Starting phenix.real_space_refine on Mon Apr 6 12:40:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q7l_72306/04_2026/9q7l_72306.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q7l_72306/04_2026/9q7l_72306.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9q7l_72306/04_2026/9q7l_72306.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q7l_72306/04_2026/9q7l_72306.map" model { file = "/net/cci-nas-00/data/ceres_data/9q7l_72306/04_2026/9q7l_72306.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q7l_72306/04_2026/9q7l_72306.cif" } resolution = 3.68 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.018 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 110 5.16 5 C 11570 2.51 5 N 3056 2.21 5 O 3535 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18286 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2839 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 342} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2839 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 342} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2839 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 342} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2839 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 342} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2839 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 342} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "a" Number of atoms: 1317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1317 Classifications: {'peptide': 166} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 160} Chain: "b" Number of atoms: 1317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1317 Classifications: {'peptide': 166} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 160} Chain: "c" Number of atoms: 1317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1317 Classifications: {'peptide': 166} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 160} 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} Time building chain proxies: 4.29, per 1000 atoms: 0.23 Number of scatterers: 18286 At special positions: 0 Unit cell: (96.66, 124.584, 185.802, 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 110 16.00 P 10 15.00 Mg 5 11.99 O 3535 8.00 N 3056 7.00 C 11570 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: 1.55 Conformation dependent library (CDL) restraints added in 792.0 milliseconds 4534 Ramachandran restraints generated. 2267 Oldfield, 0 Emsley, 2267 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4312 Finding SS restraints... Secondary structure from input PDB file: 118 helices and 30 sheets defined 45.5% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 56 through 61 removed outlier: 3.711A pdb=" N SER A 60 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS A 61 " --> pdb=" O ALA A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 91 Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.576A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 removed outlier: 3.818A pdb=" N SER A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 197 removed outlier: 3.944A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ARG A 196 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLY A 197 " --> pdb=" O LEU A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 217 removed outlier: 3.623A pdb=" N CYS A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 231 Processing helix chain 'A' and resid 251 through 256 removed outlier: 3.607A pdb=" N ARG A 254 " --> pdb=" O GLY A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 262 removed outlier: 3.758A pdb=" N THR A 260 " --> pdb=" O CYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 289 through 295 removed outlier: 4.105A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 removed outlier: 3.573A pdb=" N ARG A 312 " --> pdb=" O GLY A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 347 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.727A pdb=" N PHE A 352 " --> pdb=" O LEU A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 369 through 374 Processing helix chain 'B' and resid 56 through 61 removed outlier: 3.763A pdb=" N SER B 60 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LYS B 61 " --> pdb=" O ALA B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 91 Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.689A pdb=" N GLU B 100 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N HIS B 101 " --> pdb=" O PRO B 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 97 through 101' Processing helix chain 'B' and resid 112 through 126 Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 181 through 194 Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.830A pdb=" N CYS B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 231 Processing helix chain 'B' and resid 251 through 255 removed outlier: 3.795A pdb=" N ARG B 254 " --> pdb=" O GLY B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 262 removed outlier: 3.777A pdb=" N THR B 260 " --> pdb=" O CYS B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 267 removed outlier: 3.542A pdb=" N PHE B 266 " --> pdb=" O GLN B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 286 through 289 removed outlier: 3.845A pdb=" N ILE B 289 " --> pdb=" O ASP B 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 286 through 289' Processing helix chain 'B' and resid 290 through 295 removed outlier: 4.318A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 removed outlier: 3.583A pdb=" N ARG B 312 " --> pdb=" O GLY B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 348 removed outlier: 3.722A pdb=" N SER B 348 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.830A pdb=" N GLN B 353 " --> pdb=" O SER B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 369 through 374 Processing helix chain 'C' and resid 56 through 58 No H-bonds generated for 'chain 'C' and resid 56 through 58' Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.702A pdb=" N GLU C 100 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 97 through 101' Processing helix chain 'C' and resid 112 through 126 Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 181 through 195 removed outlier: 4.115A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.703A pdb=" N CYS C 217 " --> pdb=" O LYS C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 231 Processing helix chain 'C' and resid 251 through 255 removed outlier: 3.720A pdb=" N ARG C 254 " --> pdb=" O GLY C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 263 through 267 Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 286 through 288 No H-bonds generated for 'chain 'C' and resid 286 through 288' Processing helix chain 'C' and resid 289 through 295 removed outlier: 4.243A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 removed outlier: 3.731A pdb=" N ARG C 312 " --> pdb=" O GLY C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 348 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.501A pdb=" N PHE C 352 " --> pdb=" O LEU C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 369 through 374 Processing helix chain 'D' and resid 56 through 58 No H-bonds generated for 'chain 'D' and resid 56 through 58' Processing helix chain 'D' and resid 78 through 93 removed outlier: 3.789A pdb=" N GLU D 93 " --> pdb=" O THR D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.727A pdb=" N GLU D 100 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N HIS D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 97 through 101' Processing helix chain 'D' and resid 112 