Starting phenix.real_space_refine on Wed Mar 4 16:56:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7q8c_13864/03_2026/7q8c_13864.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q8c_13864/03_2026/7q8c_13864.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7q8c_13864/03_2026/7q8c_13864.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q8c_13864/03_2026/7q8c_13864.map" model { file = "/net/cci-nas-00/data/ceres_data/7q8c_13864/03_2026/7q8c_13864.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q8c_13864/03_2026/7q8c_13864.cif" } resolution = 2.72 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 5 5.21 5 S 115 5.16 5 C 9195 2.51 5 N 2470 2.21 5 O 3180 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14975 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2895 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 21, 'TRANS': 348} Chain: "B" Number of atoms: 2895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2895 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 21, 'TRANS': 348} Chain: "C" Number of atoms: 2895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2895 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 21, 'TRANS': 348} Chain: "D" Number of atoms: 2895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2895 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 21, 'TRANS': 348} Chain: "E" Number of atoms: 2895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2895 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 21, 'TRANS': 348} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "B" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 76 Classifications: {'water': 76} Link IDs: {None: 75} Chain: "C" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 74 Classifications: {'water': 74} Link IDs: {None: 73} Chain: "D" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 70 Classifications: {'water': 70} Link IDs: {None: 69} Chain: "E" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Time building chain proxies: 2.86, per 1000 atoms: 0.19 Number of scatterers: 14975 At special positions: 0 Unit cell: (87.0317, 100.819, 198.191, 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 115 16.00 P 10 15.00 Mg 5 11.99 O 3180 8.00 N 2470 7.00 C 9195 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.15 Conformation dependent library (CDL) restraints added in 542.8 milliseconds 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3430 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 30 sheets defined 50.0% alpha, 16.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.916A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 removed outlier: 3.568A pdb=" N LEU A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR A 143 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 175 removed outlier: 3.801A pdb=" N VAL A 175 " --> pdb=" O PRO A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 172 through 175' Processing helix chain 'A' and resid 181 through 193 Processing helix chain 'A' and resid 194 through 197 Processing helix chain 'A' and resid 202 through 217 removed outlier: 3.539A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N CYS A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 234 removed outlier: 3.632A pdb=" N LYS A 232 " --> pdb=" O THR A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 256 Processing helix chain 'A' and resid 257 through 261 Processing helix chain 'A' and resid 262 through 267 Processing helix chain 'A' and resid 273 through 283 Processing helix chain 'A' and resid 289 through 295 removed outlier: 3.511A pdb=" N GLY A 295 " --> pdb=" O ARG A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 305 Processing helix chain 'A' and resid 308 through 319 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 348 removed outlier: 3.521A pdb=" N SER A 348 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 355 removed outlier: 3.577A pdb=" N GLN A 353 " --> pdb=" O THR A 350 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N THR A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 removed outlier: 3.537A pdb=" N GLU A 364 " --> pdb=" O SER A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.925A pdb=" N ASN A 372 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.917A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 removed outlier: 3.568A pdb=" N LEU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 removed outlier: 3.800A pdb=" N VAL B 175 " --> pdb=" O PRO B 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 172 through 175' Processing helix chain 'B' and resid 181 through 193 Processing helix chain 'B' and resid 194 through 197 Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.538A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N CYS B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 234 removed outlier: 3.632A pdb=" N LYS B 232 " --> pdb=" O THR B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 256 Processing helix chain 'B' and resid 257 through 261 Processing helix chain 'B' and resid 262 through 267 Processing helix chain 'B' and resid 273 through 283 Processing helix chain 'B' and resid 289 through 295 removed outlier: 3.511A pdb=" N GLY B 295 " --> pdb=" O ARG B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 305 Processing helix chain 'B' and resid 308 through 319 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 348 removed outlier: 3.521A pdb=" N SER B 348 