Starting phenix.real_space_refine on Fri Jun 13 18:58:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a2s_15105/06_2025/8a2s_15105.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a2s_15105/06_2025/8a2s_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8a2s_15105/06_2025/8a2s_15105.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a2s_15105/06_2025/8a2s_15105.map" model { file = "/net/cci-nas-00/data/ceres_data/8a2s_15105/06_2025/8a2s_15105.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a2s_15105/06_2025/8a2s_15105.cif" } resolution = 2.22 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15141 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" 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: "A" 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: C, B, E, D Time building chain proxies: 7.85, per 1000 atoms: 0.52 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: 3.70 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 2.39 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: 5.39 Time building geometry restraints manager: 4.19 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: 0.12 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.790 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: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 34.780 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.300 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.19), residues: 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 TRP 0.021 0.004 TRP B 340 HIS 0.005 0.002 HIS B 173 PHE 0.016 0.002 PHE B 262 TYR 0.008 0.002 TYR A 143 ARG 0.006 0.001 ARG B 177 Details of bonding type rmsd hydrogen bonds : bond 0.22234 ( 728) hydrogen bonds : angle 7.80262 ( 1908) covalent geometry : bond 0.00883 (14860) covalent geometry : angle 0.67692 (20170) *********************** 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 : 1.481 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: 1.5770 time to fit residues: 465.3349 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 : 1.583 ------------------------------------------------------------------------------- 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 151 optimal weight: 0.9990 chunk 136 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 141 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 105 optimal weight: 0.7980 chunk 163 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 225 ASN A 314 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 = 0.3451 r_free = 0.3451 target = 0.121016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.102669 restraints weight = 15179.204| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.20 r_work: 0.3075 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 14860 Z= 0.125 Angle : 0.595 7.558 20170 Z= 0.290 Chirality : 0.046 0.196 2240 Planarity : 0.004 0.029 2570 Dihedral : 11.974 179.683 2068 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 1.54 % Allowed : 8.87 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.20), residues: 1800 helix: -0.12 (0.19), residues: 740 sheet: -0.10 (0.25), residues: 330 loop : 1.90 (0.26), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 79 HIS 0.004 0.001 HIS C 161 PHE 0.011 0.001 PHE D 262 TYR 0.010 0.001 TYR B 143 ARG 0.005 0.000 ARG D 28 Details of bonding type rmsd hydrogen bonds : bond 0.04226 ( 728) hydrogen bonds : angle 5.24605 ( 1908) covalent geometry : bond 0.00267 (14860) covalent geometry : angle 0.59538 (20170) *********************** 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 242 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 218 time to evaluate : 1.669 Fit side-chains REVERT: C 225 ASN cc_start: 0.8174 (m-40) cc_final: 0.7956 (m110) REVERT: A 64 ILE cc_start: 0.9384 (OUTLIER) cc_final: 0.9113 (pp) REVERT: A 66 THR cc_start: 0.8893 (OUTLIER) cc_final: 0.8617 (m) REVERT: A 191 LYS cc_start: 0.8759 (tttm) cc_final: 0.8377 (ttmm) REVERT: B 41 GLN cc_start: 0.7873 (tt0) cc_final: 0.7261 (tp-100) REVERT: B 95 ARG cc_start: 0.8097 (mtt-85) cc_final: 0.7793 (mtp85) REVERT: B 121 GLN cc_start: 0.8835 (tt0) cc_final: 0.8614 (tt0) REVERT: D 41 GLN cc_start: 0.7702 (tt0) cc_final: 0.7243 (tp40) REVERT: D 128 ASN cc_start: 0.8202 (m110) cc_final: 0.7865 (t0) REVERT: E 50 LYS cc_start: 0.8049 (mtmm) cc_final: 0.7725 (mtpt) REVERT: E 57 GLU cc_start: 0.8406 (tt0) cc_final: 0.8087 (pt0) REVERT: E 66 THR cc_start: 0.8866 (OUTLIER) cc_final: 0.8616 (m) REVERT: E 118 LYS cc_start: 0.8480 (mtmt) cc_final: 0.8218 (mtpt) outliers start: 24 outliers final: 9 residues processed: 227 average time/residue: 1.9654 time to fit residues: 483.1068 Evaluate side-chains 199 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 187 time to evaluate : 2.069 ------------------------------------------------------------------------------- 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 323 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 169 optimal weight: 0.0470 chunk 175 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 125 optimal weight: 0.9980 chunk 133 optimal weight: 0.0870 chunk 43 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 overall best weight: 0.9658 ------------------------------------------------------------------------------- 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 B 246 GLN E 59 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 = 0.120617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.102503 restraints weight = 15091.839| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.16 r_work: 0.3073 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14860 Z= 0.122 Angle : 0.572 6.993 20170 Z= 0.276 Chirality : 0.045 0.178 2240 Planarity : 0.004 0.029 2570 Dihedral : 11.028 176.247 2060 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.86 % Allowed : 10.29 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.20), residues: 1800 helix: 0.54 (0.19), residues: 750 sheet: 0.12 (0.26), residues: 330 loop : 1.91 (0.26), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 79 HIS 0.004 0.001 HIS C 161 PHE 0.009 0.001 PHE D 262 TYR 0.008 0.001 TYR A 143 ARG 0.006 0.000 ARG D 28 Details of bonding type rmsd hydrogen bonds : bond 0.03862 ( 728) hydrogen bonds : angle 4.89930 ( 1908) covalent geometry : bond 0.00266 (14860) covalent geometry : angle 0.57189 (20170) *********************** 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 229 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 200 time to evaluate : 2.144 Fit side-chains REVERT: C 276 GLU cc_start: 0.8287 (mm-30) cc_final: 0.7956 (mt-10) REVERT: A 64 ILE cc_start: 0.9407 (OUTLIER) cc_final: 0.9101 (pp) REVERT: A 66 THR cc_start: 0.8887 (OUTLIER) cc_final: 0.8621 (m) REVERT: A 125 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7942 (mm-30) REVERT: A 191 LYS cc_start: 0.8761 (tttm) cc_final: 0.8369 (ttmm) REVERT: A 292 ASP cc_start: 0.8355 (m-30) cc_final: 0.8143 (m-30) REVERT: B 41 GLN cc_start: 0.7841 (tt0) cc_final: 0.7223 (tp-100) REVERT: B 95 ARG cc_start: 0.8090 (mtt-85) cc_final: 0.7775 (mtp85) REVERT: D 41 GLN cc_start: 0.7713 (tt0) cc_final: 0.7255 (tp40) REVERT: D 128 ASN cc_start: 0.8189 (m110) cc_final: 0.7888 (t0) REVERT: E 50 LYS cc_start: 0.8059 (mtmm) cc_final: 0.7720 (mtpt) REVERT: E 57 GLU cc_start: 0.8437 (tt0) cc_final: 0.8123 (pt0) REVERT: E 117 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7962 (mt-10) REVERT: E 118 LYS cc_start: 0.8477 (mtmt) cc_final: 0.8228 (mtpt) REVERT: E 355 MET cc_start: 0.8710 (OUTLIER) cc_final: 0.8214 (mtp) outliers start: 29 outliers final: 14 residues processed: 217 average time/residue: 1.6027 time to fit residues: 377.4222 Evaluate side-chains 195 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 178 time to evaluate : 1.684 ------------------------------------------------------------------------------- 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 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 324 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain D residue 323 SER 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 66 optimal weight: 2.9990 chunk 174 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 117 optimal weight: 6.9990 chunk 175 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 99 optimal weight: 0.9990 chunk 169 optimal weight: 0.7980 chunk 120 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 B 246 GLN D 59 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.119485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.101069 restraints weight = 15117.732| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.19 r_work: 0.3049 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.1818 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 : 0.575 6.753 20170 Z= 0.278 