through 126 Processing helix chain 'D' and resid 137 through 145 Processing helix chain 'D' and resid 181 through 195 removed outlier: 3.975A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 217 removed outlier: 3.790A pdb=" N CYS D 217 " --> pdb=" O LYS D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 231 Processing helix chain 'D' and resid 252 through 257 Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 263 through 267 Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 286 through 289 Processing helix chain 'D' and resid 290 through 295 removed outlier: 4.130A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 removed outlier: 3.680A pdb=" N ARG D 312 " --> pdb=" O GLY D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 347 Processing helix chain 'D' and resid 349 through 353 Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 369 through 374 Processing helix chain 'E' and resid 55 through 60 removed outlier: 3.667A pdb=" N SER E 60 " --> pdb=" O ASP E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 92 Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.565A pdb=" N GLU E 100 " --> pdb=" O ALA E 97 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N HIS E 101 " --> pdb=" O PRO E 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 97 through 101' Processing helix chain 'E' and resid 112 through 126 Processing helix chain 'E' and resid 137 through 145 Processing helix chain 'E' and resid 181 through 195 removed outlier: 4.070A pdb=" N GLU E 195 " --> pdb=" O LYS E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 217 removed outlier: 3.830A pdb=" N CYS E 217 " --> pdb=" O LYS E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 231 Processing helix chain 'E' and resid 252 through 257 removed outlier: 3.644A pdb=" N CYS E 257 " --> pdb=" O GLU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 262 Processing helix chain 'E' and resid 263 through 267 Processing helix chain 'E' and resid 273 through 284 Processing helix chain 'E' and resid 286 through 289 removed outlier: 3.624A pdb=" N ILE E 289 " --> pdb=" O ASP E 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 286 through 289' Processing helix chain 'E' and resid 290 through 295 removed outlier: 3.667A pdb=" N TYR E 294 " --> pdb=" O ARG E 290 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALA E 295 " --> pdb=" O LYS E 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 290 through 295' Processing helix chain 'E' and resid 302 through 306 removed outlier: 3.687A pdb=" N MET E 305 " --> pdb=" O GLY E 302 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N TYR E 306 " --> pdb=" O THR E 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 302 through 306' Processing helix chain 'E' and resid 308 through 321 removed outlier: 3.828A pdb=" N ARG E 312 " --> pdb=" O GLY E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 348 Processing helix chain 'E' and resid 352 through 356 removed outlier: 3.529A pdb=" N MET E 355 " --> pdb=" O PHE E 352 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TRP E 356 " --> pdb=" O GLN E 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 352 through 356' Processing helix chain 'E' and resid 359 through 365 Processing helix chain 'E' and resid 366 through 368 No H-bonds generated for 'chain 'E' and resid 366 through 368' Processing helix chain 'E' and resid 369 through 374 Processing helix chain 'a' and resid 8 through 20 removed outlier: 3.716A pdb=" N ILE a 12 " --> pdb=" O ASN a 8 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL a 20 " --> pdb=" O ASN a 16 " (cutoff:3.500A) Processing helix chain 'a' and resid 25 through 30 Processing helix chain 'a' and resid 58 through 60 No H-bonds generated for 'chain 'a' and resid 58 through 60' Processing helix chain 'a' and resid 66 through 74 Processing helix chain 'a' and resid 110 through 120 Processing helix chain 'a' and resid 120 through 128 removed outlier: 4.141A pdb=" N ILE a 124 " --> pdb=" O SER a 120 " (cutoff:3.500A) Processing helix chain 'a' and resid 139 through 143 removed outlier: 3.622A pdb=" N ASP a 142 " --> pdb=" O GLY a 139 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE a 143 " --> pdb=" O LEU a 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 139 through 143' Processing helix chain 'a' and resid 145 through 153 removed outlier: 4.246A pdb=" N LEU a 149 " --> pdb=" O ASP a 145 " (cutoff:3.500A) Processing helix chain 'a' and resid 154 through 156 No H-bonds generated for 'chain 'a' and resid 154 through 156' Processing helix chain 'b' and resid 8 through 20 removed outlier: 3.607A pdb=" N ILE b 12 " --> pdb=" O ASN b 8 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL b 20 " --> pdb=" O ASN b 16 " (cutoff:3.500A) Processing helix chain 'b' and resid 25 through 31 Processing helix chain 'b' and resid 66 through 75 Processing helix chain 'b' and resid 110 through 120 Processing helix chain 'b' and resid 120 through 128 removed outlier: 4.100A pdb=" N ILE b 124 " --> pdb=" O SER b 120 " (cutoff:3.500A) Processing helix chain 'b' and resid 139 through 143 removed outlier: 3.563A pdb=" N ASP b 142 " --> pdb=" O GLY b 139 " (cutoff:3.500A) Processing helix chain 'b' and resid 145 through 153 removed outlier: 4.275A pdb=" N LEU b 149 " --> pdb=" O ASP b 145 " (cutoff:3.500A) Processing helix chain 'b' and resid 154 through 156 No H-bonds generated for 'chain 'b' and resid 154 through 156' Processing helix chain 'c' and resid 8 through 20 removed outlier: 3.990A pdb=" N VAL c 20 " --> pdb=" O ASN c 16 " (cutoff:3.500A) Processing helix chain 'c' and resid 58 through 60 No H-bonds generated for 'chain 'c' and resid 58 through 60' Processing helix chain 'c' and resid 66 through 75 removed outlier: 3.595A pdb=" N SER c 70 " --> pdb=" O ASP c 66 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU c 75 " --> pdb=" O PHE c 71 " (cutoff:3.500A) Processing helix chain 'c' and resid 110 through 120 Processing helix chain 'c' and resid 120 through 128 removed outlier: 4.102A pdb=" N ILE c 124 " --> pdb=" O SER c 120 " (cutoff:3.500A) Processing helix chain 'c' and resid 145 through 153 removed outlier: 4.194A pdb=" N LEU c 149 " --> pdb=" O ASP c 145 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.657A pdb=" N THR A 106 " --> pdb=" O CYS A 10 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ASN A 12 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (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 169 through 170 Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 170 removed outlier: 6.364A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA6, first strand: chain 'B' and resid 29 through 32 removed outlier: 3.792A pdb=" N THR B 106 " --> pdb=" O CYS B 10 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ASN B 12 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA8, first strand: chain 'B' and resid 176 through 178 removed outlier: 7.525A pdb=" N VAL B 298 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB1, first strand: chain 'C' and resid 29 through 32 removed outlier: 3.901A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ASN C 12 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU C 107 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB3, first strand: chain 'C' and resid 169 through 170 removed outlier: 3.568A pdb=" N TYR C 169 " --> pdb=" O TYR C 166 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 169 through 170 removed outlier: 3.568A pdb=" N TYR C 169 " --> pdb=" O TYR C 166 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AB6, first strand: chain 