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 355 removed outlier: 3.577A pdb=" N GLN B 353 " --> pdb=" O THR B 350 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N THR B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 removed outlier: 3.537A pdb=" N GLU B 364 " --> pdb=" O SER B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 373 removed outlier: 3.925A pdb=" N ASN B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.917A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 removed outlier: 3.568A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER C 144 " --> pdb=" O LEU C 140 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER C 145 " --> pdb=" O SER C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 removed outlier: 3.801A pdb=" N VAL C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 172 through 175' Processing helix chain 'C' and resid 181 through 193 Processing helix chain 'C' and resid 194 through 197 Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.538A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N CYS C 217 " --> pdb=" O LYS C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 234 removed outlier: 3.632A pdb=" N LYS C 232 " --> pdb=" O THR C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 256 Processing helix chain 'C' and resid 257 through 261 Processing helix chain 'C' and resid 262 through 267 Processing helix chain 'C' and resid 273 through 283 Processing helix chain 'C' and resid 289 through 295 removed outlier: 3.511A pdb=" N GLY C 295 " --> pdb=" O ARG C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'C' and resid 308 through 319 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 348 removed outlier: 3.520A pdb=" N SER C 348 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 355 removed outlier: 3.577A pdb=" N GLN C 353 " --> pdb=" O THR C 350 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N THR C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 removed outlier: 3.537A pdb=" N GLU C 364 " --> pdb=" O SER C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.925A pdb=" N ASN C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.916A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 removed outlier: 3.568A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR D 143 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER D 144 " --> pdb=" O LEU D 140 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER D 145 " --> pdb=" O SER D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 175 removed outlier: 3.801A pdb=" N VAL D 175 " --> pdb=" O PRO D 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 172 through 175' Processing helix chain 'D' and resid 181 through 193 Processing helix chain 'D' and resid 194 through 197 Processing helix chain 'D' and resid 202 through 217 removed outlier: 3.539A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N CYS D 217 " --> pdb=" O LYS D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 234 removed outlier: 3.632A pdb=" N LYS D 232 " --> pdb=" O THR D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 256 Processing helix chain 'D' and resid 257 through 261 Processing helix chain 'D' and resid 262 through 267 Processing helix chain 'D' and resid 273 through 283 Processing helix chain 'D' and resid 289 through 295 removed outlier: 3.511A pdb=" N GLY D 295 " --> pdb=" O ARG D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 305 Processing helix chain 'D' and resid 308 through 319 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 348 removed outlier: 3.521A pdb=" N SER D 348 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 355 removed outlier: 3.577A pdb=" N GLN D 353 " --> pdb=" O THR D 350 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N THR D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 removed outlier: 3.536A pdb=" N GLU D 364 " --> pdb=" O SER D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 removed outlier: 3.925A pdb=" N ASN D 372 " --> pdb=" O SER D 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 92 Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.916A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 146 removed outlier: 3.568A pdb=" N LEU E 142 " --> pdb=" O ALA E 138 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR E 143 " --> pdb=" O VAL E 139 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER E 144 " --> pdb=" O LEU E 140 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER E 145 " --> pdb=" O SER E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 175 removed outlier: 3.801A pdb=" N VAL E 175 " --> pdb=" O PRO E 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 172 through 175' Processing helix chain 'E' and resid 181 through 193 Processing helix chain 'E' and resid 194 through 197 Processing helix chain 'E' and resid 202 through 217 removed outlier: 3.539A pdb=" N GLU E 207 " --> pdb=" O THR E 203 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N CYS E 217 " --> pdb=" O LYS E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 234 removed outlier: 3.632A pdb=" N LYS E 232 " --> pdb=" O THR E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 256 Processing helix chain 'E' and resid 257 through 261 Processing helix chain 'E' and resid 262 through 267 Processing helix chain 'E' and resid 273 through 283 Processing helix chain 'E' and resid 289 through 295 removed outlier: 3.511A pdb=" N GLY E 295 " --> pdb=" O ARG