Starting phenix.real_space_refine on Wed Mar 4 08:17:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k20_22638/03_2026/7k20_22638.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k20_22638/03_2026/7k20_22638.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7k20_22638/03_2026/7k20_22638.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k20_22638/03_2026/7k20_22638.map" model { file = "/net/cci-nas-00/data/ceres_data/7k20_22638/03_2026/7k20_22638.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k20_22638/03_2026/7k20_22638.cif" } resolution = 3.2 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= 0.002 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 8 5.49 5 Mg 4 5.21 5 S 84 5.16 5 C 7480 2.51 5 N 1984 2.21 5 O 2268 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11828 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} 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: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} 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: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} 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: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} 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: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 48 Unusual residues: {' MG': 1, '1T4': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 48 Unusual residues: {' MG': 1, '1T4': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 48 Unusual residues: {' MG': 1, '1T4': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 48 Unusual residues: {' MG': 1, '1T4': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.91, per 1000 atoms: 0.25 Number of scatterers: 11828 At special positions: 0 Unit cell: (100.32, 77.33, 164.065, 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 84 16.00 P 8 15.00 Mg 4 11.99 O 2268 8.00 N 1984 7.00 C 7480 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 538.1 milliseconds 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2752 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 20 sheets defined 41.5% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 78 through 91 Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.995A pdb=" N GLU A 100 " --> pdb=" O ALA A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.966A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 146 removed outlier: 3.636A pdb=" N LEU A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 175 removed outlier: 3.677A pdb=" N ILE A 175 " --> pdb=" O PRO A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 172 through 175' Processing helix chain 'A' and resid 181 through 193 removed outlier: 3.676A pdb=" N LYS A 191 " --> pdb=" O ASP A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 217 removed outlier: 3.765A pdb=" N ASP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS A 215 " --> pdb=" O ASP A 211 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N CYS A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 230 removed outlier: 3.751A pdb=" N ALA A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.732A pdb=" N CYS A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 267 removed outlier: 3.506A pdb=" N ILE A 267 " --> pdb=" O PRO A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 280 Processing helix chain 'A' and resid 289 through 295 Processing helix chain 'A' and resid 301 through 305 removed outlier: 3.629A pdb=" N THR A 304 " --> pdb=" O GLY A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 318 removed outlier: 3.751A pdb=" N GLN A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR A 318 " --> pdb=" O GLN A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 347 Processing helix chain 'A' and resid 359 through 366 removed outlier: 4.013A pdb=" N GLU A 364 " --> pdb=" O GLN A 360 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA A 365 " --> pdb=" O GLU A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 374 removed outlier: 3.920A pdb=" N VAL A 370 " --> pdb=" O PRO A 367 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N HIS A 371 " --> pdb=" O SER A 368 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS A 373 " --> pdb=" O VAL A 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 61 removed outlier: 3.620A pdb=" N LYS B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 