'D' and resid 29 through 32 removed outlier: 3.836A pdb=" N THR D 106 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N ASN D 12 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AB8, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AB9, first strand: chain 'D' and resid 169 through 170 removed outlier: 3.578A pdb=" N VAL D 298 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU D 153 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER D 300 " --> pdb=" O LEU D 153 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC2, first strand: chain 'E' and resid 29 through 32 removed outlier: 3.891A pdb=" N THR E 106 " --> pdb=" O CYS E 10 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ASN E 12 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC4, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AC5, first strand: chain 'E' and resid 169 through 170 removed outlier: 6.329A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 238 through 241 Processing sheet with id=AC7, first strand: chain 'a' and resid 6 through 7 removed outlier: 7.420A pdb=" N THR a 6 " --> pdb=" O ILE a 47 " (cutoff:3.500A) removed outlier: 9.456A pdb=" N VAL a 49 " --> pdb=" O THR a 6 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL a 49 " --> pdb=" O LEU a 40 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N LEU a 40 " --> pdb=" O VAL a 49 " (cutoff:3.500A) removed outlier: 9.285A pdb=" N GLU a 51 " --> pdb=" O PHE a 38 " (cutoff:3.500A) removed outlier: 10.948A pdb=" N PHE a 38 " --> pdb=" O GLU a 51 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N LYS a 53 " --> pdb=" O VAL a 36 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N VAL a 36 " --> pdb=" O LYS a 53 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ILE a 55 " --> pdb=" O LYS a 34 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N LYS a 34 " --> pdb=" O ASP a 86 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N HIS a 133 " --> pdb=" O LEU a 99 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'a' and resid 6 through 7 removed outlier: 7.420A pdb=" N THR a 6 " --> pdb=" O ILE a 47 " (cutoff:3.500A) removed outlier: 9.456A pdb=" N VAL a 49 " --> pdb=" O THR a 6 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL a 49 " --> pdb=" O LEU a 40 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N LEU a 40 " --> pdb=" O VAL a 49 " (cutoff:3.500A) removed outlier: 9.285A pdb=" N GLU a 51 " --> pdb=" O PHE a 38 " (cutoff:3.500A) removed outlier: 10.948A pdb=" N PHE a 38 " --> pdb=" O GLU a 51 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N LYS a 53 " --> pdb=" O VAL a 36 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N VAL a 36 " --> pdb=" O LYS a 53 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ILE a 55 " --> pdb=" O LYS a 34 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N LYS a 34 " --> pdb=" O ASP a 86 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'b' and resid 6 through 7 removed outlier: 7.678A pdb=" N THR b 6 " --> pdb=" O ILE b 47 " (cutoff:3.500A) removed outlier: 9.413A pdb=" N VAL b 49 " --> pdb=" O THR b 6 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N LYS b 34 " --> pdb=" O ASP b 86 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N HIS b 133 " --> pdb=" O LEU b 99 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'b' and resid 55 through 56 removed outlier: 7.214A pdb=" N ILE b 55 " --> pdb=" O LYS b 34 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N LYS b 34 " --> pdb=" O ASP b 86 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'c' and resid 47 through 56 removed outlier: 5.676A pdb=" N LEU c 37 " --> pdb=" O GLU c 50 " (cutoff:3.500A) removed outlier: 9.585A pdb=" N ALA c 52 " --> pdb=" O ALA c 35 " (cutoff:3.500A) removed outlier: 11.261A pdb=" N ALA c 35 " --> pdb=" O ALA c 52 " (cutoff:3.500A) removed outlier: 9.902A pdb=" N GLN c 54 " --> pdb=" O LYS c 33 " (cutoff:3.500A) removed outlier: 8.896A pdb=" N LYS c 33 " --> pdb=" O GLN c 54 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LYS c 34 " --> pdb=" O ASP c 86 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N HIS c 133 " --> pdb=" O LEU c 99 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'c' and resid 47 through 56 removed outlier: 5.676A pdb=" N LEU c 37 " --> pdb=" O GLU c 50 " (cutoff:3.500A) removed outlier: 9.585A pdb=" N ALA c 52 " --> pdb=" O ALA c 35 " (cutoff:3.500A) removed outlier: 11.261A pdb=" N ALA c 35 " --> pdb=" O ALA c 52 " (cutoff:3.500A) removed outlier: 9.902A pdb=" N GLN c 54 " --> pdb=" O LYS c 33 " (cutoff:3.500A) removed outlier: 8.896A pdb=" N LYS c 33 " --> pdb=" O GLN c 54 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LYS c 34 " --> pdb=" O ASP c 86 " (cutoff:3.500A) 844 hydrogen bonds defined for protein. 2277 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: 4.47 Time building geometry restraints manager: 1.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5351 1.34 - 1.46: 4318 1.46 - 1.59: 8783 1.59 - 1.71: 15 1.71 - 1.83: 189 Bond restraints: 18656 Sorted by residual: bond pdb=" CB GLU E 334 " pdb=" CG GLU E 334 " ideal model delta sigma weight residual 1.520 1.585 -0.065 3.00e-02 1.11e+03 4.75e+00 bond pdb=" N THR a 63 " pdb=" CA THR a 63 " ideal model delta sigma weight residual 1.459 1.484 -0.025 1.15e-02 7.56e+03 4.59e+00 bond pdb=" C CYS D 257 " pdb=" N PRO D 258 " ideal model delta sigma weight residual 1.337 1.358 -0.021 1.06e-02 8.90e+03 3.93e+00 bond pdb=" CB GLN E 353 " pdb=" CG GLN E 353 " ideal model delta sigma weight residual 1.520 1.579 -0.059 3.00e-02 1.11e+03 3.84e+00 bond pdb=" N THR b 63 " pdb=" CA THR b 63 " ideal model delta sigma weight residual 1.462 1.490 -0.029 1.48e-02 4.57e+03 3.73e+00 ... (remaining 18651 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.95: 24873 3.95 - 7.90: 351 7.90 - 11.85: 38 11.85 - 15.80: 8 15.80 - 19.75: 1 Bond angle restraints: 25271 Sorted by residual: angle pdb=" C GLU C 270 " pdb=" N SER C 271 " pdb=" CA SER C 271 " ideal model delta sigma weight residual 121.54 134.74 -13.20 1.91e+00 2.74e-01 4.78e+01 angle pdb=" CA GLN c 46 " pdb=" CB GLN c 46 " pdb=" CG GLN c 46 " ideal model delta sigma weight residual 114.10 125.55 -11.45 2.00e+00 2.50e-01 3.28e+01 angle pdb=" CA LEU C 110 " pdb=" CB LEU C 110 " pdb=" CG LEU C 110 " ideal model delta sigma weight residual 116.30 136.05 -19.75 3.50e+00 8.16e-02 3.18e+01 angle pdb=" C ASP b 62 " pdb=" N THR b 63 " pdb=" CA THR b 63 " ideal model delta sigma weight residual 122.61 130.86 -8.25 1.56e+00 4.11e-01 2.80e+01 angle pdb=" CA GLU C 270 " pdb=" CB GLU C 270 " pdb=" CG GLU C 270 " ideal model delta sigma weight residual 114.10 124.53 -10.43 2.00e+00 2.50e-01 2.72e+01 ... (remaining 25266 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 10294 17.31 - 34.61: 806 34.61 - 51.92: 165 51.92 - 69.23: 26 69.23 - 86.54: 19 Dihedral angle restraints: 11310 sinusoidal: 4608 harmonic: 6702 Sorted by residual: dihedral pdb=" CA GLU c 28 " pdb=" C GLU c 28 " pdb=" N ILE c 29 " pdb=" CA ILE c 29 " ideal model delta harmonic sigma weight residual 180.00 148.41 31.59 0 5.00e+00 4.00e-02 3.99e+01 dihedral pdb=" CA MET D 325 " pdb=" C MET D 325 " pdb=" N LYS D 326 " pdb=" CA LYS D 326 " ideal model delta harmonic sigma weight residual -180.00 -153.17 -26.83 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA ARG c 45 " pdb=" C ARG c 45 " pdb=" N GLN c 46 " pdb=" CA GLN c 46 " ideal model delta harmonic sigma weight residual 180.00 -153.69 -26.31 0 5.00e+00 4.00e-02 2.77e+01 ... (remaining 11307 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 2141 0.067 - 0.134: 573 0.134 - 0.201: 88 0.201 - 0.268: 24 0.268 - 0.335: 4 Chirality restraints: 2830 Sorted by residual: chirality pdb=" CB ILE D 71 " pdb=" CA ILE D 71 " pdb=" CG1 ILE D 71 " pdb=" CG2 ILE D 71 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" CB ILE A 287 " pdb=" CA ILE A 287 " pdb=" CG1 ILE A 287 " pdb=" CG2 ILE A 287 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" CB VAL b 72 " pdb=" CA VAL b 72 " pdb=" CG1 VAL b 72 " pdb=" CG2 VAL b 72 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 2827 not shown) Planarity restraints: 3213 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR c 82 " -0.018 2.00e-02 2.50e+03 2.55e-02 1.30e+01 pdb=" CG TYR c 82 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 TYR c 82 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR c 82 " -0.030 2.00e-02 2.50e+03 pdb=" CE1 TYR c 82 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR c 82 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR c 82 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR c 82 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 342 " 0.017 2.00e-02 2.50e+03 3.39e-02 1.15e+01 pdb=" C GLY C 342 " -0.059 2.00e-02 2.50e+03 pdb=" O GLY C 342 " 0.022 2.00e-02 2.50e+03 pdb=" N GLY C 343 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN D 353 " 0.017 2.00e-02 2.50e+03 3.37e-02 1.14e+01 pdb=" CD GLN D 353 " -0.058 2.00e-02 2.50e+03 pdb=" OE1 GLN D 353 " 0.022 2.00e-02 2.50e+03 pdb=" NE2 GLN D 353 " 0.019 2.00e-02 2.50e+03 ... (remaining 3210 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 51 2.66 - 3.22: 15494 3.22 - 3.78: 27859 3.78 - 4.34: 38655 4.34 - 4.90: 62353 Nonbonded interactions: 144412 Sorted by model distance: nonbonded pdb=" O1B ADP C 400 " pdb="MG MG C 401 " model vdw 2.105 2.170 nonbonded pdb=" O1B ADP A 400 " pdb="MG MG A 401 " model vdw 2.115 2.170 nonbonded pdb=" O1B ADP B 400 " pdb="MG MG B 401 " model vdw 2.119 2.170 nonbonded pdb=" O1B ADP E 400 " pdb="MG MG E 401 " model vdw 2.123 2.170 nonbonded pdb=" O1B ADP D 400 " pdb="MG MG D 401 " model vdw 2.124 2.170 ... (remaining 144407 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' } 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 group one per residue 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: 4.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.750 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 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:1.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 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 : 0.006 0.065 18656 Z= 0.272 Angle : 1.176 19.745 25271 Z= 0.612 Chirality : 0.063 0.335 2830 Planarity : 0.009 0.095 3213 Dihedral : 13.489 86.536 6998 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.91 % Favored : 97.00 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.95 (0.16), residues: 2267 helix: -2.44 (0.13), residues: 845 sheet: -0.18 (0.24), residues: 467 loop : -0.50 (0.20), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.002 ARG E 206 TYR 0.060 0.003 TYR c 82 PHE 0.044 0.004 PHE b 71 TRP 0.029 0.003 TRP B 86 HIS 0.016 0.002 HIS E 88 Details of bonding type rmsd covalent geometry : bond 0.00567 (18656) covalent geometry : angle 1.17638 (25271) hydrogen bonds : bond 0.16263 ( 818) hydrogen bonds : angle 7.54750 ( 2277) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4534 Ramachandran restraints generated. 2267 Oldfield, 0 Emsley, 2267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4534 Ramachandran restraints generated. 2267 Oldfield, 0 Emsley, 2267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 330 ILE cc_start: 0.9316 (mp) cc_final: 0.9111 (pt) REVERT: A 355 MET cc_start: 0.9209 (mtm) cc_final: 0.7929 (mtm) REVERT: B 82 MET cc_start: 0.8825 (tpt) cc_final: 0.8416 (tpt) REVERT: B 132 MET cc_start: 0.8933 (ppp) cc_final: 0.8560 (tmm) REVERT: B 176 MET cc_start: 0.6869 (mtt) cc_final: 0.6471 (mtt) REVERT: B 283 MET cc_start: 0.8931 (mmm) cc_final: 0.8646 (mmm) REVERT: B 285 CYS cc_start: 0.8598 (m) cc_final: 0.8229 (m) REVERT: C 132 MET cc_start: 0.8292 (ppp) cc_final: 0.8070 (tmm) REVERT: C 314 GLN cc_start: 0.9379 (tm-30) cc_final: 0.8913 (tm-30) REVERT: C 355 MET cc_start: 0.8981 (mtm) cc_final: 0.8446 (mtm) REVERT: D 86 TRP cc_start: 0.9068 (m-10) cc_final: 0.8418 (m-90) REVERT: D 121 GLN cc_start: 0.9467 (pt0) cc_final: 0.9232 (pp30) REVERT: D 123 MET cc_start: 0.9404 (mmp) cc_final: 0.9186 (mmp) REVERT: D 176 MET cc_start: 0.8486 (ptp) cc_final: 0.8096 (pmm) REVERT: D 184 ASP cc_start: 0.9407 (m-30) cc_final: 0.9198 (m-30) REVERT: D 263 GLN cc_start: 0.8747 (mp10) cc_final: 0.8408 (mp10) REVERT: D 354 GLN cc_start: 0.8647 (pm20) cc_final: 0.8418 (pm20) REVERT: D 355 MET cc_start: 0.8227 (mmp) cc_final: 0.7983 (mmm) REVERT: E 11 ASP cc_start: 0.8607 (t0) cc_final: 0.8406 (t70) REVERT: E 90 PHE cc_start: 0.9659 (m-80) cc_final: 0.9239 (m-80) REVERT: E 154 ASP cc_start: 0.8635 (t0) cc_final: 0.7889 (p0) REVERT: E 206 ARG cc_start: 0.9439 (ttm110) cc_final: 0.9208 (ttm-80) REVERT: E 257 CYS cc_start: 0.8945 (t) cc_final: 0.8511 (m) REVERT: E 305 MET cc_start: 0.7920 (mmp) cc_final: 0.7568 (mmm) REVERT: E 325 MET cc_start: -0.0602 (tpt) cc_final: -0.1250 (mtp) REVERT: E 355 MET cc_start: 0.7705 (mpp) cc_final: 0.7370 (mpp) REVERT: a 166 LEU cc_start: 0.9207 (tt) cc_final: 0.8872 (mt) REVERT: b 78 ASN cc_start: 0.9188 (m-40) cc_final: 0.8902 (p0) REVERT: c 81 ARG cc_start: 0.8345 (mmp80) cc_final: 0.8015 (mmm160) REVERT: c 117 TYR cc_start: 0.7785 (m-80) cc_final: 0.6488 (m-10) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.1397 time to fit residues: 39.7987 Evaluate side-chains 144 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 7.9990 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 0.0570 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 2.9990 overall best weight: 1.8104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN B 162 ASN ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 GLN D 297 ASN D 353 GLN ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 GLN a 46 GLN a 54 GLN ** a 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 78 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.060775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.044448 restraints weight = 95110.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.045880 restraints weight = 46944.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.046816 restraints weight = 29726.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.047390 restraints weight = 21894.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.047781 restraints weight = 18005.353| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 18656 Z= 0.153 Angle : 0.633 10.834 25271 Z= 0.317 Chirality : 0.045 0.152 2830 Planarity : 0.005 0.056 3213 Dihedral : 5.710 45.910 2563 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.87 % Favored : 97.09 % Rotamer: Outliers : 0.40 % Allowed : 4.50 % Favored : 95.10 % 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: -0.33 (0.17), residues: 2267 helix: -0.41 (0.17), residues: 869 sheet: 0.08 (0.24), residues: 462 loop : 0.08 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 206 TYR 0.013 0.001 TYR B 166 PHE 0.022 0.002 PHE b 15 TRP 0.012 0.002 TRP B 86 HIS 0.005 0.001 HIS D 275 Details of bonding type rmsd covalent geometry : bond 0.00338 (18656) covalent geometry : angle 0.63344 (25271) hydrogen bonds : bond 0.03769 ( 818) hydrogen bonds : angle 5.17502 ( 2277) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4534 Ramachandran restraints generated. 