E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 305 Processing helix chain 'E' and resid 308 through 319 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 348 removed outlier: 3.521A pdb=" N SER E 348 " --> pdb=" O SER E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 355 removed outlier: 3.576A pdb=" N GLN E 353 " --> pdb=" O THR E 350 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N THR E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 366 removed outlier: 3.537A pdb=" N GLU E 364 " --> pdb=" O SER E 360 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 removed outlier: 3.925A pdb=" N ASN E 372 " --> pdb=" O SER E 368 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.545A pdb=" N HIS A 29 " --> pdb=" O ALA A 19 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ILE A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.680A pdb=" N THR A 106 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 170 removed outlier: 6.185A pdb=" N ILE A 297 " --> pdb=" O VAL A 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 237 through 240 Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 32 removed outlier: 3.545A pdb=" N HIS B 29 " --> pdb=" O ALA B 19 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ILE B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.680A pdb=" N THR B 106 " --> pdb=" O ILE B 8 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AB2, first strand: chain 'B' and resid 169 through 170 removed outlier: 6.185A pdb=" N ILE B 297 " --> pdb=" O VAL B 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 237 through 240 Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 32 removed outlier: 3.545A pdb=" N HIS C 29 " --> pdb=" O ALA C 19 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ILE C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.680A pdb=" N THR C 106 " --> pdb=" O ILE C 8 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB8, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.185A pdb=" N ILE C 297 " --> pdb=" O VAL C 330 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 237 through 240 Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 32 removed outlier: 3.545A pdb=" N HIS D 29 " --> pdb=" O ALA D 19 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ILE D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.681A pdb=" N THR D 106 " --> pdb=" O ILE D 8 " (cutoff:3.500A) removed outlier: 8.707A 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: 6.185A pdb=" N ILE D 297 " --> pdb=" O VAL D 330 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 237 through 240 Processing sheet with id=AC7, first strand: chain 'E' and resid 29 through 32 removed outlier: 3.545A pdb=" N HIS E 29 " --> pdb=" O ALA E 19 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ILE E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.680A pdb=" N THR E 106 " --> pdb=" O ILE E 8 " (cutoff:3.500A) removed outlier: 8.707A 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: 6.185A pdb=" N ILE E 297 " --> pdb=" O VAL E 330 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 237 through 240 670 hydrogen bonds defined for protein. 1710 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.38 Time building geometry restraints manager: 1.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4780 1.34 - 1.46: 2264 1.46 - 1.57: 7671 1.57 - 1.69: 15 1.69 - 1.80: 205 Bond restraints: 14935 Sorted by residual: bond pdb=" C4 ADP A 600 " pdb=" C5 ADP A 600 " ideal model delta sigma weight residual 1.490 1.462 0.028 2.00e-02 2.50e+03 1.91e+00 bond pdb=" C4 ADP C 600 " pdb=" C5 ADP C 600 " ideal model delta sigma weight residual 1.490 1.463 0.027 2.00e-02 2.50e+03 1.86e+00 bond pdb=" C4 ADP E 600 " pdb=" C5 ADP E 600 " ideal model delta sigma weight residual 1.490 1.463 0.027 2.00e-02 2.50e+03 1.83e+00 bond pdb=" C4 ADP B 600 " pdb=" C5 ADP B 600 " ideal model delta sigma weight residual 1.490 1.463 0.027 2.00e-02 2.50e+03 1.79e+00 bond pdb=" C4 ADP D 600 " pdb=" C5 ADP D 600 " ideal model delta sigma weight residual 1.490 1.463 0.027 2.00e-02 2.50e+03 1.79e+00 ... (remaining 14930 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 19710 1.49 - 2.97: 409 2.97 - 4.46: 86 4.46 - 5.95: 25 5.95 - 7.44: 20 Bond angle restraints: 20250 Sorted by residual: angle pdb=" C1' ADP D 600 " pdb=" C2' ADP D 600 " pdb=" C3' ADP D 600 " ideal model delta sigma weight residual 111.00 103.56 7.44 3.00e+00 1.11e-01 6.14e+00 angle pdb=" C1' ADP A 600 " pdb=" C2' ADP A 600 " pdb=" C3' ADP A 600 " ideal model delta sigma weight residual 111.00 103.57 7.43 3.00e+00 1.11e-01 6.13e+00 angle pdb=" C1' ADP C 600 " pdb=" C2' ADP C 600 " pdb=" C3' ADP C 600 " ideal model delta sigma weight residual 111.00 103.59 7.41 3.00e+00 1.11e-01 6.10e+00 angle pdb=" C1' ADP B 600 " pdb=" C2' ADP B 600 " pdb=" C3' ADP B 600 " ideal model delta sigma weight residual 111.00 103.59 7.41 3.00e+00 1.11e-01 6.10e+00 angle pdb=" C1' ADP E 600 " pdb=" C2' ADP E 600 " pdb=" C3' ADP E 600 " ideal model delta sigma weight residual 111.00 103.59 7.41 3.00e+00 1.11e-01 6.10e+00 ... (remaining 20245 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.68: 8870 26.68 - 53.35: 155 53.35 - 80.03: 10 80.03 - 106.70: 0 106.70 - 133.38: 5 Dihedral angle restraints: 9040 sinusoidal: 3700 harmonic: 5340 Sorted by residual: dihedral pdb=" O1B ADP A 600 " pdb=" O3A ADP A 600 " pdb=" PB ADP A 600 " pdb=" PA ADP A 600 " ideal model delta sinusoidal sigma weight residual 300.00 