91 removed outlier: 3.517A pdb=" N GLU B 83 " --> pdb=" O TRP B 79 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 101 removed outlier: 4.016A pdb=" N GLU B 100 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 3.513A 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: 3.977A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 146 removed outlier: 3.554A pdb=" N LEU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 removed outlier: 3.665A pdb=" N ILE B 175 " --> pdb=" O PRO B 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 172 through 175' Processing helix chain 'B' and resid 181 through 193 removed outlier: 3.545A pdb=" N TYR B 188 " --> pdb=" O ASP B 184 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS B 191 " --> pdb=" O ASP B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 217 removed outlier: 3.883A pdb=" N ASP B 211 " --> pdb=" O GLU B 207 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS B 215 " --> pdb=" O ASP B 211 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N CYS B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 230 removed outlier: 3.913A pdb=" N ALA B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 267 Processing helix chain 'B' and resid 273 through 284 removed outlier: 3.551A pdb=" N LYS B 284 " --> pdb=" O ASN B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 295 Processing helix chain 'B' and resid 301 through 305 removed outlier: 3.607A pdb=" N THR B 304 " --> pdb=" O GLY B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 318 removed outlier: 3.667A pdb=" N GLN B 314 " --> pdb=" O ALA B 310 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR B 318 " --> pdb=" O GLN B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 347 Processing helix chain 'B' and resid 359 through 366 removed outlier: 4.032A pdb=" N GLU B 364 " --> pdb=" O GLN B 360 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA B 365 " --> pdb=" O GLU B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 374 removed outlier: 3.837A pdb=" N VAL B 370 " --> pdb=" O PRO B 367 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N HIS B 371 " --> pdb=" O SER B 368 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS B 373 " --> pdb=" O VAL B 370 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N CYS B 374 " --> pdb=" O HIS B 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 61 removed outlier: 3.558A pdb=" N LYS C 61 " --> pdb=" O GLU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 91 removed outlier: 3.629A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.983A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 146 removed outlier: 3.558A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER C 145 " --> pdb=" O SER C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 removed outlier: 3.726A pdb=" N ILE C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 172 through 175' Processing helix chain 'C' and resid 181 through 193 removed outlier: 3.514A pdb=" N THR C 186 " --> pdb=" O GLY C 182 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 217 removed outlier: 3.737A pdb=" N ASP C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS C 215 " --> pdb=" O ASP C 211 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N CYS C 217 " --> pdb=" O LYS C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 230 removed outlier: 3.658A pdb=" N ALA C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.664A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (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 Processing helix chain 'C' and resid 301 through 306 removed outlier: 4.222A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 318 removed outlier: 3.516A pdb=" N GLN C 314 " --> pdb=" O ALA C 310 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR C 318 " --> pdb=" O GLN C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 347 Processing helix chain 'C' and resid 359 through 364 removed outlier: 4.107A pdb=" N GLU C 364 " --> pdb=" O GLN C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 374 removed outlier: 3.584A pdb=" N ILE C 369 " --> pdb=" O GLY C 366 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N HIS C 371 " --> pdb=" O SER C 368 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS C 373 " --> pdb=" O VAL C 370 