: 0.7752 (mt-10) REVERT: D 64 ILE cc_start: 0.9217 (OUTLIER) cc_final: 0.8981 (pp) REVERT: D 128 ASN cc_start: 0.8175 (m110) cc_final: 0.7790 (t0) REVERT: D 355 MET cc_start: 0.8752 (OUTLIER) cc_final: 0.7955 (mtp) REVERT: E 25 ASP cc_start: 0.8072 (OUTLIER) cc_final: 0.7704 (p0) REVERT: E 50 LYS cc_start: 0.8051 (mtmm) cc_final: 0.7675 (mtpt) REVERT: E 57 GLU cc_start: 0.8442 (tt0) cc_final: 0.8063 (pt0) REVERT: E 100 GLU cc_start: 0.8163 (pt0) cc_final: 0.7747 (pm20) REVERT: E 117 GLU cc_start: 0.8262 (mt-10) cc_final: 0.8010 (mt-10) REVERT: E 118 LYS cc_start: 0.8496 (mtmt) cc_final: 0.8200 (mtpt) REVERT: E 191 LYS cc_start: 0.8657 (tttm) cc_final: 0.8416 (ttmm) REVERT: E 215 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8313 (mppt) REVERT: E 234 SER cc_start: 0.8077 (OUTLIER) cc_final: 0.7802 (t) REVERT: E 314 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8326 (tt0) REVERT: E 355 MET cc_start: 0.8693 (OUTLIER) cc_final: 0.8278 (mtp) outliers start: 27 outliers final: 13 residues processed: 207 average time/residue: 0.7621 time to fit residues: 170.3509 Evaluate side-chains 208 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 185 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 215 LYS Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 323 SER Chi-restraints excluded: chain E residue 355 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 117 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 179 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 122 optimal weight: 0.8980 chunk 133 optimal weight: 0.6980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN C 354 GLN B 246 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.119476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.101064 restraints weight = 15137.069| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.19 r_work: 0.3046 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 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 : 0.003 0.025 14860 Z= 0.128 Angle : 0.581 6.708 20170 Z= 0.281 Chirality : 0.046 0.179 2240 Planarity : 0.004 0.041 2570 Dihedral : 10.500 176.204 2060 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.54 % Allowed : 12.67 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.20), residues: 1800 helix: 0.90 (0.20), residues: 750 sheet: 0.32 (0.26), residues: 335 loop : 2.00 (0.25), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 95 TYR 0.008 0.001 TYR C 143 PHE 0.010 0.001 PHE D 262 TRP 0.015 0.002 TRP D 340 HIS 0.004 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00283 (14860) covalent geometry : angle 0.58070 (20170) hydrogen bonds : bond 0.03646 ( 728) hydrogen bonds : angle 4.68972 ( 1908) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 188 time to evaluate : 0.600 Fit side-chains REVERT: C 125 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.7341 (mp0) REVERT: C 225 ASN cc_start: 0.8112 (m-40) cc_final: 0.7905 (m-40) REVERT: C 276 GLU cc_start: 0.8313 (mm-30) cc_final: 0.7929 (mt-10) REVERT: C 334 GLU cc_start: 0.7879 (pm20) cc_final: 0.7596 (pm20) REVERT: A 64 ILE cc_start: 0.9375 (OUTLIER) cc_final: 0.9109 (pp) REVERT: A 191 LYS cc_start: 0.8751 (tttm) cc_final: 0.8343 (ttmm) REVERT: B 41 GLN cc_start: 0.7860 (tt0) cc_final: 0.7255 (tp-100) REVERT: B 44 MET cc_start: 0.8840 (mtp) cc_final: 0.8436 (mtp) REVERT: B 121 GLN cc_start: 0.8713 (tt0) cc_final: 0.8513 (tt0) REVERT: D 41 GLN cc_start: 0.7718 (tt0) cc_final: 0.7251 (tp40) REVERT: D 57 GLU cc_start: 0.8175 (tt0) cc_final: 0.7734 (mt-10) REVERT: D 64 ILE cc_start: 0.9209 (OUTLIER) cc_final: 0.8968 (pp) REVERT: D 128 ASN cc_start: 0.8147 (m110) cc_final: 0.7786 (t0) REVERT: D 355 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.7948 (mtp) REVERT: E 25 ASP cc_start: 0.8026 (OUTLIER) cc_final: 0.7675 (p0) REVERT: E 50 LYS cc_start: 0.8045 (mtmm) cc_final: 0.7663 (mtpt) REVERT: E 57 GLU cc_start: 0.8425 (tt0) cc_final: 0.8044 (pt0) REVERT: E 95 ARG cc_start: 0.7769 (mtt-85) cc_final: 0.7364 (mtt180) REVERT: E 100 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7755 (pm20) REVERT: E 117 GLU cc_start: 0.8272 (mt-10) cc_final: 0.7965 (mt-10) REVERT: E 118 LYS cc_start: 0.8493 (mtmt) cc_final: 0.8199 (mtpt) REVERT: E 191 LYS cc_start: 0.8638 (tttm) cc_final: 0.8402 (ttmm) REVERT: E 215 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8277 (mppt) REVERT: E 234 SER cc_start: 0.8126 (OUTLIER) cc_final: 0.7850 (t) REVERT: E 314 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.8291 (tt0) REVERT: E 355 MET cc_start: 0.8676 (OUTLIER) cc_final: 0.8280 (mtp) outliers start: 24 outliers final: 13 residues processed: 201 average time/residue: 0.7776 time to fit residues: 168.8508 Evaluate side-chains 211 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 188 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 215 LYS Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 323 SER Chi-restraints excluded: chain E residue 355 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 18 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 