166.62 133.38 1 2.00e+01 2.50e-03 4.05e+01 dihedral pdb=" O1B ADP E 600 " pdb=" O3A ADP E 600 " pdb=" PB ADP E 600 " pdb=" PA ADP E 600 " ideal model delta sinusoidal sigma weight residual 300.00 166.63 133.36 1 2.00e+01 2.50e-03 4.05e+01 dihedral pdb=" O1B ADP B 600 " pdb=" O3A ADP B 600 " pdb=" PB ADP B 600 " pdb=" PA ADP B 600 " ideal model delta sinusoidal sigma weight residual 300.00 166.64 133.36 1 2.00e+01 2.50e-03 4.05e+01 ... (remaining 9037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1062 0.031 - 0.062: 762 0.062 - 0.093: 208 0.093 - 0.124: 186 0.124 - 0.155: 17 Chirality restraints: 2235 Sorted by residual: chirality pdb=" C3' ADP B 600 " pdb=" C2' ADP B 600 " pdb=" C4' ADP B 600 " pdb=" O3' ADP B 600 " both_signs ideal model delta sigma weight residual False -2.51 -2.67 0.15 2.00e-01 2.50e+01 5.97e-01 chirality pdb=" C3' ADP E 600 " pdb=" C2' ADP E 600 " pdb=" C4' ADP E 600 " pdb=" O3' ADP E 600 " both_signs ideal model delta sigma weight residual False -2.51 -2.66 0.15 2.00e-01 2.50e+01 5.92e-01 chirality pdb=" C3' ADP D 600 " pdb=" C2' ADP D 600 " pdb=" C4' ADP D 600 " pdb=" O3' ADP D 600 " both_signs ideal model delta sigma weight residual False -2.51 -2.66 0.15 2.00e-01 2.50e+01 5.83e-01 ... (remaining 2232 not shown) Planarity restraints: 2605 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 163 " -0.026 5.00e-02 4.00e+02 3.89e-02 2.42e+00 pdb=" N PRO B 164 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO B 164 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 164 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 163 " -0.025 5.00e-02 4.00e+02 3.86e-02 2.38e+00 pdb=" N PRO E 164 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO E 164 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO E 164 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 163 " 0.025 5.00e-02 4.00e+02 3.86e-02 2.38e+00 pdb=" N PRO D 164 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO D 164 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 164 " 0.021 5.00e-02 4.00e+02 ... (remaining 2602 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 130 2.54 - 3.13: 10877 3.13 - 3.72: 21511 3.72 - 4.31: 34343 4.31 - 4.90: 55049 Nonbonded interactions: 121910 Sorted by model distance: nonbonded pdb="MG MG E 601 " pdb=" O HOH E 765 " model vdw 1.953 2.170 nonbonded pdb="MG MG D 601 " pdb=" O HOH D 767 " model vdw 1.956 2.170 nonbonded pdb="MG MG B 601 " pdb=" O HOH B 771 " model vdw 1.957 2.170 nonbonded pdb="MG MG A 601 " pdb=" O HOH A 769 " model vdw 1.957 2.170 nonbonded pdb="MG MG C 601 " pdb=" O HOH C 770 " model vdw 1.957 2.170 ... (remaining 121905 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.610 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: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.610 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 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 : 0.005 0.040 14935 Z= 0.189 Angle : 0.618 7.435 20250 Z= 0.300 Chirality : 0.050 0.155 2235 Planarity : 0.005 0.039 2605 Dihedral : 10.883 133.379 5610 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.20), residues: 1840 helix: -0.61 (0.18), residues: 675 sheet: 0.75 (0.27), residues: 365 loop : 0.87 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 255 TYR 0.011 0.001 TYR E 294 PHE 0.010 0.001 PHE C 254 TRP 0.012 0.002 TRP E 79 HIS 0.004 0.001 HIS E 161 Details of bonding type rmsd covalent geometry : bond 0.00460 (14935) covalent geometry : angle 0.61849 (20250) hydrogen bonds : bond 0.29447 ( 660) hydrogen bonds : angle 8.00821 ( 1710) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.602 Fit side-chains REVERT: A 132 LEU cc_start: 0.8791 (tp) cc_final: 0.8507 (tp) REVERT: B 82 MET cc_start: 0.8965 (tpt) cc_final: 0.8260 (tpt) REVERT: C 25 ASP cc_start: 0.7262 (p0) cc_final: 0.7034 (p0) REVERT: C 42 GLN cc_start: 0.8469 (tp40) cc_final: 0.8139 (mm-40) REVERT: C 82 MET cc_start: 0.8930 (tpt) cc_final: 0.8475 (tpt) REVERT: C 227 MET cc_start: 0.8252 (mmm) cc_final: 0.7985 (tpt) REVERT: C 248 MET cc_start: 0.8077 (mmt) cc_final: 0.7862 (mmp) REVERT: D 190 MET cc_start: 0.8201 (ttp) cc_final: 0.7979 (ttp) REVERT: E 227 MET cc_start: 0.8310 (mmm) cc_final: 0.8027 (tpt) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.8989 time to fit residues: 176.5314 Evaluate side-chains 128 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 6.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 GLN D 114 GLN D 353 GLN E 353 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.094147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.078339 restraints weight = 20413.921| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 1.20 r_work: 0.2810 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8947 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 14935 Z= 0.213 Angle : 0.746 8.721 20250 Z= 0.376 Chirality : 0.053 0.203 2235 Planarity : 0.005 0.044 2605 Dihedral : 9.585 136.345 2045 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.98 % Allowed : 7.78 % Favored : 90.