Chirality : 0.046 0.180 2240 Planarity : 0.004 0.030 2570 Dihedral : 10.800 177.235 2060 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.74 % Allowed : 11.77 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.21), residues: 1800 helix: 0.72 (0.20), residues: 750 sheet: 0.15 (0.26), residues: 335 loop : 1.98 (0.25), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 340 HIS 0.004 0.001 HIS C 161 PHE 0.009 0.001 PHE D 262 TYR 0.008 0.001 TYR A 143 ARG 0.004 0.000 ARG D 95 Details of bonding type rmsd hydrogen bonds : bond 0.03723 ( 728) hydrogen bonds : angle 4.81363 ( 1908) covalent geometry : bond 0.00282 (14860) covalent geometry : angle 0.57480 (20170) *********************** 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 214 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 187 time to evaluate : 1.576 Fit side-chains REVERT: C 276 GLU cc_start: 0.8307 (mm-30) cc_final: 0.7948 (mt-10) REVERT: A 64 ILE cc_start: 0.9399 (OUTLIER) cc_final: 0.9117 (pp) REVERT: A 66 THR cc_start: 0.8846 (OUTLIER) cc_final: 0.8588 (m) REVERT: A 191 LYS cc_start: 0.8760 (tttm) cc_final: 0.8355 (ttmm) REVERT: A 292 ASP cc_start: 0.8399 (m-30) cc_final: 0.8179 (m-30) REVERT: B 41 GLN cc_start: 0.7838 (tt0) cc_final: 0.7215 (tp-100) REVERT: B 95 ARG cc_start: 0.8110 (mtt-85) cc_final: 0.7774 (mtp85) REVERT: D 41 GLN cc_start: 0.7713 (tt0) cc_final: 0.7250 (tp40) REVERT: D 64 ILE cc_start: 0.9219 (OUTLIER) cc_final: 0.8978 (pp) REVERT: D 125 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7192 (mp0) REVERT: D 128 ASN cc_start: 0.8205 (m110) cc_final: 0.7876 (t0) REVERT: D 355 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.7990 (mtp) REVERT: E 50 LYS cc_start: 0.8046 (mtmm) cc_final: 0.7699 (mtpt) REVERT: E 57 GLU cc_start: 0.8419 (tt0) cc_final: 0.8063 (pt0) REVERT: E 117 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7928 (mt-10) REVERT: E 118 LYS cc_start: 0.8467 (mtmt) cc_final: 0.8206 (mtpt) REVERT: E 234 SER cc_start: 0.8074 (OUTLIER) cc_final: 0.7727 (t) REVERT: E 355 MET cc_start: 0.8682 (OUTLIER) cc_final: 0.8230 (mtp) outliers start: 27 outliers final: 12 residues processed: 200 average time/residue: 1.7432 time to fit residues: 378.0089 Evaluate side-chains 202 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 183 time to evaluate : 1.654 ------------------------------------------------------------------------------- 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 64 ILE Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 122 ILE 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 13 optimal weight: 3.9990 chunk 94 optimal weight: 0.4980 chunk 85 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 175 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 98 optimal weight: 8.9990 chunk 22 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- 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 225 ASN B 246 GLN E 87 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.117856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.099258 restraints weight = 15259.903| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.20 r_work: 0.3020 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14860 Z= 0.175 Angle : 0.613 7.057 20170 Z= 0.301 Chirality : 0.048 0.193 2240 Planarity : 0.004 0.030 2570 Dihedral : 10.943 176.435 2060 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 2.06 % Allowed : 11.51 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.20), residues: 1800 helix: 0.72 (0.19), residues: 750 sheet: 0.21 (0.26), residues: 335 loop : 1.95 (0.25), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP D 340 HIS 0.005 0.001 HIS E 87 PHE 0.013 0.001 PHE D 262 TYR 0.008 0.001 TYR A 143 ARG 0.005 0.001 ARG D 95 Details of bonding type rmsd hydrogen bonds : bond 0.04343 ( 728) hydrogen bonds : angle 4.91505 ( 1908) covalent geometry : bond 0.00396 (14860) covalent geometry : angle 0.61324 (20170) *********************** 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 230 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 198 time to evaluate : 1.940 Fit side-chains REVERT: C 125 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.7319 (mp0) REVERT: C 276 GLU cc_start: 0.8348 (mm-30) cc_final: 0.7966 (mt-10) REVERT: C 334 GLU cc_start: 0.7885 (pm20) cc_final: 0.7644 (pm20) REVERT: A 64 ILE cc_start: 0.9398 (OUTLIER) cc_final: 0.9134 (pp) REVERT: A 66 THR cc_start: 0.8870 (OUTLIER) cc_final: 0.8630 (m) REVERT: A 191 LYS cc_start: 0.8780 (tttm) cc_final: 0.8385 (ttmm) REVERT: A 292 ASP cc_start: 0.8426 (m-30) cc_final: 0.8222 (m-30) REVERT: B 41 GLN cc_start: 0.7856 (tt0) cc_final: 0.7244 (tp-100) REVERT: B 64 ILE cc_start: 0.9450 (OUTLIER) cc_final: 0.8825 (pp) REVERT: D 41 GLN cc_start: 0.7722 (tt0) cc_final: 0.7243 (tp40) REVERT: D 64 ILE cc_start: 0.9207 (OUTLIER) cc_final: 0.8974 (pp) REVERT: D 128 ASN cc_start: 0.8200 (m110) cc_final: 0.7838 (t0) REVERT: D 355 MET cc_start: 0.8784 (OUTLIER) cc_final: 0.7991 (mtp) REVERT: E 50 LYS cc_start: 0.8042 (mtmm) cc_final: 0.7682 (mtpt) REVERT: E 57 GLU cc_start: 0.8457 (tt0) cc_final: 0.8072 (pt0) REVERT: E 100 GLU cc_start: 0.8146 (pt0) cc_final: 0.7741 (pm20) REVERT: E 118 LYS cc_start: 0.8486 (mtmt) cc_final: 0.8160 (mtpt) REVERT: E 191 LYS cc_start: 0.8652 (tttm) cc_final: 0.8412 (ttmm) REVERT: E 215 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8333 (mppt) REVERT: E 234 SER cc_start: 0.8099 (OUTLIER) cc_final: 0.7767 (t) REVERT: E 355 MET cc_start: 0.8705 (OUTLIER) cc_final: 0.8270 (mtp) outliers start: 32 outliers final: 16 residues processed: 215 average time/residue: 1.7498 time to fit residues: 409.3240 Evaluate side-chains 215 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 190 time to evaluate : 1.594 ------------------------------------------------------------------------------- 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 66 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 323 SER 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 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 323 SER Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 355 MET 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 355 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 149 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 50 optimal weight: 8.9990 chunk 117 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 7 optimal weight: 0.2980 chunk 86 optimal weight: 0.5980 chunk 22 optimal weight: 10.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 = 0.3404 r_free = 0.3404 target = 0.117798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.099267 restraints weight = 15192.350| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.19 r_work: 0.3019 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.1827 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= 0.183 Angle : 0.620 7.111 20170 Z= 0.305 Chirality : 0.048 0.193 2240 Planarity : 0.004 0.030 2570 Dihedral : 10.944 173.882 2060 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.20), residues: 1800 helix: 0.66 (0.19), residues: 765 sheet: 0.20 (0.26), residues: 335 loop : 1.78 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP D 340 HIS 0.004 0.001 HIS D 173 PHE 0.013 0.002 PHE D 262 TYR 0.007 0.001 TYR A 143 ARG 0.005 0.001 ARG E 95 Details of bonding type rmsd hydrogen bonds : bond 0.04374 ( 728) hydrogen bonds : angle 4.91220 ( 1908) covalent geometry : bond 0.00417 (14860) covalent geometry : angle 0.62021 (20170) *********************** 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 217 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 191 time to evaluate : 1.726 Fit side-chains REVERT: C 125 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.7301 (mp0) REVERT: C 276 GLU cc_start: 0.8348 (mm-30) cc_final: 0.7963 (mt-10) REVERT: C 334 GLU cc_start: 0.7895 (pm20) cc_final: 0.7640 (pm20) REVERT: A 64 ILE cc_start: 0.9384 (OUTLIER) cc_final: 0.9116 (pp) REVERT: A 66 THR cc_start: 0.8869 (OUTLIER) cc_final: 0.8640 (m) REVERT: A 191 LYS cc_start: 0.8788 (tttm) cc_final: 0.8391 (ttmm) REVERT: A 292 ASP cc_start: 0.8441 (m-30) cc_final: 0.8235 (m-30) REVERT: B 41 GLN cc_start: 0.7867 (tt0) cc_final: 0.7244 (tp-100) REVERT: B 64 ILE cc_start: 0.9448 (OUTLIER) cc_final: 0.8822 (pp) REVERT: D 41 GLN cc_start: 0.7720 (tt0) cc_final: 0.7240 (tp40) REVERT: D 64 ILE cc_start: 0.9210 (OUTLIER) cc_final: 0.8976 (pp) REVERT: D 128 ASN cc_start: 0.8184 (m110) cc_final: 0.7804 (t0) REVERT: D 355 MET cc_start: 0.8773 (OUTLIER) cc_final: 0.7982 (mtp) REVERT: E 25 ASP cc_start: 0.8127 (OUTLIER) cc_final: 0.7715 (p0) REVERT: E 50 LYS cc_start: 0.8054 (mtmm) cc_final: 0.7690 (mtpt) REVERT: E 57 GLU cc_start: 0.8452 (tt0) cc_final: 0.8071 (pt0) REVERT: E 100 GLU cc_start: 0.8149 (pt0) cc_final: 0.7738 (pm20) REVERT: E 117 GLU cc_start: 0.8272 (mt-10) cc_final: 0.7982 (mt-10) REVERT: E 118 LYS cc_start: 0.8471 (mtmt) cc_final: 0.8146 (mtpt) REVERT: E 191 LYS cc_start: 0.8660 (tttm) cc_final: 0.8415 (ttmm) REVERT: E 215 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8340 (mppt) REVERT: E 234 SER cc_start: 0.8103 (OUTLIER) cc_final: 0.7777 (t) REVERT: E 355 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.8268 (mtp) outliers start: 26 outliers final: 14 residues processed: 207 average time/residue: 1.5940 time to fit residues: 357.6511 Evaluate side-chains 211 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 187 time to evaluate : 1.592 ------------------------------------------------------------------------------- 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 66 THR Chi-restraints excluded: chain A residue 122 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 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 324 THR 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 355 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 178 optimal weight: 8.9990 chunk 18 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 40 optimal weight: 0.2980 chunk 67 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN C 225 ASN C 354 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 = 0.3407 r_free = 0.3407 target = 0.118020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.099508 restraints weight = 15196.057| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 1.19 r_work: 0.3016 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14860 Z= 0.175 Angle : 0.616 7.082 20170 Z= 0.303 Chirality : 0.048 0.192 2240 Planarity : 0.004 0.043 2570 Dihedral : 10.909 173.234 2060 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.93 % Allowed : 11.77 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.20), residues: 1800 helix: 0.69 (0.19), residues: 765 sheet: 0.22 (0.26), residues: 335 loop : 1.78 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP D 340 HIS 0.004 0.001 HIS D 173 PHE 0.013 0.001 PHE D 262 TYR 0.007 0.001 TYR A 143 ARG 0.009 0.001 ARG E 95 Details of bonding type rmsd hydrogen bonds : bond 0.04292 ( 728) hydrogen bonds : angle 4.88703 ( 1908) covalent geometry : bond 0.00398 (14860) covalent geometry : angle 0.61559 (20170) *********************** 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 224 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 194 time to evaluate : 1.584 Fit side-chains REVERT: C 125 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.7290 (mp0) REVERT: C 276 GLU cc_start: 0.8344 (mm-30) cc_final: 0.7961 (mt-10) REVERT: C 334 GLU cc_start: 0.7892 (pm20) cc_final: 0.7636 (pm20) REVERT: A 64 ILE cc_start: 0.9382 (OUTLIER) cc_final: 0.9112 (pp) REVERT: A 66 THR cc_start: 0.8877 (OUTLIER) cc_final: 0.8656 (m) REVERT: A 191 LYS cc_start: 0.8782 (tttm) cc_final: 0.8386 (ttmm) REVERT: A 292 ASP cc_start: 0.8436 (m-30) cc_final: 0.8226 (m-30) REVERT: B 41 GLN cc_start: 0.7859 (tt0) cc_final: 0.7247 (tp-100) REVERT: B 64 ILE cc_start: 0.9447 (OUTLIER) cc_final: 0.8817 (pp) REVERT: B 95 ARG cc_start: 0.8067 (mtt-85) cc_final: 0.7759 (mtp85) REVERT: D 41 GLN cc_start: 0.7723 (tt0) cc_final: 0.7240 (tp40) REVERT: D 64 ILE cc_start: 0.9216 (OUTLIER) cc_final: 0.8980 (pp) REVERT: D 125 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7134 (mp0) REVERT: D 128 ASN cc_start: 0.8203 (m110) cc_final: 0.7820 (t0) REVERT: D 355 MET cc_start: 0.8770 (OUTLIER) cc_final: 0.7980 (mtp) REVERT: E 25 ASP cc_start: 0.8101 (OUTLIER) cc_final: 0.7696 (p0) REVERT: E 50 LYS cc_start: 0.8059 (mtmm) cc_final: 0.7695 (mtpt) REVERT: E 57 GLU cc_start: 0.8448 (tt0) cc_final: 0.8071 (pt0) REVERT: E 100 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7729 (pm20) REVERT: E 117 GLU cc_start: 0.8278 (mt-10) cc_final: 0.7988 (mt-10) REVERT: E 118 LYS cc_start: 0.8474 (mtmt) cc_final: 0.8156 (mtpt) REVERT: E 191 LYS cc_start: 0.8655 (tttm) cc_final: 0.8413 (ttmm) REVERT: E 215 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8331 (mppt) REVERT: E 234 SER cc_start: 0.8099 (OUTLIER) cc_final: 0.7789 (t) REVERT: E 355 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.8266 (mtp) outliers start: 30 outliers final: 16 residues processed: 213 average time/residue: 1.5757 time to fit residues: 363.4925 Evaluate side-chains 219 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 