2267 Oldfield, 0 Emsley, 2267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4534 Ramachandran restraints generated. 2267 Oldfield, 0 Emsley, 2267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 143 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 MET cc_start: 0.8945 (mtp) cc_final: 0.8711 (mtp) REVERT: B 176 MET cc_start: 0.7194 (mtt) cc_final: 0.6933 (mtt) REVERT: C 82 MET cc_start: 0.9169 (tpp) cc_final: 0.8965 (tpp) REVERT: C 355 MET cc_start: 0.8686 (mtm) cc_final: 0.8451 (mtm) REVERT: D 82 MET cc_start: 0.9396 (tpp) cc_final: 0.9135 (tpp) REVERT: D 184 ASP cc_start: 0.9338 (m-30) cc_final: 0.9117 (m-30) REVERT: D 263 GLN cc_start: 0.8845 (mp10) cc_final: 0.8482 (mp10) REVERT: D 354 GLN cc_start: 0.8497 (pm20) cc_final: 0.8253 (pm20) REVERT: E 90 PHE cc_start: 0.9681 (m-80) cc_final: 0.9125 (m-80) REVERT: E 123 MET cc_start: 0.8767 (mmp) cc_final: 0.8435 (mmp) REVERT: E 154 ASP cc_start: 0.8589 (t0) cc_final: 0.7961 (p0) REVERT: E 257 CYS cc_start: 0.8865 (t) cc_final: 0.8638 (t) REVERT: E 305 MET cc_start: 0.8046 (mmp) cc_final: 0.7767 (mmm) REVERT: E 306 TYR cc_start: 0.8798 (m-80) cc_final: 0.7673 (m-80) REVERT: E 355 MET cc_start: 0.7786 (mpp) cc_final: 0.7387 (mpp) REVERT: a 26 GLN cc_start: 0.8973 (pt0) cc_final: 0.8758 (pp30) REVERT: a 166 LEU cc_start: 0.9136 (tt) cc_final: 0.8866 (mt) REVERT: c 81 ARG cc_start: 0.8561 (mmp80) cc_final: 0.7868 (mmt-90) REVERT: c 115 MET cc_start: 0.8459 (tmm) cc_final: 0.7996 (tmm) outliers start: 8 outliers final: 4 residues processed: 150 average time/residue: 0.1377 time to fit residues: 32.8658 Evaluate side-chains 137 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 133 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain E residue 153 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 176 optimal weight: 10.0000 chunk 151 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 209 optimal weight: 1.9990 chunk 189 optimal weight: 7.9990 chunk 18 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 160 optimal weight: 0.7980 chunk 9 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 71 optimal weight: 8.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN C 128 ASN ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 ASN ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.060039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.043557 restraints weight = 97275.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.044989 restraints weight = 48063.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.045925 restraints weight = 30497.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.046496 restraints weight = 22593.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.046899 restraints weight = 18631.293| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 18656 Z= 0.151 Angle : 0.605 9.218 25271 Z= 0.297 Chirality : 0.044 0.147 2830 Planarity : 0.004 0.051 3213 Dihedral : 5.344 41.974 2563 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.96 % Favored : 97.00 % Rotamer: Outliers : 0.45 % Allowed : 5.91 % Favored : 93.63 % 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: 0.21 (0.18), residues: 2267 helix: 0.28 (0.18), residues: 899 sheet: 0.08 (0.25), residues: 464 loop : 0.28 (0.21), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 62 TYR 0.011 0.001 TYR A 166 PHE 0.026 0.001 PHE b 15 TRP 0.011 0.001 TRP B 79 HIS 0.004 0.001 HIS D 88 Details of bonding type rmsd covalent geometry : bond 0.00340 (18656) covalent geometry : angle 0.60467 (25271) hydrogen bonds : bond 0.03407 ( 818) hydrogen bonds : angle 4.77531 ( 2277) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4534 Ramachandran restraints generated. 2267 Oldfield, 0 Emsley, 2267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4534 Ramachandran restraints generated. 2267 Oldfield, 0 Emsley, 2267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 144 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 143 TYR cc_start: 0.9308 (m-80) cc_final: 0.8455 (m-80) REVERT: C 355 MET cc_start: 0.8688 (mtm) cc_final: 0.8391 (mtt) REVERT: D 176 MET cc_start: 0.8132 (ptp) cc_final: 0.7847 (pmm) REVERT: D 263 GLN cc_start: 0.8826 (mp10) cc_final: 0.8527 (mp10) REVERT: E 90 PHE cc_start: 0.9694 (m-80) cc_final: 0.9088 (m-80) REVERT: E 123 MET cc_start: 0.8836 (mmp) cc_final: 0.8403 (mmp) REVERT: E 154 ASP cc_start: 0.8482 (t0) cc_final: 0.7806 (p0) REVERT: E 269 MET cc_start: 0.8454 (mmp) cc_final: 0.8120 (mmp) REVERT: E 305 MET cc_start: 0.7987 (mmp) cc_final: 0.7658 (mmm) REVERT: E 306 TYR cc_start: 0.8750 (m-80) cc_final: 0.7555 (m-80) REVERT: E 355 MET cc_start: 0.7837 (mpp) cc_final: 0.7477 (mpp) REVERT: a 26 GLN cc_start: 0.9001 (pt0) cc_final: 0.8774 (pp30) REVERT: c 146 ARG cc_start: 0.8681 (ptt180) cc_final: 0.8450 (ptp-170) outliers start: 9 outliers final: 5 residues processed: 150 average time/residue: 0.1346 time to fit residues: 32.0120 Evaluate side-chains 137 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 132 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain c residue 25 THR Chi-restraints excluded: chain c residue 129 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 143 optimal weight: 10.0000 chunk 118 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 62 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 207 optimal weight: 0.9990 chunk 131 optimal weight: 6.9990 chunk 153 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 157 optimal weight: 9.9990 chunk 37 optimal weight: 7.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN C 162 ASN E 162 ASN ** a 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.059777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.043282 restraints weight = 97542.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.044702 restraints weight = 48320.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.045639 restraints weight = 30752.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.046240 restraints weight = 22734.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.046599 restraints weight = 18627.497| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18656 Z= 0.136 Angle : 0.585 8.312 25271 Z= 0.286 Chirality : 0.044 0.145 2830 Planarity : 0.004 0.050 3213 Dihedral : 5.155 44.354 2563 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.04 % Favored : 96.91 % Rotamer: Outliers : 0.86 % Allowed : 7.12 % Favored : 92.02 % 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: 0.51 (0.18), residues: 2267 helix: 0.60 (0.18), residues: 899 sheet: -0.02 (0.24), residues: 480 loop : 0.54 (0.22), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 147 TYR 0.011 0.001 TYR c 117 PHE 0.029 0.001 PHE b 15 TRP 0.011 0.001 TRP B 86 HIS 0.004 0.001 HIS D 88 Details of bonding type rmsd covalent geometry : bond 0.00305 (18656) covalent geometry : angle 0.58535 (25271) hydrogen bonds : bond 0.03163 ( 818) hydrogen bonds : angle 4.54852 ( 2277) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4534 Ramachandran restraints generated. 2267 Oldfield, 0 Emsley, 2267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4534 Ramachandran restraints generated. 