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.19), residues: 1840 helix: -0.01 (0.19), residues: 730 sheet: 0.88 (0.27), residues: 360 loop : 0.74 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 116 TYR 0.012 0.002 TYR C 294 PHE 0.012 0.001 PHE A 254 TRP 0.017 0.003 TRP A 340 HIS 0.008 0.002 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00505 (14935) covalent geometry : angle 0.74571 (20250) hydrogen bonds : bond 0.06692 ( 660) hydrogen bonds : angle 5.41696 ( 1710) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 138 time to evaluate : 0.493 Fit side-chains REVERT: A 45 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.7699 (mtt) REVERT: A 240 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7991 (tt0) REVERT: B 95 ARG cc_start: 0.8364 (mtp-110) cc_final: 0.8149 (mtp85) REVERT: B 227 MET cc_start: 0.8580 (tpt) cc_final: 0.8280 (tpt) REVERT: C 25 ASP cc_start: 0.7851 (p0) cc_final: 0.7586 (p0) REVERT: C 42 GLN cc_start: 0.8667 (tp40) cc_final: 0.8429 (mm-40) REVERT: C 176 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.7979 (mtp180) REVERT: C 227 MET cc_start: 0.8218 (mmm) cc_final: 0.7860 (tpt) REVERT: C 248 MET cc_start: 0.8702 (mmt) cc_final: 0.8455 (mmp) REVERT: D 45 MET cc_start: 0.7983 (OUTLIER) cc_final: 0.7632 (mtt) REVERT: D 190 MET cc_start: 0.9194 (ttp) cc_final: 0.8973 (ttp) REVERT: E 227 MET cc_start: 0.8318 (mmm) cc_final: 0.8036 (tpt) outliers start: 32 outliers final: 6 residues processed: 159 average time/residue: 0.8206 time to fit residues: 140.3566 Evaluate side-chains 143 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 133 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain C residue 68 LYS Chi-restraints excluded: chain C residue 176 ARG Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain E residue 240 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 102 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 59 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 184 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 175 optimal weight: 5.9990 chunk 159 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 45 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 353 GLN E 353 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.093530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.077712 restraints weight = 20666.270| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 1.20 r_work: 0.2796 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8965 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 : 0.005 0.042 14935 Z= 0.213 Angle : 0.733 8.604 20250 Z= 0.368 Chirality : 0.053 0.197 2235 Planarity : 0.005 0.045 2605 Dihedral : 9.783 140.300 2045 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.85 % Allowed : 8.89 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.19), residues: 1840 helix: 0.41 (0.20), residues: 705 sheet: 0.83 (0.28), residues: 360 loop : 0.48 (0.22), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 255 TYR 0.012 0.002 TYR A 279 PHE 0.013 0.002 PHE B 254 TRP 0.017 0.003 TRP A 340 HIS 0.008 0.002 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00510 (14935) covalent geometry : angle 0.73349 (20250) hydrogen bonds : bond 0.06596 ( 660) hydrogen bonds : angle 5.15144 ( 1710) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 0.649 Fit side-chains REVERT: A 45 MET cc_start: 0.8005 (OUTLIER) cc_final: 0.7779 (mtt) REVERT: A 240 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.8038 (tt0) REVERT: B 227 MET cc_start: 0.8518 (tpt) cc_final: 0.8069 (tpt) REVERT: C 227 MET cc_start: 0.8189 (mmm) cc_final: 0.7762 (tpt) REVERT: D 45 MET cc_start: 0.8001 (OUTLIER) cc_final: 0.7685 (mtt) REVERT: E 227 MET cc_start: 0.8303 (mmm) cc_final: 0.8091 (tpt) outliers start: 30 outliers final: 14 residues processed: 154 average time/residue: 0.8184 time to fit residues: 135.3920 Evaluate side-chains 147 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 68 LYS Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain D residue 240 GLU Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain E residue 240 GLU Chi-restraints excluded: chain E residue 262 LYS Chi-restraints excluded: chain E residue 375 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 25 optimal weight: 0.7980 chunk 100 optimal weight: 10.0000 chunk 180 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 124 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 96 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 143 optimal weight: 0.0770 chunk 33 optimal weight: 9.9990 overall best weight: 1.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN D 353 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.095504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.080003 restraints weight = 20693.335| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 1.19 r_work: 0.2841 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8929 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14935 Z= 0.126 Angle : 0.631 7.909 20250 Z= 0.309 Chirality : 0.048 0.196 2235 Planarity : 0.004 0.043 2605 Dihedral : 9.213 132.530 2045 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.60 % Allowed : 9.63 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.20), residues: 1840 helix: 0.71 (0.20), residues: 695 sheet: 0.86 (0.26), residues: 395 loop : 0.27 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 147 TYR 0.013 0.001 TYR A 279 PHE 0.010 0.001 PHE B 254 TRP 0.013 0.002 TRP E 79 HIS 0.004 0.001 HIS E 161 Details of bonding type rmsd covalent geometry : bond 0.00279 (14935) covalent geometry : angle 0.63076 (20250) hydrogen bonds : bond 0.04500 ( 660) hydrogen bonds : angle 4.91839 ( 1710) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 0.532 Fit side-chains REVERT: A 240 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7994 (tt0) REVERT: B 227 MET cc_start: 0.8546 (tpt) cc_final: 