Starting phenix.real_space_refine on Sun Oct 25 00:46:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/12rv_76718/10_2026/12rv_76718.cif Found real_map, /net/cci-nas-00/data/ceres_data/12rv_76718/10_2026/12rv_76718.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/12rv_76718/10_2026/12rv_76718.map" default_real_map = "/net/cci-nas-00/data/ceres_data/12rv_76718/10_2026/12rv_76718.map" model { file = "/net/cci-nas-00/data/ceres_data/12rv_76718/10_2026/12rv_76718.cif" } default_model = "/net/cci-nas-00/data/ceres_data/12rv_76718/10_2026/12rv_76718.cif" } resolution = 3.24 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 ------------------------------------------------------------------------------- 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= 0.016 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 9260 2.51 5 N 2470 2.21 5 O 2846 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14701 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2910 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} 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: 2910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2910 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} 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: 2910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2910 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} 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: 2910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2910 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} 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: 2910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2910 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "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: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 3.32, per 1000 atoms: 0.23 Number of scatterers: 14701 At special positions: 0 Unit cell: (79.104, 108.768, 194.464, 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 2846 8.00 N 2470 7.00 C 9260 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: 1.14 Conformation dependent library (CDL) restraints added in 491.9 milliseconds 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3450 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 30 sheets defined 50.2% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.592A pdb=" N HIS A 101 " --> pdb=" O PRO A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.625A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 145 Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 181 through 197 removed outlier: 3.876A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ARG A 196 " --> pdb=" O ILE A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 252 through 257 Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 273 through 285 removed outlier: 3.555A pdb=" N CYS A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 296 removed outlier: 4.280A pdb=" N LYS A 291 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ASP A 292 " --> pdb=" O ASP A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 306 removed outlier: 4.384A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 337 through 349 Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 367 through 372 Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 92 Processing helix chain 'E' and resid 97 through 101 Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.596A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 146 Processing helix chain 'E' and resid 172 through 175 Processing helix chain 'E' and resid 181 through 197 removed outlier: 3.796A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLU E 195 " --> pdb=" O LYS E 191 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ARG E 196 " --> pdb=" O ILE E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 217 Processing helix chain 'E' and resid 222 through 233 Processing helix chain 'E' and resid 252 through 260 Proline residue: E 258 - end of helix Processing helix chain 'E' and resid 273 through 285 removed outlier: 3.620A pdb=" N CYS E 285 " --> pdb=" O SER E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 296 removed outlier: 4.184A pdb=" N LYS E 291 " --> pdb=" O VAL E 287 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ASP E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 305 Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 334 through 336 No H-bonds generated for 'chain 'E' and resid 334 through 336' Processing helix chain 'E' and resid 337 through 349 Processing helix chain 'E' and resid 350 through 354 removed outlier: 3.633A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 367 through 372 removed outlier: 4.136A