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N CYS C 374 " --> pdb=" O HIS C 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 63 No H-bonds generated for 'chain 'D' and resid 61 through 63' Processing helix chain 'D' and resid 78 through 91 removed outlier: 3.503A pdb=" N LYS D 84 " --> pdb=" O ASP D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.987A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 146 removed outlier: 3.639A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR D 143 " --> pdb=" O VAL D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 175 removed outlier: 3.772A pdb=" N ILE D 175 " --> pdb=" O PRO D 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 172 through 175' Processing helix chain 'D' and resid 181 through 193 removed outlier: 3.538A pdb=" N TYR D 188 " --> pdb=" O ASP D 184 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS D 191 " --> pdb=" O ASP D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 217 removed outlier: 3.897A pdb=" N ASP D 211 " --> pdb=" O GLU D 207 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS D 215 " --> pdb=" O ASP D 211 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N CYS D 217 " --> pdb=" O LYS D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 230 removed outlier: 3.653A pdb=" N ALA D 228 " --> pdb=" O GLU D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 273 through 283 Processing helix chain 'D' and resid 289 through 295 removed outlier: 3.639A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 305 removed outlier: 3.598A pdb=" N THR D 304 " --> pdb=" O GLY D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 318 removed outlier: 3.549A pdb=" N THR D 318 " --> pdb=" O GLN D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 347 Processing helix chain 'D' and resid 359 through 366 removed outlier: 4.090A pdb=" N GLU D 364 " --> pdb=" O GLN D 360 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA D 365 " --> pdb=" O GLU D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 374 removed outlier: 4.105A pdb=" N VAL D 370 " --> pdb=" O PRO D 367 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N HIS D 371 " --> pdb=" O SER D 368 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS D 373 " --> pdb=" O VAL D 370 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N CYS D 374 " --> pdb=" O HIS D 371 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 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: 3.569A pdb=" N VAL A 163 " --> pdb=" O VAL A 152 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 6.066A 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 31 removed outlier: 7.113A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (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 169 through 170 Processing sheet with id=AA9, first strand: chain 'B' and resid 169 through 170 removed outlier: 3.564A pdb=" N VAL B 163 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB2, first strand: chain 'C' and resid 29 through 31 removed outlier: 3.688A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ASN C 12 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB4, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB5, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.317A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AB7, first strand: chain 'D' and resid 29 through 31 removed outlier: 7.103A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AB9, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AC1, first strand: chain 'D' and resid 169 through 170 removed outlier: 3.506A pdb=" N ASP D 154 " --> pdb=" O HIS D 161 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL D 163 " --> pdb=" O VAL D 152 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 238 through 241 429 hydrogen bonds defined for protein. 1083 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: 2.04 Time building geometry restraints manager: 1.