191 time to evaluate : 1.717 ------------------------------------------------------------------------------- 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 66 THR 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 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 324 THR 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 323 SER 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 65 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 167 optimal weight: 0.8980 chunk 72 optimal weight: 10.0000 chunk 70 optimal weight: 6.9990 chunk 151 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN C 225 ASN C 354 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 = 0.3417 r_free = 0.3417 target = 0.118781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.100340 restraints weight = 15120.933| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 1.19 r_work: 0.3031 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14860 Z= 0.143 Angle : 0.592 6.937 20170 Z= 0.289 Chirality : 0.046 0.185 2240 Planarity : 0.004 0.043 2570 Dihedral : 10.724 175.694 2060 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 2.06 % Allowed : 11.70 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.20), residues: 1800 helix: 0.82 (0.20), residues: 750 sheet: 0.25 (0.26), residues: 335 loop : 1.94 (0.25), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 340 HIS 0.003 0.001 HIS C 161 PHE 0.011 0.001 PHE D 262 TYR 0.007 0.001 TYR A 143 ARG 0.009 0.000 ARG E 95 Details of bonding type rmsd hydrogen bonds : bond 0.03912 ( 728) hydrogen bonds : angle 4.79210 ( 1908) covalent geometry : bond 0.00318 (14860) covalent geometry : angle 0.59216 (20170) *********************** 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 224 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 192 time to evaluate : 1.689 Fit side-chains REVERT: C 125 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.7305 (mp0) REVERT: C 276 GLU cc_start: 0.8319 (mm-30) cc_final: 0.7939 (mt-10) REVERT: C 334 GLU cc_start: 0.7875 (pm20) cc_final: 0.7615 (pm20) REVERT: A 64 ILE cc_start: 0.9383 (OUTLIER) cc_final: 0.9115 (pp) REVERT: A 66 THR cc_start: 0.8862 (OUTLIER) cc_final: 0.8647 (m) REVERT: A 191 LYS cc_start: 0.8772 (tttm) cc_final: 0.8370 (ttmm) REVERT: A 292 ASP cc_start: 0.8430 (m-30) cc_final: 0.8224 (m-30) REVERT: B 41 GLN cc_start: 0.7860 (tt0) cc_final: 0.7251 (tp-100) REVERT: B 64 ILE cc_start: 0.9450 (OUTLIER) cc_final: 0.8815 (pp) REVERT: B 95 ARG cc_start: 0.8062 (mtt-85) cc_final: 0.7754 (mtp85) REVERT: D 41 GLN cc_start: 0.7719 (tt0) cc_final: 0.7241 (tp40) REVERT: D 64 ILE cc_start: 0.9209 (OUTLIER) cc_final: 0.8967 (pp) REVERT: D 125 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7127 (mp0) REVERT: D 128 ASN cc_start: 0.8162 (m110) cc_final: 0.7800 (t0) REVERT: D 355 MET cc_start: 0.8759 (OUTLIER) cc_final: 0.7985 (mtp) REVERT: E 25 ASP cc_start: 0.8066 (OUTLIER) cc_final: 0.7670 (p0) REVERT: E 50 LYS cc_start: 0.8046 (mtmm) cc_final: 0.7683 (mtpt) REVERT: E 57 GLU cc_start: 0.8440 (tt0) cc_final: 0.8063 (pt0) REVERT: E 64 ILE cc_start: 0.8989 (OUTLIER) cc_final: 0.8756 (pp) REVERT: E 100 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7744 (pm20) REVERT: E 117 GLU cc_start: 0.8278 (mt-10) cc_final: 0.8024 (mt-10) REVERT: E 118 LYS cc_start: 0.8469 (mtmt) cc_final: 0.8151 (mtpt) REVERT: E 191 LYS cc_start: 0.8641 (tttm) cc_final: 0.8400 (ttmm) REVERT: E 215 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8301 (mppt) REVERT: E 234 SER cc_start: 0.8097 (OUTLIER) cc_final: 0.7806 (t) REVERT: E 355 MET cc_start: 0.8682 (OUTLIER) cc_final: 0.8271 (mtp) outliers start: 32 outliers final: 15 residues processed: 212 average time/residue: 1.6440 time to fit residues: 376.6888 Evaluate side-chains 217 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 189 time to evaluate : 1.706 ------------------------------------------------------------------------------- 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 66 THR 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 350 SER Chi-restraints excluded: chain A residue 351 THR 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 324 THR Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 25 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 67 optimal weight: 6.9990 chunk 53 optimal weight: 8.9990 chunk 140 optimal weight: 0.0070 chunk 71 optimal weight: 8.9990 chunk 92 optimal weight: 2.9990 chunk 121 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 163 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 150 optimal weight: 0.9990 overall best weight: 0.