pdb=" N VAL E 370 " --> pdb=" O PRO E 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.510A pdb=" N GLU B 100 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 3.742A 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 removed outlier: 3.750A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 181 through 197 removed outlier: 4.090A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ARG B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 216 Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 252 through 260 Proline residue: B 258 - end of helix Processing helix chain 'B' and resid 273 through 285 removed outlier: 3.510A pdb=" N CYS B 285 " --> pdb=" O SER B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 296 removed outlier: 4.261A pdb=" N LYS B 291 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ASP B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 305 Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 337 through 349 Processing helix chain 'B' and resid 350 through 356 removed outlier: 4.160A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N TRP B 356 " --> pdb=" O GLN B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 367 through 372 removed outlier: 3.557A pdb=" N VAL B 370 " --> pdb=" O PRO B 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.676A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.639A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 197 removed outlier: 4.054A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 257 Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 273 through 285 Processing helix chain 'C' and resid 286 through 295 removed outlier: 4.194A pdb=" N LYS C 291 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 305 removed outlier: 3.514A pdb=" N THR C 304 " --> pdb=" O GLY C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 337 through 349 Processing helix chain 'C' and resid 350 through 356 removed outlier: 3.698A pdb=" N TRP C 356 " --> pdb=" O GLN C 353 " (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 55 through 61 Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 97 through 101 Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.687A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 Processing helix chain 'D' and resid 181 through 197 removed outlier: 3.897A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ARG D 196 " --> pdb=" O ILE D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 252 through 257 Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 273 through 285 removed outlier: 3.633A pdb=" N CYS D 285 " --> pdb=" O SER D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 296 removed outlier: 4.249A pdb=" N LYS D 291 " --> pdb=" O VAL D 287 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ASP D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 305 Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 349 Processing helix chain 'D' and resid 350 through 354 removed outlier: 3.713A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 369 through 374 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.741A pdb=" N PHE A 31 " --> pdb=" O CYS A 17 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N VAL A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ALA A 135 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 6.982A 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 removed outlier: 3.607A pdb=" N ARG A 37 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'A' and resid 176 through 178 removed outlier: 3.630A pdb=" N VAL A 152 " --> pdb=" O VAL A 163 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 176 through 178 removed outlier: 3.800A pdb=" N GLN C 41 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'E' and resid 29 through 32 removed outlier: 7.143A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.507A pdb=" N VAL E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR E 133 " --> pdb=" O VAL E 103 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 35 through 36 Processing sheet with id=AA9, first strand: chain 'E' and resid 41 through 42 removed outlier: 3.928A pdb=" N GLN E 41 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 41 through 42 removed outlier: 3.928A pdb=" N GLN E 41 " --> pdb=" O ALA C 170 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL C 152 " --> pdb=" O VAL C 163 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AB3, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AB4, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AB5, first strand: chain 'E' and resid 238 through 241 Processing sheet with id=AB6, first strand: chain 'B' and resid 29 through 32 removed outlier: 3.674A pdb=" N PHE B 31 " --> pdb=" O