0.8078 (tpt) REVERT: C 25 ASP cc_start: 0.7829 (p0) cc_final: 0.7609 (p0) REVERT: C 176 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.7960 (mtp180) REVERT: D 45 MET cc_start: 0.7941 (OUTLIER) cc_final: 0.7671 (mtt) REVERT: D 82 MET cc_start: 0.9194 (OUTLIER) cc_final: 0.8806 (tpt) REVERT: E 227 MET cc_start: 0.8317 (mmm) cc_final: 0.8075 (tpt) outliers start: 26 outliers final: 12 residues processed: 150 average time/residue: 0.8128 time to fit residues: 131.1091 Evaluate side-chains 143 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 68 LYS Chi-restraints excluded: chain C residue 176 ARG Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 240 GLU Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain E residue 240 GLU Chi-restraints excluded: chain E residue 262 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 57 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 148 optimal weight: 20.0000 chunk 39 optimal weight: 8.9990 chunk 8 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 160 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 353 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.093679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.078075 restraints weight = 20820.334| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 1.19 r_work: 0.2807 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 14935 Z= 0.195 Angle : 0.705 8.323 20250 Z= 0.351 Chirality : 0.052 0.193 2235 Planarity : 0.005 0.042 2605 Dihedral : 9.625 138.312 2045 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.10 % Allowed : 9.94 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.20), residues: 1840 helix: 0.68 (0.20), residues: 695 sheet: 0.67 (0.26), residues: 400 loop : 0.23 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 255 TYR 0.012 0.002 TYR A 279 PHE 0.014 0.001 PHE B 254 TRP 0.016 0.003 TRP A 340 HIS 0.007 0.002 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00467 (14935) covalent geometry : angle 0.70528 (20250) hydrogen bonds : bond 0.05849 ( 660) hydrogen bonds : angle 4.92555 ( 1710) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 126 time to evaluate : 0.639 Fit side-chains REVERT: A 240 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.8058 (tt0) REVERT: B 227 MET cc_start: 0.8568 (tpt) cc_final: 0.8064 (tpt) REVERT: C 45 MET cc_start: 0.7895 (mtt) cc_final: 0.7649 (mtt) REVERT: C 227 MET cc_start: 0.8621 (tpt) cc_final: 0.8388 (tpt) REVERT: D 45 MET cc_start: 0.7910 (OUTLIER) cc_final: 0.7635 (mtt) REVERT: E 227 MET cc_start: 0.8300 (mmm) cc_final: 0.8043 (tpt) outliers start: 34 outliers final: 21 residues processed: 151 average time/residue: 0.7956 time to fit residues: 129.4193 Evaluate side-chains 150 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 68 LYS Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 240 GLU Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain E residue 131 SER Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 240 GLU Chi-restraints excluded: chain E residue 262 LYS Chi-restraints excluded: chain E residue 375 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 14 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 155 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 146 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 162 optimal weight: 10.0000 chunk 126 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 112 optimal weight: 0.9980 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 353 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.093284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.077539 restraints weight = 20582.224| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 1.19 r_work: 0.2794 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8977 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14935 Z= 0.219 Angle : 0.738 8.643 20250 Z= 0.370 Chirality : 0.053 0.193 2235 Planarity : 0.005 0.043 2605 Dihedral : 9.817 142.090 2045 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.22 % Allowed : 10.12 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.19), residues: 1840 helix: 0.58 (0.20), residues: 695 sheet: 0.58 (0.26), residues: 400 loop : 0.14 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 255 TYR 0.011 0.002 TYR A 279 PHE 0.014 0.002 PHE B 254 TRP 0.017 0.003 TRP A 340 HIS 0.007 0.002 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00530 (14935) covalent geometry : angle 0.73790 (20250) hydrogen bonds : bond 0.06284 ( 660) hydrogen bonds : angle 4.94602 ( 1710) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 128 time to evaluate : 0.397 Fit side-chains REVERT: A 240 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8098 (tt0) REVERT: B 227 MET cc_start: 0.8616 (tpt) cc_final: 0.8077 (tpt) REVERT: C 45 MET cc_start: 0.7951 (mtt) cc_final: 0.7713 (mtt) REVERT: D 45 MET cc_start: 0.7870 (OUTLIER) cc_final: 0.7647 (mtt) REVERT: D 82 MET cc_start: 0.9220 (OUTLIER) cc_final: 0.8907 (tpt) REVERT: D 114 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7695 (mp-120) REVERT: E 227 MET cc_start: 0.8307 (mmm) cc_final: 0.8041 (tpt) REVERT: E 269 ASP cc_start: 0.8394 (OUTLIER) cc_final: 0.8115 (m-30) outliers start: 36 outliers final: 20 residues processed: 156 average time/residue: 0.7512 time to fit residues: 126.6037 Evaluate side-chains 153 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 68 LYS Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 114 GLN Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain E residue 131 SER Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 240 GLU Chi-restraints excluded: chain E residue 262 LYS Chi-restraints excluded: chain E residue 269 ASP Chi-restraints excluded: chain E residue 375 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 147 optimal weight: 9.9990 chunk 163 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 18 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 155 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 157 optimal weight: 0.8980 chunk 134 optimal weight: 5.