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN C 225 ASN C 354 GLN A 246 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 = 0.3439 r_free = 0.3439 target = 0.120477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.102145 restraints weight = 15156.008| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.19 r_work: 0.3062 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 14860 Z= 0.108 Angle : 0.561 6.487 20170 Z= 0.270 Chirality : 0.045 0.167 2240 Planarity : 0.004 0.042 2570 Dihedral : 10.223 176.383 2060 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.80 % Allowed : 11.96 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.20), residues: 1800 helix: 0.92 (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 TRP 0.014 0.002 TRP D 340 HIS 0.003 0.001 HIS B 161 PHE 0.009 0.001 PHE E 31 TYR 0.008 0.001 TYR C 143 ARG 0.010 0.000 ARG E 95 Details of bonding type rmsd hydrogen bonds : bond 0.03345 ( 728) hydrogen bonds : angle 4.62204 ( 1908) covalent geometry : bond 0.00231 (14860) covalent geometry : angle 0.56115 (20170) *********************** 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 220 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 192 time to evaluate : 1.926 Fit side-chains REVERT: C 125 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.7346 (mp0) REVERT: C 276 GLU cc_start: 0.8312 (mm-30) cc_final: 0.7933 (mt-10) REVERT: C 334 GLU cc_start: 0.7836 (pm20) cc_final: 0.7582 (pm20) REVERT: A 64 ILE cc_start: 0.9383 (OUTLIER) cc_final: 0.9121 (pp) REVERT: A 66 THR cc_start: 0.8825 (OUTLIER) cc_final: 0.8611 (m) REVERT: A 191 LYS cc_start: 0.8741 (tttm) cc_final: 0.8329 (ttmm) REVERT: A 292 ASP cc_start: 0.8427 (m-30) cc_final: 0.8216 (m-30) REVERT: B 41 GLN cc_start: 0.7833 (tt0) cc_final: 0.7222 (tp-100) REVERT: B 95 ARG cc_start: 0.8075 (mtt-85) cc_final: 0.7681 (mtp85) REVERT: D 41 GLN cc_start: 0.7719 (tt0) cc_final: 0.7247 (tp40) REVERT: D 64 ILE cc_start: 0.9203 (OUTLIER) cc_final: 0.8982 (pp) REVERT: D 125 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7149 (mp0) REVERT: D 128 ASN cc_start: 0.8141 (m110) cc_final: 0.7806 (t0) REVERT: E 25 ASP cc_start: 0.8028 (OUTLIER) cc_final: 0.7650 (p0) REVERT: E 50 LYS cc_start: 0.8040 (mtmm) cc_final: 0.7674 (mtpt) REVERT: E 57 GLU cc_start: 0.8403 (tt0) cc_final: 0.8043 (pt0) REVERT: E 95 ARG cc_start: 0.7764 (mtt-85) cc_final: 0.7307 (mtt-85) REVERT: E 100 GLU cc_start: 0.8134 (pt0) cc_final: 0.7738 (pm20) REVERT: E 117 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7943 (mt-10) REVERT: E 118 LYS cc_start: 0.8484 (mtmt) cc_final: 0.8201 (mtpt) REVERT: E 191 LYS cc_start: 0.8621 (tttm) cc_final: 0.8362 (ttmm) REVERT: E 215 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8240 (mppt) REVERT: E 234 SER cc_start: 0.8117 (OUTLIER) cc_final: 0.7842 (t) REVERT: E 355 MET cc_start: 0.8662 (OUTLIER) cc_final: 0.8271 (mtp) outliers start: 28 outliers final: 14 residues processed: 210 average time/residue: 1.6799 time to fit residues: 381.8621 Evaluate side-chains 210 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 187 time to evaluate : 1.755 ------------------------------------------------------------------------------- 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 66 THR 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 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 64 ILE Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 323 SER 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 355 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 179 optimal weight: 1.9990 chunk 146 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 chunk 169 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 175 optimal weight: 0.0010 chunk 119 optimal weight: 0.6980 chunk 47 optimal weight: 4.9990 chunk 153 optimal weight: 7.9990 chunk 46 optimal weight: 0.0970 overall best weight: 0.5184 ------------------------------------------------------------------------------- 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 E 87 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.122321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.104078 