CYS B 17 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N VAL B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.642A pdb=" N ARG B 37 " --> pdb=" O THR B 66 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB9, first strand: chain 'B' and resid 176 through 178 removed outlier: 3.606A pdb=" N VAL B 152 " --> pdb=" O VAL B 163 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 176 through 178 removed outlier: 3.894A pdb=" N GLN D 41 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AC3, first strand: chain 'C' and resid 29 through 32 removed outlier: 3.677A pdb=" N PHE C 31 " --> pdb=" O CYS C 17 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N VAL C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.534A pdb=" N ARG C 37 " --> pdb=" O THR C 66 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AC6, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AC7, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.896A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N VAL D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR D 133 " --> pdb=" O VAL D 103 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.673A pdb=" N ARG D 37 " --> pdb=" O THR D 66 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AD1, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AD2, first strand: chain 'D' and resid 169 through 170 removed outlier: 3.614A pdb=" N VAL D 152 " --> pdb=" O VAL D 163 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N MET D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 238 through 241 752 hydrogen bonds defined for protein. 1950 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.54 Time building geometry restraints manager: 1.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4786 1.35 - 1.46: 3385 1.46 - 1.58: 6634 1.58 - 1.70: 15 1.70 - 1.82: 190 Bond restraints: 15010 Sorted by residual: bond pdb=" CB MET A 325 " pdb=" CG MET A 325 " ideal model delta sigma weight residual 1.520 1.488 0.032 3.00e-02 1.11e+03 1.12e+00 bond pdb=" C4 ADP A 401 " pdb=" C5 ADP A 401 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 9.87e-01 bond pdb=" C4 ADP B 401 " pdb=" C5 ADP B 401 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 9.71e-01 bond pdb=" C4 ADP E 401 " pdb=" C5 ADP E 401 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 9.70e-01 bond pdb=" C4 ADP D 401 " pdb=" C5 ADP D 401 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 9.52e-01 ... (remaining 15005 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 20074 2.04 - 4.09: 239 4.09 - 6.13: 43 6.13 - 8.18: 7 8.18 - 10.22: 2 Bond angle restraints: 20365 Sorted by residual: angle pdb=" CA MET C 47 " pdb=" CB MET C 47 " pdb=" CG MET C 47 " ideal model delta sigma weight residual 114.10 121.53 -7.43 2.00e+00 2.50e-01 1.38e+01 angle pdb=" CB MET C 47 " pdb=" CG MET C 47 " pdb=" SD MET C 47 " ideal model delta sigma weight residual 112.70 122.92 -10.22 3.00e+00 1.11e-01 1.16e+01 angle pdb=" CB MET E 283 " pdb=" CG MET E 283 " pdb=" SD MET E 283 " ideal model delta sigma weight residual 112.70 121.80 -9.10 3.00e+00 1.11e-01 9.21e+00 angle pdb=" O1B ADP B 401 " pdb=" PB ADP B 401 " pdb=" O3B ADP B 401 " ideal model delta sigma weight residual 119.90 113.06 6.84 3.00e+00 1.11e-01 5.20e+00 angle pdb=" O1B ADP C 401 " pdb=" PB ADP C 401 " pdb=" O3B ADP C 401 " ideal model delta sigma weight residual 119.90 113.26 6.64 3.00e+00 1.11e-01 4.91e+00 ... (remaining 20360 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.09: 8222 19.09 - 38.18: 644 38.18 - 57.27: 96 57.27 - 76.36: 58 76.36 - 95.45: 10 Dihedral angle restraints: 9030 sinusoidal: 3645 harmonic: 5385 Sorted by residual: dihedral pdb=" O1B ADP D 401 " pdb=" O3A ADP D 401 " pdb=" PB ADP D 401 " pdb=" PA ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 -155.45 95.45 1 2.00e+01 2.50e-03 2.63e+01 dihedral pdb=" O1B ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PB ADP B 401 " pdb=" PA ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 -153.74 93.74 1 2.00e+01 2.50e-03 2.56e+01 dihedral pdb=" O1B ADP A 401 " pdb=" O3A ADP A 401 " pdb=" PB ADP A 401 " pdb=" PA ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 -150.94 90.93 1 2.00e+01 2.50e-03 2.44e+01 ... (remaining 9027 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1320 0.026 - 0.053: 555 0.053 - 0.079: 178 0.079 - 0.105: 162 0.105 - 0.132: 45 Chirality restraints: 2260 Sorted by residual: chirality pdb=" CA ILE A 165 " pdb=" N ILE A 165 " pdb=" C ILE A 165 " pdb=" CB ILE A 165 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.33e-01 chirality pdb=" CA ASN E 12 " pdb=" N ASN E 12 " pdb=" C ASN E 12 " pdb=" CB ASN E 12 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.29e-01 