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3356 1.33 - 1.45: 2025 1.45 - 1.57: 6555 1.57 - 1.68: 12 1.68 - 1.80: 148 Bond restraints: 12096 Sorted by residual: bond pdb=" CE1 HIC B 73 " pdb=" NE2 HIC B 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.65e+00 bond pdb=" C2 1T4 B 803 " pdb=" N1 1T4 B 803 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.45e+00 bond pdb=" CE1 HIC D 73 " pdb=" NE2 HIC D 73 " ideal model delta sigma weight residual 1.347 1.401 -0.054 2.00e-02 2.50e+03 7.41e+00 bond pdb=" CB THR C 160 " pdb=" CG2 THR C 160 " ideal model delta sigma weight residual 1.521 1.432 0.089 3.30e-02 9.18e+02 7.22e+00 bond pdb=" CE1 HIC A 73 " pdb=" NE2 HIC A 73 " ideal model delta sigma weight residual 1.347 1.401 -0.054 2.00e-02 2.50e+03 7.21e+00 ... (remaining 12091 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 15593 2.11 - 4.22: 728 4.22 - 6.32: 77 6.32 - 8.43: 23 8.43 - 10.54: 7 Bond angle restraints: 16428 Sorted by residual: angle pdb=" C19 1T4 C 803 " pdb=" C17 1T4 C 803 " pdb=" N1 1T4 C 803 " ideal model delta sigma weight residual 114.67 125.21 -10.54 3.00e+00 1.11e-01 1.23e+01 angle pdb=" C19 1T4 B 803 " pdb=" C17 1T4 B 803 " pdb=" N1 1T4 B 803 " ideal model delta sigma weight residual 114.67 125.13 -10.46 3.00e+00 1.11e-01 1.22e+01 angle pdb=" CB MET B 325 " pdb=" CG MET B 325 " pdb=" SD MET B 325 " ideal model delta sigma weight residual 112.70 102.31 10.39 3.00e+00 1.11e-01 1.20e+01 angle pdb=" C19 1T4 A 803 " pdb=" C17 1T4 A 803 " pdb=" N1 1T4 A 803 " ideal model delta sigma weight residual 114.67 124.77 -10.10 3.00e+00 1.11e-01 1.13e+01 angle pdb=" CB MET A 325 " pdb=" CG MET A 325 " pdb=" SD MET A 325 " ideal model delta sigma weight residual 112.70 102.72 9.98 3.00e+00 1.11e-01 1.11e+01 ... (remaining 16423 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.28: 6950 18.28 - 36.56: 219 36.56 - 54.85: 37 54.85 - 73.13: 9 73.13 - 91.41: 5 Dihedral angle restraints: 7220 sinusoidal: 2920 harmonic: 4300 Sorted by residual: dihedral pdb=" O1B ADP A 802 " pdb=" O3A ADP A 802 " pdb=" PB ADP A 802 " pdb=" PA ADP A 802 " ideal model delta sinusoidal sigma weight residual -60.00 -151.41 91.41 1 2.00e+01 2.50e-03 2.46e+01 dihedral pdb=" CA PHE C 124 " pdb=" C PHE C 124 " pdb=" N GLU C 125 " pdb=" CA GLU C 125 " ideal model delta harmonic sigma weight residual 180.00 155.92 24.08 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CA PHE A 124 " pdb=" C PHE A 124 " pdb=" N GLU A 125 " pdb=" CA GLU A 125 " ideal model delta harmonic sigma weight residual 180.00 156.10 23.90 0 5.00e+00 4.00e-02 2.28e+01 ... (remaining 7217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1166 0.058 - 0.115: 532 0.115 - 0.172: 93 0.172 - 0.230: 10 0.230 - 0.287: 7 Chirality restraints: 1808 Sorted by residual: chirality pdb=" CB ILE C 250 " pdb=" CA ILE C 250 " pdb=" CG1 ILE C 250 " pdb=" CG2 ILE C 250 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CB ILE A 250 " pdb=" CA ILE A 250 " pdb=" CG1 ILE A 250 " pdb=" CG2 ILE A 250 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CB ILE D 250 " pdb=" CA ILE D 250 " pdb=" CG1 ILE D 250 " pdb=" CG2 ILE D 250 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 1805 not shown) Planarity restraints: 2092 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 340 " -0.027 2.00e-02 2.50e+03 1.55e-02 6.01e+00 pdb=" CG TRP B 340 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP B 340 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP B 340 " 0.013 2.00e-02 2.50e+03 pdb=" NE1 TRP B 340 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B 340 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 340 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 340 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 340 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B 340 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 242 " -0.041 5.00e-02 4.00e+02 6.10e-02 5.96e+00 pdb=" N PRO A 243 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO A 243 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 243 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 242 " -0.038 5.00e-02 4.00e+02 5.75e-02 5.29e+00 pdb=" N PRO C 243 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO C 243 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 243 " -0.032 5.00e-02 4.00e+02 ... (remaining 2089 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 465 2.69 - 3.24: 11220 3.24 - 3.80: 18891 3.80 - 4.35: 25732 4.35 - 4.90: 43113 Nonbonded interactions: 99421 Sorted by model distance: nonbonded pdb="MG MG B 801 " pdb=" O1B ADP B 802 " model vdw 2.141 2.170 nonbonded pdb="MG MG C 801 " pdb=" O1B ADP C 802 " model vdw 2.158 2.170 nonbonded pdb="MG MG D 801 " pdb=" O1B ADP D 802 " model