restraints weight = 15282.712| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.20 r_work: 0.3090 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14860 Z= 0.094 Angle : 0.547 6.384 20170 Z= 0.261 Chirality : 0.044 0.141 2240 Planarity : 0.004 0.040 2570 Dihedral : 9.489 172.388 2060 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 1.48 % Allowed : 12.67 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.20), residues: 1800 helix: 1.05 (0.20), residues: 750 sheet: 0.48 (0.27), residues: 325 loop : 1.91 (0.25), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 79 HIS 0.006 0.001 HIS E 87 PHE 0.009 0.001 PHE E 31 TYR 0.008 0.001 TYR C 143 ARG 0.009 0.000 ARG E 95 Details of bonding type rmsd hydrogen bonds : bond 0.02984 ( 728) hydrogen bonds : angle 4.46761 ( 1908) covalent geometry : bond 0.00200 (14860) covalent geometry : angle 0.54746 (20170) ********************** 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 210 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 187 time to evaluate : 1.825 Fit side-chains REVERT: C 276 GLU cc_start: 0.8328 (mm-30) cc_final: 0.7954 (mt-10) REVERT: C 334 GLU cc_start: 0.7766 (pm20) cc_final: 0.7516 (pm20) REVERT: A 64 ILE cc_start: 0.9389 (OUTLIER) cc_final: 0.9130 (pp) REVERT: A 66 THR cc_start: 0.8842 (OUTLIER) cc_final: 0.8601 (m) REVERT: A 191 LYS cc_start: 0.8719 (tttm) cc_final: 0.8304 (ttmm) REVERT: A 292 ASP cc_start: 0.8378 (m-30) cc_final: 0.8177 (m-30) REVERT: B 41 GLN cc_start: 0.7794 (tt0) cc_final: 0.7204 (tp-100) REVERT: D 41 GLN cc_start: 0.7714 (tt0) cc_final: 0.7245 (tp40) REVERT: D 128 ASN cc_start: 0.8133 (m110) cc_final: 0.7805 (t0) REVERT: E 25 ASP cc_start: 0.7974 (OUTLIER) cc_final: 0.7766 (p0) REVERT: E 50 LYS cc_start: 0.8031 (mtmm) cc_final: 0.7665 (mtpt) REVERT: E 57 GLU cc_start: 0.8385 (tt0) cc_final: 0.8085 (pt0) REVERT: E 100 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7750 (pm20) REVERT: E 117 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7951 (mt-10) REVERT: E 118 LYS cc_start: 0.8483 (mtmt) cc_final: 0.8200 (mtpt) REVERT: E 215 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.8222 (mppt) REVERT: E 234 SER cc_start: 0.8059 (OUTLIER) cc_final: 0.7816 (t) REVERT: E 355 MET cc_start: 0.8656 (OUTLIER) cc_final: 0.8260 (mtp) outliers start: 23 outliers final: 8 residues processed: 200 average time/residue: 1.6020 time to fit residues: 347.3148 Evaluate side-chains 199 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 184 time to evaluate : 1.740 ------------------------------------------------------------------------------- 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 64 ILE Chi-restraints excluded: chain A residue 66 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 351 THR 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 355 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 92 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 160 optimal weight: 1.9990 chunk 35 optimal weight: 0.0270 chunk 16 optimal weight: 0.9990 chunk 123 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 147 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 overall best weight: 1.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN C 225 ASN C 354 GLN B 246 GLN D 87 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.119766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.101305 restraints weight = 15113.184| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.19 r_work: 0.3049 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14860 Z= 0.133 Angle : 0.583 6.326 20170 Z= 0.283 Chirality : 0.046 0.163 2240 Planarity : 0.004 0.040 2570 Dihedral : 9.710 168.663 2060 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.09 % Allowed : 13.31 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.20), residues: 1800 helix: 0.98 (0.20), residues: 750 sheet: 0.46 (0.27), residues: 325 loop : 1.93 (0.25), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 340 HIS 0.005 0.001 HIS D 87 PHE 0.010 0.001 PHE D 262 TYR 0.007 0.001 TYR C 143 ARG 0.009 0.000 ARG E 95 Details of bonding type rmsd hydrogen bonds : bond 0.03699 ( 728) hydrogen bonds : angle 4.63165 ( 1908) covalent geometry : bond 0.00296 (14860) covalent geometry : angle 0.58296 (20170) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13567.10 seconds wall clock time: 237 minutes 32.90 seconds (14252.90 seconds total)