chirality pdb=" CA VAL C 30 " pdb=" N VAL C 30 " pdb=" C VAL C 30 " pdb=" CB VAL C 30 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.93e-01 ... (remaining 2257 not shown) Planarity restraints: 2605 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN E 12 " 0.007 2.00e-02 2.50e+03 1.39e-02 1.94e+00 pdb=" C ASN E 12 " -0.024 2.00e-02 2.50e+03 pdb=" O ASN E 12 " 0.009 2.00e-02 2.50e+03 pdb=" N GLY E 13 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 124 " -0.002 2.00e-02 2.50e+03 1.01e-02 1.77e+00 pdb=" CG PHE E 124 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE E 124 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE E 124 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE E 124 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE E 124 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE E 124 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 242 " -0.021 5.00e-02 4.00e+02 3.15e-02 1.59e+00 pdb=" N PRO C 243 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO C 243 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 243 " -0.018 5.00e-02 4.00e+02 ... (remaining 2602 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 40 2.59 - 3.17: 12247 3.17 - 3.74: 23826 3.74 - 4.32: 33420 4.32 - 4.90: 55128 Nonbonded interactions: 124661 Sorted by model distance: nonbonded pdb=" O3B ADP B 401 " pdb="MG MG B 402 " model vdw 2.012 2.170 nonbonded pdb=" O3B ADP A 401 " pdb="MG MG A 402 " model vdw 2.024 2.170 nonbonded pdb=" O3B ADP C 401 " pdb="MG MG C 402 " model vdw 2.026 2.170 nonbonded pdb=" O3B ADP E 401 " pdb="MG MG E 402 " model vdw 2.050 2.170 nonbonded pdb="MG MG B 402 " pdb=" O HOH B 501 " model vdw 2.053 2.170 ... (remaining 124656 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.670 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 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 : 0.002 0.032 15010 Z= 0.103 Angle : 0.560 10.221 20365 Z= 0.274 Chirality : 0.041 0.132 2260 Planarity : 0.004 0.031 2605 Dihedral : 14.718 95.452 5580 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.70 % Allowed : 11.43 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.20), residues: 1840 helix: 1.38 (0.19), residues: 770 sheet: -0.57 (0.29), residues: 295 loop : 0.95 (0.24), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 206 TYR 0.016 0.001 TYR C 143 PHE 0.020 0.001 PHE E 124 TRP 0.010 0.001 TRP C 79 HIS 0.002 0.000 HIS E 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00195 / 0.10 (15010) covalent geometry : angle 0.56031 / 0.27 (20365) hydrogen bonds : bond 0.15211 / 10.12 ( 737) hydrogen bonds : angle 6.39819 / 4.63 ( 1950) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 0.504 Fit side-chains REVERT: E 82 MET cc_start: 0.8227 (tpt) cc_final: 0.7524 (tpt) REVERT: B 78 ASN cc_start: 0.8082 (t0) cc_final: 0.7778 (t0) REVERT: B 352 PHE cc_start: 0.7505 (t80) cc_final: 0.7245 (t80) outliers start: 11 outliers final: 9 residues processed: 136 average time/residue: 0.1023 time to fit residues: 22.4320 Evaluate side-chains 129 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 120 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain D residue 217 CYS Chi-restraints excluded: chain D residue 267 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 0.3980 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 ASN ** C 371 HIS ** 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 = 0.3237 r_free = 0.3237 target = 0.077182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.067906 restraints weight = 36000.707| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 2.68 r_work: 0.2942 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.0968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 15010 Z= 0.206 Angle : 0.586 6.725 20365 Z= 0.283 Chirality : 0.044 0.147 2260 Planarity : 0.004 0.030 2605 Dihedral : 7.455 95.078 2104 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.03 % Allowed : 11.37 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.20), residues: 1840 helix: 1.24 (0.19), residues: 775 sheet: -0.39 (0.29), residues: 285 loop : 0.76 (0.24), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 206 TYR 0.017 0.001 TYR C 143 PHE 0.010 0.001 PHE B 352 TRP 0.015 0.002 TRP D 79 HIS 0.004 0.001 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.21 (15010) covalent geometry : angle 0.58600 / 0.28 (20365) hydrogen bonds : bond 0.03532 / 2.40 ( 737) hydrogen bonds : angle 5.09300 / 3.71 ( 1950) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 123 time to evaluate : 0.600 Fit side-chains REVERT: A 132 MET cc_start: 0.8613 (tmm) cc_final: 0.8185 (ttp) REVERT: E 78 ASN cc_start: 0.7873 (t0) cc_final: 0.7604 (t0) REVERT: E 82 MET cc_start: 0.8386 (tpt) cc_final: 0.7656 (tpt) REVERT: B 78 ASN cc_start: 0.8430 (t0) cc_final: 0.8165 (t0) REVERT: B 132 MET cc_start: 0.8261 (ttp) cc_final: 0.8016 (ttp) REVERT: D 8 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.8029 (mt) REVERT: D 305 MET cc_start: 0.8905 (mtp) cc_final: 0.8593 (tpp) outliers start: 32 outliers final: 13 residues processed: 151 average time/residue: 0.0885 time to fit residues: 21.9761 Evaluate side-chains 126 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain C residue 338 SER Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: [12, 105, 113, 14, 99, 54, 104, 107, 5, 125, 56] chunk 12 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 5 optimal weight: 6.9990 chunk 125 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 ASN ** C 371 HIS ** 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 = 0.3243 r_free = 0.3243 target = 0.077495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.068190 restraints weight = 36135.319| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.68 r_work: 0.2947 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15010 Z= 0.142 Angle : 0.536 6.841 20365 Z= 0.254 Chirality : 0.042 0.142 2260 Planarity : 0.003 0.034 2605 Dihedral : 7.128 91.514 2094 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.59 % Allowed : 12.32 % Favored : 86.10 % 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: 1.05 (0.20), residues: 1840 helix: 1.30 (0.19), residues: 775 sheet: -0.30 (0.29), residues: 295 loop : 0.70 (0.24), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 147 TYR 0.013 0.001 TYR E 362 PHE 0.009 0.001 PHE E 124 TRP 0.011 0.001 TRP D 79 HIS 0.003 0.001 HIS E 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (15010) covalent geometry : angle 0.53555 / 0.25 (20365) hydrogen bonds : bond 0.03174 / 2.14 ( 737) hydrogen bonds : angle 4.81945 / 3.52 ( 1950) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 0.509 Fit side-chains REVERT: E 50 LYS cc_start: 0.8811 (mtmm) cc_final: 0.8565 (mtmm) REVERT: E 82 MET cc_start: 0.8424 (tpt) cc_final: 0.7776 (tpt) REVERT: D 82 MET cc_start: 0.8360 (mmm) cc_final: 0.7855 (tpt) REVERT: D 305 MET cc_start: 0.8909 (mtp) cc_final: 0.8555 (tpp) outliers start: 25 outliers final: 14 residues processed: 147 average time/residue: 0.0948 time to fit residues: 23.0742 Evaluate side-chains 128 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 103 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: [34, 67, 47, 144, 95, 136, 176, 48, 73, 141, 117] chunk 34 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 144 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 136 optimal weight: 3.9990 chunk 176 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 ASN A 115 ASN ** C 371 HIS ** 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 = 0.3222 r_free = 0.3222 target = 0.076134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.067052 restraints weight = 35865.977| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.56 r_work: 0.2939 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8952 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15010 Z= 0.159 Angle : 0.546 7.021 20365 Z= 0.258 Chirality : 0.043 0.142 2260 Planarity : 0.003 0.029 2605 Dihedral : 7.133 91.274 2093 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.71 % Allowed : 12.89 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.20), residues: 1840 helix: 1.32 (0.19), residues: 770 sheet: -0.31 (0.29), residues: 305 loop : 0.69 (0.24), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 147 TYR 0.013 0.001 TYR E 362 PHE 0.007 0.001 PHE E 124 TRP 0.012 0.002 TRP D 79 HIS 0.008 0.001 HIS E 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (15010) covalent geometry : angle 0.54645 / 0.26 (20365) hydrogen bonds : bond 0.03061 / 2.07 ( 737) hydrogen bonds : angle 4.73942 / 3.46 ( 1950) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 117 time to evaluate : 0.578 Fit side-chains REVERT: A 355 MET cc_start: 0.9164 (mmm) cc_final: 0.8924 (mtt) REVERT: B 78 ASN cc_start: 0.8747 (t0) cc_final: 0.8264 (t0) REVERT: D 82 MET cc_start: 0.8555 (mmm) cc_final: 0.8119 (tpt) REVERT: D 305 MET cc_start: 0.9093 (mtp) cc_final: 0.8764 (tpp) outliers start: 27 outliers final: 19 residues processed: 139 average time/residue: 0.0957 time to fit residues: 21.9478 Evaluate side-chains 133 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 103 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: [30, 102, 47, 22, 92, 91, 20, 5, 23, 119, 68] chunk 30 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 22 optimal weight: 4.9990 chunk 92 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 119 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 