158 optimal weight: 9.9990 chunk 122 optimal weight: 8.9990 chunk 148 optimal weight: 9.9990 chunk 107 optimal weight: 0.9980 chunk 61 optimal weight: 0.4980 chunk 19 optimal weight: 0.6980 chunk 15 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN B 246 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.119101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.100575 restraints weight = 15187.250| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.19 r_work: 0.3041 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14860 Z= 0.135 Angle : 0.587 6.645 20170 Z= 0.285 Chirality : 0.046 0.180 2240 Planarity : 0.004 0.040 2570 Dihedral : 10.412 176.989 2060 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.67 % Allowed : 12.67 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.20), residues: 1800 helix: 0.90 (0.20), residues: 750 sheet: 0.34 (0.26), residues: 335 loop : 1.99 (0.25), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 95 TYR 0.008 0.001 TYR C 143 PHE 0.010 0.001 PHE D 262 TRP 0.015 0.002 TRP D 340 HIS 0.004 0.001 HIS E 161 Details of bonding type rmsd covalent geometry : bond 0.00301 (14860) covalent geometry : angle 0.58702 (20170) hydrogen bonds : bond 0.03765 ( 728) hydrogen bonds : angle 4.70541 ( 1908) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 191 time to evaluate : 0.512 Fit side-chains REVERT: C 125 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.7513 (mp0) REVERT: C 225 ASN cc_start: 0.8112 (m-40) cc_final: 0.7905 (m-40) REVERT: C 276 GLU cc_start: 0.8337 (mm-30) cc_final: 0.7950 (mt-10) REVERT: C 334 GLU cc_start: 0.7870 (pm20) cc_final: 0.7603 (pm20) REVERT: A 64 ILE cc_start: 0.9370 (OUTLIER) cc_final: 0.9103 (pp) REVERT: A 191 LYS cc_start: 0.8750 (tttm) cc_final: 0.8345 (ttmm) REVERT: B 41 GLN cc_start: 0.7833 (tt0) cc_final: 0.7242 (tp-100) REVERT: B 44 MET cc_start: 0.8837 (mtp) cc_final: 0.8432 (mtp) REVERT: B 64 ILE cc_start: 0.9434 (OUTLIER) cc_final: 0.8808 (pp) REVERT: B 121 GLN cc_start: 0.8713 (tt0) cc_final: 0.8496 (tt0) REVERT: B 125 GLU cc_start: 0.8236 (mm-30) cc_final: 0.8033 (mm-30) REVERT: D 41 GLN cc_start: 0.7706 (tt0) cc_final: 0.7239 (tp40) REVERT: D 57 GLU cc_start: 0.8183 (tt0) cc_final: 0.7743 (mt-10) REVERT: D 64 ILE cc_start: 0.9212 (OUTLIER) cc_final: 0.8975 (pp) REVERT: D 128 ASN cc_start: 0.8153 (m110) cc_final: 0.7787 (t0) REVERT: D 355 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.7935 (mtp) REVERT: E 25 ASP cc_start: 0.8008 (OUTLIER) cc_final: 0.7802 (p0) REVERT: E 50 LYS cc_start: 0.8050 (mtmm) cc_final: 0.7669 (mtpt) REVERT: E 57 GLU cc_start: 0.8429 (tt0) cc_final: 0.8047 (pt0) REVERT: E 95 ARG cc_start: 0.7780 (mtt-85) cc_final: 0.7372 (mtt180) REVERT: E 100 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7715 (pm20) REVERT: E 117 GLU cc_start: 0.8278 (mt-10) cc_final: 0.7962 (mt-10) REVERT: E 118 LYS cc_start: 0.8495 (mtmt) cc_final: 0.8195 (mtpt) REVERT: E 191 LYS cc_start: 0.8650 (tttm) cc_final: 0.8420 (ttmm) REVERT: E 215 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8284 (mppt) REVERT: E 234 SER cc_start: 0.8106 (OUTLIER) cc_final: 0.7838 (t) REVERT: E 314 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.8308 (tt0) REVERT: E 355 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.8283 (mtp) outliers start: 26 outliers final: 14 residues processed: 205 average time/residue: 0.7780 time to fit residues: 172.0091 Evaluate side-chains 216 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 191 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 215 LYS Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 323 SER Chi-restraints excluded: chain E residue 355 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 160 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 175 optimal weight: 0.5980 chunk 118 optimal weight: 0.5980 chunk 161 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN C 354 GLN A 40 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.120846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.102559 restraints weight = 15110.778| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.19 r_work: 0.3071 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 14860 Z= 0.104 Angle : 0.558 6.331 20170 Z= 0.268 Chirality : 0.045 0.155 2240 Planarity : 0.004 0.039 2570 Dihedral : 9.956 174.863 2060 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 1.48 % Allowed : 12.73 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.20), residues: 1800 helix: 1.00 (0.20), residues: 750 sheet: 0.42 (0.27), residues: 325 loop : 1.93 (0.25), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 95 TYR 0.008 0.001 TYR C 143 PHE 0.009 0.001 PHE E 31 TRP 0.014 0.002 TRP D 340 HIS 0.004 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00224 (14860) covalent geometry : angle 0.55826 (20170) hydrogen bonds : bond 0.03228 ( 728) hydrogen bonds : angle 4.55283 ( 1908) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6354.89 seconds wall clock time: 108 minutes 43.22 seconds (6523.22 seconds total)