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 353 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.094815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.079314 restraints weight = 20656.222| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 1.19 r_work: 0.2830 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8942 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14935 Z= 0.137 Angle : 0.644 7.974 20250 Z= 0.317 Chirality : 0.049 0.198 2235 Planarity : 0.004 0.042 2605 Dihedral : 9.347 134.431 2045 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.67 % Allowed : 10.74 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.20), residues: 1840 helix: 0.71 (0.20), residues: 695 sheet: 0.70 (0.26), residues: 395 loop : 0.16 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 177 TYR 0.011 0.001 TYR A 279 PHE 0.011 0.001 PHE B 254 TRP 0.014 0.002 TRP E 79 HIS 0.005 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00310 (14935) covalent geometry : angle 0.64443 (20250) hydrogen bonds : bond 0.04692 ( 660) hydrogen bonds : angle 4.82035 ( 1710) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 0.587 Fit side-chains REVERT: A 240 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.8033 (tt0) REVERT: B 227 MET cc_start: 0.8590 (tpt) cc_final: 0.8076 (tpt) REVERT: C 45 MET cc_start: 0.7905 (mtt) cc_final: 0.7660 (mtt) REVERT: C 269 ASP cc_start: 0.8125 (OUTLIER) cc_final: 0.7889 (m-30) REVERT: E 227 MET cc_start: 0.8282 (mmm) cc_final: 0.8027 (tpt) outliers start: 27 outliers final: 14 residues processed: 148 average time/residue: 0.7916 time to fit residues: 126.0631 Evaluate side-chains 142 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 68 LYS Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 269 ASP Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain E residue 262 LYS Chi-restraints excluded: chain E residue 375 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 136 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 163 optimal weight: 7.9990 chunk 118 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 168 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 chunk 162 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 68 optimal weight: 0.8980 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 353 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.094542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.078800 restraints weight = 20667.438| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 1.20 r_work: 0.2818 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8954 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14935 Z= 0.160 Angle : 0.669 8.154 20250 Z= 0.331 Chirality : 0.050 0.194 2235 Planarity : 0.005 0.041 2605 Dihedral : 9.472 136.245 2045 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.60 % Allowed : 11.11 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.20), residues: 1840 helix: 0.71 (0.20), residues: 695 sheet: 0.61 (0.26), residues: 400 loop : 0.17 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 255 TYR 0.012 0.001 TYR A 279 PHE 0.012 0.001 PHE B 254 TRP 0.013 0.002 TRP E 79 HIS 0.006 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00374 (14935) covalent geometry : angle 0.66905 (20250) hydrogen bonds : bond 0.05214 ( 660) hydrogen bonds : angle 4.82676 ( 1710) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 0.581 Fit side-chains REVERT: A 240 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.8050 (tt0) REVERT: B 227 MET cc_start: 0.8610 (tpt) cc_final: 0.8064 (tpt) REVERT: C 45 MET cc_start: 0.7904 (mtt) cc_final: 0.7665 (mtt) REVERT: C 269 ASP cc_start: 0.8149 (OUTLIER) cc_final: 0.7919 (m-30) REVERT: D 114 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7671 (mp-120) REVERT: D 305 MET cc_start: 0.9069 (mmm) cc_final: 0.8733 (mmt) REVERT: E 227 MET cc_start: 0.8242 (mmm) cc_final: 0.7984 (tpt) outliers start: 26 outliers final: 15 residues processed: 148 average time/residue: 0.7723 time to fit residues: 123.4890 Evaluate side-chains 144 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 68 LYS Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 269 ASP Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain D residue 114 GLN Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain E residue 131 SER Chi-restraints excluded: chain E residue 375 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 36 optimal weight: 0.1980 chunk 42 optimal weight: 7.9990 chunk 167 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 121 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 93 optimal weight: 7.9990 chunk 184 optimal weight: 9.9990 chunk 34 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 151 optimal weight: 7.