ASN A 40 HIS ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 HIS ** 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 = 0.3250 r_free = 0.3250 target = 0.077553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.068433 restraints weight = 35623.388| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.57 r_work: 0.2970 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15010 Z= 0.101 Angle : 0.522 6.912 20365 Z= 0.243 Chirality : 0.041 0.133 2260 Planarity : 0.003 0.027 2605 Dihedral : 6.934 88.606 2093 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 1.65 % Allowed : 13.33 % Favored : 85.02 % 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: 1.17 (0.20), residues: 1840 helix: 1.41 (0.19), residues: 770 sheet: -0.21 (0.29), residues: 305 loop : 0.75 (0.24), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 147 TYR 0.010 0.001 TYR C 143 PHE 0.005 0.001 PHE E 124 TRP 0.011 0.002 TRP D 79 HIS 0.009 0.001 HIS E 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (15010) covalent geometry : angle 0.52164 / 0.24 (20365) hydrogen bonds : bond 0.02702 / 1.84 ( 737) hydrogen bonds : angle 4.59731 / 3.36 ( 1950) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 0.589 Fit side-chains REVERT: A 355 MET cc_start: 0.9159 (mmm) cc_final: 0.8827 (mtp) REVERT: B 78 ASN cc_start: 0.8760 (t0) cc_final: 0.8267 (t0) REVERT: C 355 MET cc_start: 0.9255 (mmm) cc_final: 0.9028 (mtt) REVERT: D 82 MET cc_start: 0.8539 (mmm) cc_final: 0.8107 (tpt) REVERT: D 305 MET cc_start: 0.9079 (mtp) cc_final: 0.8779 (tpp) outliers start: 26 outliers final: 17 residues processed: 141 average time/residue: 0.0924 time to fit residues: 21.5071 Evaluate side-chains 131 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: [24, 74, 145, 16, 161, 98, 156, 174, 55, 75, 166] chunk 24 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 chunk 145 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 156 optimal weight: 1.9990 chunk 174 optimal weight: 0.6980 chunk 55 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 166 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 ASN ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 HIS ** 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 = 0.3209 r_free = 0.3209 target = 0.075488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.066143 restraints weight = 35996.429| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 2.68 r_work: 0.2921 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15010 Z= 0.170 Angle : 0.552 6.925 20365 Z= 0.260 Chirality : 0.043 0.147 2260 Planarity : 0.003 0.027 2605 Dihedral : 7.016 90.477 2093 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.78 % Allowed : 12.95 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.20), residues: 1840 helix: 1.35 (0.20), residues: 770 sheet: -0.15 (0.29), residues: 305 loop : 0.68 (0.24), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 290 TYR 0.014 0.001 TYR E 362 PHE 0.008 0.001 PHE D 223 TRP 0.014 0.002 TRP D 79 HIS 0.008 0.001 HIS E 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 (15010) covalent geometry : angle 0.55152 / 0.26 (20365) hydrogen bonds : bond 0.03091 / 2.09 ( 737) hydrogen bonds : angle 4.62960 / 3.38 ( 1950) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 115 time to evaluate : 0.545 Fit side-chains REVERT: A 132 MET cc_start: 0.8660 (tmm) cc_final: 0.8092 (tmm) REVERT: A 355 MET cc_start: 0.9130 (mmm) cc_final: 0.8810 (mtp) REVERT: E 16 MET cc_start: 0.8730 (mmm) cc_final: 0.8488 (mmm) REVERT: E 82 MET cc_start: 0.8397 (tpt) cc_final: 0.7671 (tpt) REVERT: B 78 ASN cc_start: 0.8705 (t0) cc_final: 0.8201 (t0) REVERT: C 355 MET cc_start: 0.9245 (mmm) cc_final: 0.9040 (mtt) REVERT: D 305 MET cc_start: 0.8967 (mtp) cc_final: 0.8641 (tpp) outliers start: 28 outliers final: 21 residues processed: 139 average time/residue: 0.0921 time to fit residues: 21.1596 Evaluate side-chains 135 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: [18, 54, 165, 29, 14, 163, 112, 161, 149, 92, 127] chunk 18 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 165 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 14 optimal weight: 0.2980 chunk 163 optimal weight: 5.9990 chunk 112 optimal weight: 7.9990 chunk 161 optimal weight: 0.7980 chunk 149 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 127 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 HIS ** 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 = 0.3244 r_free = 0.3244 target = 0.077619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.068368 restraints weight = 35927.922| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.67 r_work: 0.2955 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15010 Z= 