vdw 2.159 2.170 nonbonded pdb=" OE2 GLU C 270 " pdb=" OG1 THR D 203 " model vdw 2.234 3.040 nonbonded pdb=" OD1 ASP B 157 " pdb=" O3' ADP B 802 " model vdw 2.244 3.040 ... (remaining 99416 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.310 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: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.130 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 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 : 0.013 0.224 12100 Z= 0.671 Angle : 1.021 10.540 16428 Z= 0.521 Chirality : 0.064 0.287 1808 Planarity : 0.007 0.061 2092 Dihedral : 10.523 91.411 4468 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % 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: -5.12 (0.16), residues: 1468 helix: -4.45 (0.09), residues: 636 sheet: -2.85 (0.27), residues: 236 loop : -2.06 (0.22), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG B 39 TYR 0.018 0.003 TYR C 218 PHE 0.030 0.004 PHE D 266 TRP 0.037 0.005 TRP B 340 HIS 0.007 0.002 HIS C 40 Details of bonding type rmsd covalent geometry : bond 0.01289 (12096) covalent geometry : angle 1.02058 (16428) hydrogen bonds : bond 0.29859 ( 421) hydrogen bonds : angle 10.75294 ( 1083) Misc. bond : bond 0.21022 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 227 MET cc_start: 0.9017 (mmm) cc_final: 0.8717 (mmm) REVERT: C 184 ASP cc_start: 0.8042 (m-30) cc_final: 0.7790 (m-30) REVERT: C 286 ASP cc_start: 0.7268 (t0) cc_final: 0.6896 (t0) REVERT: C 355 MET cc_start: 0.8304 (mmm) cc_final: 0.8081 (mmm) REVERT: D 113 LYS cc_start: 0.8942 (mmtm) cc_final: 0.8507 (mptt) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.1208 time to fit residues: 23.3102 Evaluate side-chains 87 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 HIS B 59 GLN ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 GLN D 59 GLN ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.078481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.065043 restraints weight = 25279.397| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 2.39 r_work: 0.2801 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12100 Z= 0.142 Angle : 0.584 6.414 16428 Z= 0.292 Chirality : 0.045 0.138 1808 Planarity : 0.005 0.049 2092 Dihedral : 8.273 77.634 1672 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.40 % Allowed : 5.65 % Favored : 93.95 % 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: -3.37 (0.19), residues: 1468 helix: -3.07 (0.15), residues: 612 sheet: -1.83 (0.30), residues: 236 loop : -1.20 (0.23), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 95 TYR 0.010 0.001 TYR A 169 PHE 0.010 0.001 PHE D 266 TRP 0.020 0.002 TRP B 340 HIS 0.004 0.001 HIS D 87 Details of bonding type rmsd covalent geometry : bond 0.00321 (12096) covalent geometry : angle 0.58414 (16428) hydrogen bonds : bond 0.03513 ( 421) hydrogen bonds : angle 5.60229 ( 1083) Misc. bond : bond 0.00055 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 108 time to evaluate : 0.435 Fit side-chains REVERT: A 123 MET cc_start: 0.9450 (mmt) cc_final: 0.9191 (mmt) REVERT: A 283 MET cc_start: 0.8753 (mmm) cc_final: 0.8516 (mmm) REVERT: B 157 ASP cc_start: 0.8427 (t70) cc_final: 0.8017 (t0) REVERT: B 227 MET cc_start: 0.9027 (mmm) cc_final: 0.8424 (mmm) REVERT: B 372 ARG cc_start: 0.8533 (ptp-170) cc_final: 0.8187 (ptt-90) REVERT: C 355 MET cc_start: 0.8932 (mmm) cc_final: 0.8664 (mmm) REVERT: D 113 LYS cc_start: 0.8758 (mmtm) cc_final: 0.8547 (mptt) REVERT: D 184 ASP cc_start: 0.8804 (m-30) cc_final: 0.8592 (m-30) REVERT: D 227 MET cc_start: 0.9008 (mmm) cc_final: 0.8759 (mmm) REVERT: D 313 MET cc_start: 0.9215 (mmm) cc_final: 0.9005 (mmm) outliers start: 5 outliers final: 1 residues processed: 113 average time/residue: 0.1061 time to fit residues: 17.7386 Evaluate side-chains 86 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 85 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 374 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 97 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 19 optimal weight: 5.9990 chunk 4 optimal weight: 0.0870 chunk 66 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 chunk 80 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 161 HIS ** C 161 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 = 0.3191 r_free = 0.3191 target = 