2267 Oldfield, 0 Emsley, 2267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 138 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 MET cc_start: 0.9016 (mmm) cc_final: 0.8648 (tmm) REVERT: C 143 TYR cc_start: 0.9290 (m-80) cc_final: 0.8579 (m-80) REVERT: C 355 MET cc_start: 0.8645 (mtm) cc_final: 0.8318 (mtt) REVERT: D 263 GLN cc_start: 0.8855 (mp10) cc_final: 0.8587 (mp10) REVERT: E 123 MET cc_start: 0.8900 (mmp) cc_final: 0.8430 (mmp) REVERT: E 305 MET cc_start: 0.8043 (mmp) cc_final: 0.7714 (mmm) REVERT: E 306 TYR cc_start: 0.8818 (m-80) cc_final: 0.7716 (m-80) REVERT: E 355 MET cc_start: 0.7855 (mpp) cc_final: 0.7497 (mpp) REVERT: a 115 MET cc_start: 0.8494 (tpp) cc_final: 0.8135 (tpp) REVERT: b 89 TYR cc_start: 0.8936 (p90) cc_final: 0.8702 (p90) REVERT: c 115 MET cc_start: 0.8417 (tmm) cc_final: 0.8016 (tmm) REVERT: c 146 ARG cc_start: 0.8623 (ptt180) cc_final: 0.8384 (ptp-170) outliers start: 17 outliers final: 8 residues processed: 150 average time/residue: 0.1316 time to fit residues: 31.7924 Evaluate side-chains 137 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 129 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain b residue 71 PHE Chi-restraints excluded: chain c residue 129 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 182 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 184 optimal weight: 2.9990 chunk 201 optimal weight: 10.0000 chunk 216 optimal weight: 7.9990 chunk 185 optimal weight: 9.9990 chunk 33 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 165 optimal weight: 7.9990 chunk 209 optimal weight: 0.9980 chunk 116 optimal weight: 5.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 59 GLN D 353 GLN ** a 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.059607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.043236 restraints weight = 97463.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.044659 restraints weight = 48043.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.045604 restraints weight = 30475.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.046197 restraints weight = 22401.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.046585 restraints weight = 18362.592| |-----------------------------------------------------------------------------| r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 18656 Z= 0.129 Angle : 0.582 8.238 25271 Z= 0.282 Chirality : 0.043 0.142 2830 Planarity : 0.004 0.050 3213 Dihedral : 5.057 45.310 2563 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.13 % Favored : 96.82 % Rotamer: Outliers : 0.81 % Allowed : 8.08 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.18), residues: 2267 helix: 0.73 (0.19), residues: 904 sheet: 0.00 (0.24), residues: 480 loop : 0.59 (0.22), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 147 TYR 0.017 0.001 TYR c 68 PHE 0.015 0.001 PHE c 101 TRP 0.011 0.001 TRP C 340 HIS 0.004 0.001 HIS D 88 Details of bonding type rmsd covalent geometry : bond 0.00291 (18656) covalent geometry : angle 0.58224 (25271) hydrogen bonds : bond 0.03085 ( 818) hydrogen bonds : angle 4.43902 ( 2277) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4534 Ramachandran restraints generated. 2267 Oldfield, 0 Emsley, 2267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4534 Ramachandran restraints generated. 2267 Oldfield, 0 Emsley, 2267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 MET cc_start: 0.8635 (tpp) cc_final: 0.8237 (mmm) REVERT: B 82 MET cc_start: 0.9052 (mmm) cc_final: 0.8639 (tmm) REVERT: C 143 TYR cc_start: 0.9253 (m-80) cc_final: 0.8622 (m-80) REVERT: C 355 MET cc_start: 0.8634 (mtm) cc_final: 0.8267 (mtt) REVERT: D 263 GLN cc_start: 0.8863 (mp10) cc_final: 0.8530 (mp10) REVERT: D 283 MET cc_start: 0.8256 (mmp) cc_final: 0.8015 (mmm) REVERT: E 119 MET cc_start: 0.8905 (ptm) cc_final: 0.8619 (ppp) REVERT: E 123 MET cc_start: 0.8867 (mmp) cc_final: 0.8387 (mmp) REVERT: E 305 MET cc_start: 0.8064 (mmp) cc_final: 0.7861 (mmm) REVERT: E 355 MET cc_start: 0.7871 (mpp) cc_final: 0.7513 (mpp) REVERT: a 115 MET cc_start: 0.8527 (tpp) cc_final: 0.8314 (tpp) REVERT: a 166 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8595 (mt) REVERT: b 15 PHE cc_start: 0.8897 (t80) cc_final: 0.8673 (t80) REVERT: b 80 CYS cc_start: 0.8329 (t) cc_final: 0.8031 (t) REVERT: b 89 TYR cc_start: 0.8964 (p90) cc_final: 0.8634 (p90) REVERT: c 46 GLN cc_start: 0.7650 (tp40) cc_final: 0.7244 (tp40) REVERT: c 146 ARG cc_start: 0.8609 (ptt180) cc_final: 0.8399 (ptp-170) outliers start: 16 outliers final: 10 residues processed: 147 average time/residue: 0.1268 time to fit residues: 30.1506 Evaluate side-chains 138 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain a residue 166 LEU Chi-restraints excluded: chain b residue 71 PHE Chi-restraints excluded: chain c residue 25 THR Chi-restraints excluded: chain c residue 129 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 103 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 112 optimal weight: 0.0770 chunk 207 optimal weight: 0.7980 chunk 130 optimal weight: 8.9990 chunk 126 optimal weight: 8.9990 chunk 183 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 128 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 overall best weight: 3.1744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN ** a 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 46 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.058666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.042594 restraints weight = 98604.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.044005 restraints weight = 49831.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.044901 restraints weight = 31888.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.045462 restraints weight = 23738.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.045831 restraints weight = 19576.132| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 18656 Z= 0.232 Angle : 0.678 10.882 25271 Z= 0.334 Chirality : 0.045 0.145 2830 Planarity : 0.004 0.056 3213 Dihedral : 5.328 48.481 2563 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.62 % Favored : 96.34 % Rotamer: Outliers : 1.21 % Allowed : 8.49 % Favored : 90.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.66 (0.18), residues: 2267 helix: 0.77 (0.19), residues: 874 sheet: 0.10 (0.24), residues: 459 loop : 0.54 (0.21), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG c 45 TYR 0.014 0.001 TYR B 91 PHE 0.016 0.002 PHE A 255 TRP 0.015 0.002 TRP B 79 HIS 0.006 0.001 HIS D 173 Details of bonding type rmsd covalent geometry : bond 0.00513 (18656) covalent geometry : angle 0.67754 (25271) hydrogen bonds : bond 0.03773 ( 818) hydrogen bonds : angle 4.65671 ( 2277) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4534 Ramachandran restraints generated. 2267 Oldfield, 0 Emsley, 2267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4534 Ramachandran restraints generated. 2267 Oldfield, 0 Emsley, 2267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 MET cc_start: 0.9123 (mmm) cc_final: 0.8852 (mmm) REVERT: C 143 TYR cc_start: 0.9277 (m-80) cc_final: 0.8593 (m-80) REVERT: C 355 MET cc_start: 0.8596 (mtm) cc_final: 0.8288 (mtt) REVERT: D 82 MET cc_start: 0.9424 (tpp) cc_final: 0.9144 (tpp) REVERT: D 132 MET cc_start: 0.8121 (tmm) cc_final: 0.7824 (tmm) REVERT: D 283 MET cc_start: 0.8260 (mmp) cc_final: 0.7980 (mmm) REVERT: D 299 MET cc_start: 0.8814 (mmt) cc_final: 0.8515 (mmm) REVERT: E 119 MET cc_start: 0.8900 (ptm) cc_final: 0.8624 (ppp) REVERT: E 123 MET cc_start: 0.9058 (mmp) cc_final: 0.8619 (mmp) REVERT: E 305 MET cc_start: 0.8050 (mmp) cc_final: 0.7672 (mmp) REVERT: E 355 MET cc_start: 0.7997 (mpp) cc_final: 0.7611 (mpp) REVERT: b 7 VAL cc_start: 0.8857 (OUTLIER) cc_final: 0.8596 (p) REVERT: b 15 PHE cc_start: 0.8964 (t80) cc_final: 0.8696 (t80) REVERT: c 18 MET cc_start: 0.8398 (mmm) cc_final: 0.8129 (mmm) REVERT: c 115 MET cc_start: 0.8502 (tmm) cc_final: 0.8209 (tmm) REVERT: c 146 ARG cc_start: 0.8634 (ptt180) cc_final: 0.8355 (ptp-170) outliers start: 24 outliers final: 16 residues processed: 142 average time/residue: 0.1289 time to fit residues: 29.5719 Evaluate side-chains 139 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain b residue 7 VAL Chi-restraints excluded: chain b residue 71 PHE Chi-restraints excluded: chain c residue 25 THR Chi-restraints excluded: chain c residue 129 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 171 optimal weight: 0.0170 chunk 167 optimal weight: 3.9990 chunk 224 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 159 optimal weight: 3.9990 chunk 151 optimal weight: 7.9990 chunk 174 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 71 optimal weight: 7.9990 chunk 200 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 overall best weight: 2.