0.100 Angle : 0.525 7.381 20365 Z= 0.244 Chirality : 0.041 0.134 2260 Planarity : 0.003 0.029 2605 Dihedral : 6.708 87.518 2093 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.59 % Allowed : 13.46 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.20), residues: 1840 helix: 1.46 (0.20), residues: 770 sheet: -0.04 (0.30), residues: 295 loop : 0.66 (0.24), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 147 TYR 0.010 0.001 TYR E 362 PHE 0.007 0.001 PHE E 124 TRP 0.011 0.001 TRP D 79 HIS 0.009 0.001 HIS E 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (15010) covalent geometry : angle 0.52526 / 0.24 (20365) hydrogen bonds : bond 0.02622 / 1.79 ( 737) hydrogen bonds : angle 4.49887 / 3.29 ( 1950) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 0.569 Fit side-chains REVERT: A 132 MET cc_start: 0.8633 (tmm) cc_final: 0.8057 (tmm) REVERT: A 355 MET cc_start: 0.9111 (mmm) cc_final: 0.8791 (mtp) REVERT: E 82 MET cc_start: 0.8390 (tpt) cc_final: 0.7708 (tpt) REVERT: B 78 ASN cc_start: 0.8701 (t0) cc_final: 0.8202 (t0) REVERT: D 305 MET cc_start: 0.8952 (mtp) cc_final: 0.8634 (tpp) outliers start: 25 outliers final: 19 residues processed: 143 average time/residue: 0.0966 time to fit residues: 22.7058 Evaluate side-chains 133 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 151 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: [40, 89, 46, 25, 101, 76, 152, 24, 178, 114, 158] chunk 40 optimal weight: 0.8980 chunk 89 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 152 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 178 optimal weight: 5.9990 chunk 114 optimal weight: 0.0370 chunk 158 optimal weight: 0.6980 overall best weight: 0.9060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 360 GLN ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 HIS ** 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 = 0.3234 r_free = 0.3234 target = 0.076781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.067821 restraints weight = 35938.474| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.53 r_work: 0.2959 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15010 Z= 0.110 Angle : 0.531 8.074 20365 Z= 0.244 Chirality : 0.041 0.136 2260 Planarity : 0.003 0.028 2605 Dihedral : 6.551 86.629 2093 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.59 % Allowed : 13.52 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.20), residues: 1840 helix: 1.44 (0.19), residues: 775 sheet: 0.01 (0.30), residues: 295 loop : 0.71 (0.23), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 147 TYR 0.009 0.001 TYR E 362 PHE 0.006 0.001 PHE E 124 TRP 0.011 0.001 TRP D 79 HIS 0.009 0.001 HIS E 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (15010) covalent geometry : angle 0.53138 / 0.24 (20365) hydrogen bonds : bond 0.02622 / 1.79 ( 737) hydrogen bonds : angle 4.45254 / 3.26 ( 1950) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 0.373 Fit side-chains REVERT: A 355 MET cc_start: 0.9178 (mmm) cc_final: 0.8871 (mtp) REVERT: E 82 MET cc_start: 0.8506 (tpt) cc_final: 0.7888 (tpt) REVERT: B 78 ASN cc_start: 0.8774 (t0) cc_final: 0.8239 (t0) REVERT: D 305 MET cc_start: 0.9097 (mtp) cc_final: 0.8783 (tpp) outliers start: 25 outliers final: 21 residues processed: 135 average time/residue: 0.0946 time to fit residues: 20.8782 Evaluate side-chains 131 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 124 PHE Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 151 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: [158, 25, 104, 61, 4, 166, 176, 105, 45, 107, 3] chunk 158 optimal weight: 0.0970 chunk 25 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 4 optimal weight: 6.9990 chunk 166 optimal weight: 4.9990 chunk 176 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 107 optimal weight: 0.0030 chunk 3 optimal weight: 0.7980 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 HIS ** 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 = 0.3266 r_free = 0.3266 target = 0.078466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.069167 restraints weight = 35690.119| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.67 r_work: 0.2979 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 15010 Z= 0.086 Angle : 0.528 8.552 20365 Z= 0.242 Chirality : 0.041 0.132 2260 Planarity : 0.003 0.029 2605 Dihedral : 6.083 82.831 2093 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.14 % Allowed : 13.84 % Favored : 85.02 % 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: 1.35 (0.20), residues: 1840 helix: 1.53 (0.19), residues: 775 sheet: 0.07 (0.30), residues: 295 loop : 0.77 (0.23), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 335 TYR 0.011 0.001 TYR A 143 PHE 0.007 0.001 