0.078555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.065262 restraints weight = 25512.103| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 2.40 r_work: 0.2803 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12100 Z= 0.122 Angle : 0.536 6.149 16428 Z= 0.260 Chirality : 0.044 0.136 1808 Planarity : 0.004 0.049 2092 Dihedral : 7.525 77.260 1672 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.88 % Allowed : 6.69 % Favored : 92.44 % 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: -2.32 (0.20), residues: 1468 helix: -2.13 (0.18), residues: 612 sheet: -1.46 (0.30), residues: 236 loop : -0.63 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 95 TYR 0.006 0.001 TYR A 169 PHE 0.008 0.001 PHE C 124 TRP 0.014 0.001 TRP B 340 HIS 0.003 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00281 (12096) covalent geometry : angle 0.53625 (16428) hydrogen bonds : bond 0.02881 ( 421) hydrogen bonds : angle 4.79086 ( 1083) Misc. bond : bond 0.00037 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 0.522 Fit side-chains REVERT: A 157 ASP cc_start: 0.8184 (t70) cc_final: 0.7813 (t0) REVERT: A 187 ASP cc_start: 0.8691 (m-30) cc_final: 0.8487 (m-30) REVERT: A 283 MET cc_start: 0.8714 (mmm) cc_final: 0.8449 (mmm) REVERT: B 157 ASP cc_start: 0.8423 (t70) cc_final: 0.8036 (t0) REVERT: B 227 MET cc_start: 0.8973 (mmm) cc_final: 0.8631 (mmm) REVERT: B 372 ARG cc_start: 0.8424 (ptp-170) cc_final: 0.8045 (ptt-90) REVERT: C 288 ASP cc_start: 0.7482 (p0) cc_final: 0.7221 (p0) REVERT: C 355 MET cc_start: 0.8925 (mmm) cc_final: 0.8685 (mmm) REVERT: D 113 LYS cc_start: 0.8848 (mmtm) cc_final: 0.8618 (mptt) REVERT: D 269 MET cc_start: 0.8492 (mtp) cc_final: 0.7990 (mtm) REVERT: D 313 MET cc_start: 0.9167 (mmm) cc_final: 0.8931 (mmm) outliers start: 11 outliers final: 7 residues processed: 114 average time/residue: 0.1087 time to fit residues: 18.2887 Evaluate side-chains 97 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 349 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 46 optimal weight: 0.0570 chunk 3 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 90 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN C 297 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.078656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.065532 restraints weight = 25487.762| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.36 r_work: 0.2811 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2655 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12100 Z= 0.117 Angle : 0.517 6.199 16428 Z= 0.249 Chirality : 0.044 0.133 1808 Planarity : 0.004 0.046 2092 Dihedral : 7.156 77.459 1672 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.88 % Allowed : 7.32 % Favored : 91.80 % 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: -1.53 (0.22), residues: 1468 helix: -1.49 (0.21), residues: 592 sheet: -1.18 (0.31), residues: 236 loop : -0.18 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 95 TYR 0.010 0.001 TYR A 143 PHE 0.008 0.001 PHE C 124 TRP 0.011 0.001 TRP B 340 HIS 0.003 0.001 HIS D 87 Details of bonding type rmsd covalent geometry : bond 0.00273 (12096) covalent geometry : angle 0.51671 (16428) hydrogen bonds : bond 0.02569 ( 421) hydrogen bonds : angle 4.43075 ( 1083) Misc. bond : bond 0.00027 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.432 Fit side-chains REVERT: A 123 MET cc_start: 0.9522 (mmt) cc_final: 0.9185 (mmt) REVERT: A 157 ASP cc_start: 0.8221 (t70) cc_final: 0.7809 (t0) REVERT: A 349 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8302 (mp) REVERT: B 157 ASP cc_start: 0.8339 (t70) cc_final: 0.7825 (t0) REVERT: B 227 MET cc_start: 0.8953 (mmm) cc_final: 0.8582 (mmm) REVERT: B 372 ARG cc_start: 0.8439 (ptp-170) cc_final: 0.8061 (ptt-90) REVERT: C 288 ASP cc_start: 0.7425 (p0) cc_final: 0.7121 (p0) REVERT: C 355 MET cc_start: 0.8904 (mmm) cc_final: 0.8658 (mmm) REVERT: D 82 MET cc_start: 0.9401 (tpt) cc_final: 0.9044 (tpt) REVERT: D 113 LYS cc_start: 0.8972 (mmtm) cc_final: 0.8711 (mptt) REVERT: D 269 MET cc_start: 0.8498 (mtp) cc_final: 0.7958 (mtm) outliers start: 11 outliers final: 6 residues processed: 109 average time/residue: 0.0999 time to fit residues: 16.5402 Evaluate side-chains 99 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 349 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 10 