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.059263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.043173 restraints weight = 98578.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.044594 restraints weight = 49541.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.045515 restraints weight = 31632.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.046103 restraints weight = 23447.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.046467 restraints weight = 19227.043| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 18656 Z= 0.163 Angle : 0.622 9.484 25271 Z= 0.303 Chirality : 0.044 0.146 2830 Planarity : 0.004 0.055 3213 Dihedral : 5.219 49.375 2563 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.18 % Favored : 96.78 % Rotamer: Outliers : 1.01 % Allowed : 9.25 % Favored : 89.74 % 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: 0.71 (0.18), residues: 2267 helix: 0.82 (0.19), residues: 874 sheet: -0.03 (0.24), residues: 472 loop : 0.65 (0.21), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG c 81 TYR 0.022 0.001 TYR c 117 PHE 0.017 0.001 PHE A 255 TRP 0.012 0.002 TRP C 79 HIS 0.004 0.001 HIS D 173 Details of bonding type rmsd covalent geometry : bond 0.00367 (18656) covalent geometry : angle 0.62163 (25271) hydrogen bonds : bond 0.03346 ( 818) hydrogen bonds : angle 4.49787 ( 2277) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4534 Ramachandran restraints generated. 2267 Oldfield, 0 Emsley, 2267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4534 Ramachandran restraints generated. 2267 Oldfield, 0 Emsley, 2267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 MET cc_start: 0.9111 (mmm) cc_final: 0.8786 (mmm) REVERT: C 143 TYR cc_start: 0.9226 (m-80) cc_final: 0.8593 (m-80) REVERT: C 305 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8414 (mmp) REVERT: C 355 MET cc_start: 0.8529 (mtm) cc_final: 0.8231 (mtt) REVERT: D 132 MET cc_start: 0.8104 (tmm) cc_final: 0.7804 (tmm) REVERT: D 263 GLN cc_start: 0.8828 (mp10) cc_final: 0.8623 (mp10) REVERT: D 283 MET cc_start: 0.8177 (mmp) cc_final: 0.7854 (mmm) REVERT: E 119 MET cc_start: 0.8860 (ptm) cc_final: 0.8606 (ppp) REVERT: E 123 MET cc_start: 0.8994 (mmp) cc_final: 0.8520 (mmp) REVERT: E 305 MET cc_start: 0.8044 (mmp) cc_final: 0.7704 (mmp) REVERT: E 355 MET cc_start: 0.7975 (mpp) cc_final: 0.7604 (mpp) REVERT: c 18 MET cc_start: 0.8442 (mmm) cc_final: 0.8163 (mmm) REVERT: c 115 MET cc_start: 0.8571 (tmm) cc_final: 0.8313 (tmm) REVERT: c 146 ARG cc_start: 0.8680 (ptt180) cc_final: 0.8384 (ptp-170) outliers start: 20 outliers final: 14 residues processed: 138 average time/residue: 0.1331 time to fit residues: 29.8511 Evaluate side-chains 138 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain b residue 71 PHE Chi-restraints excluded: chain b residue 140 LEU Chi-restraints excluded: chain c residue 25 THR Chi-restraints excluded: chain c residue 129 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 170 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 199 optimal weight: 9.9990 chunk 210 optimal weight: 10.0000 chunk 12 optimal weight: 0.8980 chunk 224 optimal weight: 7.9990 chunk 2 optimal weight: 0.9980 chunk 172 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 154 optimal weight: 5.9990 chunk 212 optimal weight: 4.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 162 ASN ** a 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.058480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.042503 restraints weight = 99693.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.043904 restraints weight = 50115.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.044812 restraints weight = 32006.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.045396 restraints weight = 23736.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.045767 restraints weight = 19505.525| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 18656 Z= 0.215 Angle : 0.674 11.626 25271 Z= 0.329 Chirality : 0.045 0.157 2830 Planarity : 0.004 0.056 3213 Dihedral : 5.345 51.681 2563 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.66 % Favored : 96.29 % Rotamer: Outliers : 0.96 % Allowed : 9.30 % Favored : 89.74 % 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 (0.18), residues: 2267 helix: 0.72 (0.18), residues: 879 sheet: 0.08 (0.24), residues: 454 loop : 0.38 (0.21), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG b 81 TYR 0.012 0.001 TYR c 68 PHE 0.015 0.002 PHE c 103 TRP 0.013 0.002 TRP b 135 HIS 0.005 0.001 HIS D 173 Details of bonding type rmsd covalent geometry : bond 0.00481 (18656) covalent geometry : angle 0.67363 (25271) hydrogen bonds : bond 0.03652 ( 818) hydrogen bonds : angle 4.61989 ( 2277) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4534 Ramachandran restraints generated. 2267 Oldfield, 0 Emsley, 2267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4534 Ramachandran restraints generated. 2267 Oldfield, 0 Emsley, 2267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 123 MET cc_start: 0.9353 (mmp) cc_final: 0.9120 (mmm) REVERT: C 143 TYR cc_start: 0.9275 (m-80) cc_final: 0.8627 (m-80) REVERT: C 305 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.8479 (mmp) REVERT: C 355 MET cc_start: 0.8539 (mtm) cc_final: 0.8102 (mtt) REVERT: D 82 MET cc_start: 0.9324 (tpp) cc_final: 0.9115 (tpp) REVERT: D 132 MET cc_start: 0.8185 (tmm) cc_final: 0.7875 (tmm) REVERT: D 283 MET cc_start: 0.8122 (mmp) cc_final: 0.7812 (mmm) REVERT: E 90 PHE cc_start: 0.9623 (m-10) cc_final: 0.9201 (m-80) REVERT: E 119 MET cc_start: 0.8866 (ptm) cc_final: 0.8617 (ppp) REVERT: E 123 MET cc_start: 0.9080 (mmp) cc_final: 0.8593 (mmp) REVERT: E 305 MET cc_start: 0.8154 (mmp) cc_final: 0.7732 (mmp) REVERT: E 355 MET cc_start: 0.8023 (mpp) cc_final: 0.7637 (mpp) REVERT: c 18 MET cc_start: 0.8404 (mmm) cc_final: 0.8124 (mmm) REVERT: c 115 MET cc_start: 0.8685 (tmm) cc_final: 0.8416 (tmm) REVERT: c 146 ARG cc_start: 0.8696 (ptt180) cc_final: 0.8205 (ptm160) outliers start: 19 outliers final: 17 residues processed: 136 average time/residue: 0.1306 time to fit residues: 28.8548 Evaluate side-chains 139 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain a residue 166 LEU Chi-restraints excluded: chain b residue 71 PHE Chi-restraints excluded: chain c residue 25 THR Chi-restraints excluded: chain c residue 129 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 26 optimal weight: 2.9990 chunk 196 optimal weight: 9.9990 chunk 190 optimal weight: 0.7980 chunk 220 optimal weight: 8.9990 chunk 173 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 204 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 chunk 36 optimal weight: 8.9990 chunk 81 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.059570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.043584 restraints weight = 97803.