PHE E 124 TRP 0.009 0.001 TRP D 79 HIS 0.009 0.001 HIS E 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00188 / 0.09 (15010) covalent geometry : angle 0.52793 / 0.24 (20365) hydrogen bonds : bond 0.02360 / 1.61 ( 737) hydrogen bonds : angle 4.36999 / 3.20 ( 1950) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 0.469 Fit side-chains REVERT: A 82 MET cc_start: 0.8307 (tpt) cc_final: 0.8083 (tpt) REVERT: A 132 MET cc_start: 0.8353 (tmm) cc_final: 0.8141 (ttp) REVERT: A 355 MET cc_start: 0.9113 (mmm) cc_final: 0.8825 (mtp) REVERT: B 78 ASN cc_start: 0.8718 (t0) cc_final: 0.8207 (t0) REVERT: D 305 MET cc_start: 0.8904 (mtp) cc_final: 0.8589 (tpp) outliers start: 18 outliers final: 17 residues processed: 139 average time/residue: 0.0930 time to fit residues: 21.2408 Evaluate side-chains 133 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 124 PHE Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 151 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: [168, 121, 73, 113, 110, 10, 5, 45, 37, 167, 163] chunk 168 optimal weight: 5.9990 chunk 121 optimal weight: 0.5980 chunk 73 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 110 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 chunk 167 optimal weight: 0.6980 chunk 163 optimal weight: 0.0270 overall best weight: 0.6240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 HIS ** 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 = 0.3261 r_free = 0.3261 target = 0.078220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.069039 restraints weight = 35594.296| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.64 r_work: 0.2977 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15010 Z= 0.094 Angle : 0.532 8.746 20365 Z= 0.243 Chirality : 0.041 0.131 2260 Planarity : 0.003 0.029 2605 Dihedral : 5.717 81.834 2093 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.89 % Allowed : 14.41 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.20), residues: 1840 helix: 1.56 (0.19), residues: 775 sheet: 0.12 (0.30), residues: 295 loop : 0.81 (0.23), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 147 TYR 0.009 0.001 TYR C 143 PHE 0.005 0.001 PHE A 352 TRP 0.015 0.001 TRP E 86 HIS 0.009 0.001 HIS E 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.09 (15010) covalent geometry : angle 0.53249 / 0.24 (20365) hydrogen bonds : bond 0.02428 / 1.66 ( 737) hydrogen bonds : angle 4.34535 / 3.18 ( 1950) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.715 Fit side-chains REVERT: A 132 MET cc_start: 0.8449 (tmm) cc_final: 0.8106 (ttp) REVERT: A 355 MET cc_start: 0.9132 (mmm) cc_final: 0.8857 (mtp) REVERT: B 78 ASN cc_start: 0.8716 (t0) cc_final: 0.8195 (t0) REVERT: D 305 MET cc_start: 0.8892 (mtp) cc_final: 0.8581 (tpp) outliers start: 14 outliers final: 14 residues processed: 130 average time/residue: 0.0952 time to fit residues: 20.3948 Evaluate side-chains 127 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 124 PHE Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain D residue 5 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: [141, 36, 166, 128, 175, 41, 146, 10, 3, 111, 31] chunk 141 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 166 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 chunk 175 optimal weight: 4.9990 chunk 41 optimal weight: 0.4980 chunk 146 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 111 optimal weight: 10.0000 chunk 31 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 HIS ** 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 = 0.3234 r_free = 0.3234 target = 0.076813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.067642 restraints weight = 35629.405| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.64 r_work: 0.2950 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15010 Z= 0.134 Angle : 0.547 8.223 20365 Z= 0.252 Chirality : 0.042 0.135 2260 Planarity : 0.003 0.028 2605 Dihedral : 5.580 82.994 2091 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.33 % Allowed : 14.22 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.20), residues: 1840 helix: 1.51 (0.19), residues: 775 sheet: 0.10 (0.30), residues: 295 loop : 0.78 (0.23), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 147 TYR 0.014 0.001 TYR C 169 PHE 0.006 0.001 PHE A 352 TRP 0.009 0.001 TRP D 79 HIS 0.008 0.001 HIS E 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (15010) covalent geometry : angle 0.54750 / 0.25 (20365) hydrogen bonds : bond 0.02664 / 1.82 ( 737) hydrogen bonds : angle 4.39305 / 3.20 ( 1950) =============================================================================== Job complete usr+sys time: 2730.56 seconds wall clock time: 47 minutes 57.30 seconds (2877.30 seconds total)