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 353 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.094210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.078752 restraints weight = 20668.204| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 1.19 r_work: 0.2818 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8951 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14935 Z= 0.160 Angle : 0.668 8.172 20250 Z= 0.330 Chirality : 0.050 0.193 2235 Planarity : 0.005 0.041 2605 Dihedral : 9.458 137.179 2045 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.79 % Allowed : 10.99 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.20), residues: 1840 helix: 0.70 (0.20), residues: 695 sheet: 0.62 (0.26), residues: 400 loop : 0.17 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 37 TYR 0.012 0.001 TYR A 279 PHE 0.012 0.001 PHE B 254 TRP 0.013 0.002 TRP E 79 HIS 0.006 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00373 (14935) covalent geometry : angle 0.66835 (20250) hydrogen bonds : bond 0.05167 ( 660) hydrogen bonds : angle 4.81646 ( 1710) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 125 time to evaluate : 0.582 Fit side-chains REVERT: A 240 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.8043 (tt0) REVERT: B 227 MET cc_start: 0.8614 (tpt) cc_final: 0.8058 (tpt) REVERT: C 45 MET cc_start: 0.7931 (mtt) cc_final: 0.7692 (mtt) REVERT: C 269 ASP cc_start: 0.8153 (OUTLIER) cc_final: 0.7925 (m-30) REVERT: D 114 GLN cc_start: 0.8224 (OUTLIER) cc_final: 0.7667 (mp-120) REVERT: E 227 MET cc_start: 0.8236 (mmm) cc_final: 0.7975 (tpt) REVERT: E 269 ASP cc_start: 0.8354 (OUTLIER) cc_final: 0.8056 (m-30) outliers start: 29 outliers final: 16 residues processed: 150 average time/residue: 0.7570 time to fit residues: 122.7721 Evaluate side-chains 146 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 68 LYS Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 269 ASP Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain D residue 114 GLN Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain E residue 131 SER Chi-restraints excluded: chain E residue 269 ASP Chi-restraints excluded: chain E residue 375 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 179 optimal weight: 0.0270 chunk 157 optimal weight: 0.0980 chunk 110 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 120 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 overall best weight: 1.1640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 353 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.097029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.081377 restraints weight = 20519.274| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 1.21 r_work: 0.2867 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14935 Z= 0.105 Angle : 0.596 7.500 20250 Z= 0.289 Chirality : 0.047 0.187 2235 Planarity : 0.004 0.041 2605 Dihedral : 8.690 124.528 2045 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.86 % Allowed : 11.91 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.20), residues: 1840 helix: 0.89 (0.20), residues: 695 sheet: 0.74 (0.26), residues: 395 loop : 0.27 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 335 TYR 0.013 0.001 TYR A 279 PHE 0.009 0.001 PHE B 254 TRP 0.013 0.002 TRP E 79 HIS 0.004 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00224 (14935) covalent geometry : angle 0.59566 (20250) hydrogen bonds : bond 0.03751 ( 660) hydrogen bonds : angle 4.70116 ( 1710) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 0.411 Fit side-chains REVERT: A 240 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7951 (tt0) REVERT: B 227 MET cc_start: 0.8551 (tpt) cc_final: 0.7999 (tpt) REVERT: C 25 ASP cc_start: 0.7797 (p0) cc_final: 0.7571 (p0) REVERT: C 45 MET cc_start: 0.7880 (mtt) cc_final: 0.7647 (mtt) REVERT: E 227 MET cc_start: 0.8200 (mmm) cc_final: 0.7925 (tpt) outliers start: 14 outliers final: 10 residues processed: 141 average time/residue: 0.7871 time to fit residues: 119.5813 Evaluate side-chains 137 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain E residue 131 SER Chi-restraints excluded: chain E residue 375 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 47 optimal weight: 0.4980 chunk 172 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 141 optimal weight: 5.9990 chunk 168 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 76 optimal weight: 0.6980 chunk 150 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 353 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.096693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.080988 restraints weight = 20574.768| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 1.21 r_work: 0.2858 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14935 Z= 0.111 Angle : 0.603 7.586 20250 Z= 0.293 Chirality : 0.047 0.190 2235 Planarity : 0.004 0.040 2605 Dihedral : 8.607 121.304 2045 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.86 % Allowed : 12.04 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.20), residues: 1840 helix: 0.73 (0.20), residues: 725 sheet: 0.66 (0.26), residues: 400 loop : 0.33 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 291 TYR 0.012 0.001 TYR A 279 PHE 0.010 0.001 PHE B 254 TRP 0.013 0.002 TRP E 79 HIS 0.004 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00241 (14935) covalent geometry : angle 0.60291 (20250) hydrogen bonds : bond 0.04021 ( 660) hydrogen bonds : angle 4.66742 ( 1710) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4555.49 seconds wall clock time: 78 minutes 16.47 seconds (4696.47 seconds total)