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.045012 restraints weight = 48868.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.045945 restraints weight = 31102.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.046538 restraints weight = 22966.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.046883 restraints weight = 18790.201| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18656 Z= 0.120 Angle : 0.613 10.498 25271 Z= 0.296 Chirality : 0.044 0.141 2830 Planarity : 0.004 0.053 3213 Dihedral : 5.153 51.117 2563 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.91 % Favored : 97.04 % Rotamer: Outliers : 1.16 % Allowed : 9.50 % Favored : 89.34 % 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: 0.72 (0.18), residues: 2267 helix: 0.89 (0.19), residues: 879 sheet: 0.03 (0.24), residues: 472 loop : 0.55 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG c 45 TYR 0.018 0.001 TYR c 68 PHE 0.017 0.001 PHE c 103 TRP 0.015 0.001 TRP C 340 HIS 0.005 0.001 HIS D 173 Details of bonding type rmsd covalent geometry : bond 0.00272 (18656) covalent geometry : angle 0.61303 (25271) hydrogen bonds : bond 0.03162 ( 818) hydrogen bonds : angle 4.38772 ( 2277) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4534 Ramachandran restraints generated. 2267 Oldfield, 0 Emsley, 2267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4534 Ramachandran restraints generated. 2267 Oldfield, 0 Emsley, 2267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 123 MET cc_start: 0.9296 (mmp) cc_final: 0.9081 (mmm) REVERT: C 143 TYR cc_start: 0.9220 (m-80) cc_final: 0.8621 (m-80) REVERT: C 305 MET cc_start: 0.8825 (OUTLIER) cc_final: 0.8494 (mmp) REVERT: C 355 MET cc_start: 0.8483 (mtm) cc_final: 0.8078 (mtt) REVERT: D 283 MET cc_start: 0.8097 (mmp) cc_final: 0.7777 (mmm) REVERT: E 355 MET cc_start: 0.7993 (mpp) cc_final: 0.7616 (mpp) REVERT: b 80 CYS cc_start: 0.8626 (m) cc_final: 0.8026 (t) REVERT: c 18 MET cc_start: 0.8411 (mmm) cc_final: 0.8112 (mmm) REVERT: c 115 MET cc_start: 0.8598 (tmm) cc_final: 0.8386 (tmm) REVERT: c 146 ARG cc_start: 0.8678 (ptt180) cc_final: 0.8200 (ptm160) outliers start: 23 outliers final: 18 residues processed: 141 average time/residue: 0.1335 time to fit residues: 30.1394 Evaluate side-chains 143 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain b residue 71 PHE Chi-restraints excluded: chain b residue 140 LEU Chi-restraints excluded: chain c residue 25 THR Chi-restraints excluded: chain c residue 129 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 225 optimal weight: 9.9990 chunk 112 optimal weight: 3.9990 chunk 71 optimal weight: 10.0000 chunk 17 optimal weight: 0.8980 chunk 210 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 181 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 212 optimal weight: 5.9990 chunk 204 optimal weight: 7.9990 chunk 215 optimal weight: 10.0000 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 173 HIS c 54 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.059457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.043459 restraints weight = 98696.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.044873 restraints weight = 49290.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.045797 restraints weight = 31426.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.046384 restraints weight = 23249.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.046760 restraints weight = 19104.265| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 18656 Z= 0.141 Angle : 0.642 11.041 25271 Z= 0.309 Chirality : 0.044 0.196 2830 Planarity : 0.004 0.054 3213 Dihedral : 5.118 51.262 2563 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.26 % Favored : 96.69 % Rotamer: Outliers : 1.06 % Allowed : 9.65 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.18), residues: 2267 helix: 0.88 (0.19), residues: 879 sheet: 0.10 (0.24), residues: 477 loop : 0.56 (0.21), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG c 45 TYR 0.011 0.001 TYR c 68 PHE 0.017 0.001 PHE c 103 TRP 0.067 0.002 TRP E 86 HIS 0.009 0.001 HIS D 173 Details of bonding type rmsd covalent geometry : bond 0.00320 (18656) covalent geometry : angle 0.64180 (25271) hydrogen bonds : bond 0.03236 ( 818) hydrogen bonds : angle 4.41211 ( 2277) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4534 Ramachandran restraints generated. 2267 Oldfield, 0 Emsley, 2267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4534 Ramachandran restraints generated. 2267 Oldfield, 0 Emsley, 2267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 143 TYR cc_start: 0.9234 (m-80) cc_final: 0.8645 (m-80) REVERT: C 355 MET cc_start: 0.8480 (mtm) cc_final: 0.8072 (mtt) REVERT: D 283 MET cc_start: 0.8094 (mmp) cc_final: 0.7772 (mmm) REVERT: E 86 TRP cc_start: 0.8435 (m-90) cc_final: 0.7805 (m-90) REVERT: E 305 MET cc_start: 0.7725 (mmm) cc_final: 0.7459 (mmm) REVERT: E 355 MET cc_start: 0.8150 (mpp) cc_final: 0.7769 (mpp) REVERT: b 80 CYS cc_start: 0.8606 (m) cc_final: 0.8035 (t) REVERT: c 18 MET cc_start: 0.8407 (mmm) cc_final: 0.8096 (mmm) REVERT: c 115 MET cc_start: 0.8548 (tmm) cc_final: 0.8328 (tmm) REVERT: c 146 ARG cc_start: 0.8691 (ptt180) cc_final: 0.8196 (ptm160) outliers start: 21 outliers final: 19 residues processed: 137 average time/residue: 0.1278 time to fit residues: 28.4599 Evaluate side-chains 143 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain a residue 111 LEU Chi-restraints excluded: chain a residue 166 LEU Chi-restraints excluded: chain b residue 71 PHE Chi-restraints excluded: chain b residue 140 LEU Chi-restraints excluded: chain c residue 25 THR Chi-restraints excluded: chain c residue 129 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 24 optimal weight: 2.9990 chunk 179 optimal weight: 0.5980 chunk 117 optimal weight: 6.9990 chunk 166 optimal weight: 8.9990 chunk 180 optimal weight: 0.0870 chunk 109 optimal weight: 10.0000 chunk 190 optimal weight: 1.9990 chunk 170 optimal weight: 1.9990 chunk 214 optimal weight: 9.9990 chunk 106 optimal weight: 0.8980 chunk 216 optimal weight: 2.9990 overall best weight: 1.1162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.059367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.043034 restraints weight = 98232.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.044534 restraints weight = 48248.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.045506 restraints weight = 30201.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.046130 restraints weight = 22049.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.046539 restraints weight = 17908.666| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18656 Z= 0.111 Angle : 0.623 11.400 25271 Z= 0.297 Chirality : 0.044 0.159 2830 Planarity : 0.004 0.053 3213 Dihedral : 5.004 50.156 2563 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.82 % Favored : 97.13 % Rotamer: Outliers : 1.01 % Allowed : 9.65 % Favored : 89.34 % 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 (0.18), residues: 2267 helix: 0.91 (0.19), residues: 884 sheet: 0.14 (0.24), residues: 467 loop : 0.62 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG c 45 TYR 0.022 0.001 TYR c 117 PHE 0.017 0.001 PHE c 103 TRP 0.062 0.002 TRP E 86 HIS 0.004 0.001 HIS D 88 Details of bonding type rmsd covalent geometry : bond 0.00254 (18656) covalent geometry : angle 0.62335 (25271) hydrogen bonds : bond 0.03024 ( 818) hydrogen bonds : angle 4.32882 ( 2277) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3172.78 seconds wall clock time: 55 minutes 41.35 seconds (3341.35 seconds total)