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 79 optimal weight: 0.0670 chunk 6 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 82 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 297 ASN D 59 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.078568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.065485 restraints weight = 25552.576| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 2.37 r_work: 0.2809 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12100 Z= 0.115 Angle : 0.514 6.184 16428 Z= 0.245 Chirality : 0.044 0.132 1808 Planarity : 0.004 0.045 2092 Dihedral : 6.889 76.032 1672 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.11 % Allowed : 7.80 % Favored : 91.08 % 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: -1.14 (0.22), residues: 1468 helix: -1.19 (0.22), residues: 584 sheet: -0.92 (0.31), residues: 236 loop : 0.02 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 95 TYR 0.008 0.001 TYR B 294 PHE 0.007 0.001 PHE C 124 TRP 0.010 0.001 TRP B 340 HIS 0.003 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00272 (12096) covalent geometry : angle 0.51394 (16428) hydrogen bonds : bond 0.02472 ( 421) hydrogen bonds : angle 4.25667 ( 1083) Misc. bond : bond 0.00019 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.456 Fit side-chains REVERT: A 123 MET cc_start: 0.9497 (mmt) cc_final: 0.9190 (mmt) REVERT: A 157 ASP cc_start: 0.8238 (t70) cc_final: 0.7877 (t0) REVERT: A 349 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8339 (mp) REVERT: B 157 ASP cc_start: 0.8320 (t70) cc_final: 0.7767 (t0) REVERT: B 227 MET cc_start: 0.8942 (mmm) cc_final: 0.8642 (mmm) REVERT: B 372 ARG cc_start: 0.8447 (ptp-170) cc_final: 0.8067 (ptt-90) REVERT: C 355 MET cc_start: 0.8937 (mmm) cc_final: 0.8686 (mmm) REVERT: D 82 MET cc_start: 0.9398 (tpt) cc_final: 0.9057 (tpt) outliers start: 14 outliers final: 8 residues processed: 112 average time/residue: 0.0954 time to fit residues: 15.9965 Evaluate side-chains 103 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 349 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 118 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 128 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN D 297 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.075997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.062795 restraints weight = 25697.818| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 2.33 r_work: 0.2744 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2587 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 12100 Z= 0.303 Angle : 0.625 6.050 16428 Z= 0.306 Chirality : 0.048 0.131 1808 Planarity : 0.004 0.042 2092 Dihedral : 7.484 87.124 1672 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.43 % Allowed : 8.36 % Favored : 90.21 % 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: -1.18 (0.22), residues: 1468 helix: -1.34 (0.21), residues: 596 sheet: -0.79 (0.31), residues: 236 loop : 0.08 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 290 TYR 0.017 0.002 TYR A 143 PHE 0.011 0.002 PHE D 200 TRP 0.013 0.002 TRP B 340 HIS 0.004 0.001 HIS C 40 Details of bonding type rmsd covalent geometry : bond 0.00706 (12096) covalent geometry : angle 0.62515 (16428) hydrogen bonds : bond 0.03125 ( 421) hydrogen bonds : angle 4.60214 ( 1083) Misc. bond : bond 0.00018 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.442 Fit side-chains REVERT: A 157 ASP cc_start: 0.8378 (t70) cc_final: 0.8135 (t0) REVERT: A 349 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8255 (mp) REVERT: B 157 ASP cc_start: 0.8317 (t70) cc_final: 0.7872 (t0) REVERT: B 372 ARG cc_start: 0.8458 (ptp-170) cc_final: 0.8101 (ptt-90) REVERT: C 286 ASP cc_start: 0.7505 (t0) cc_final: 0.7288 (t0) REVERT: C 355 MET cc_start: 0.9030 (mmm) cc_final: 0.8763 (mmm) REVERT: D 313 MET cc_start: 0.9217 (mmm) cc_final: 0.8935 (mmm) outliers start: 18 outliers final: 10 residues processed: 110 average time/residue: 0.0994 time to fit residues: 16.5347 Evaluate side-chains 103 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 349 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 90 optimal weight: 0.1980 chunk 20 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 110 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.078284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.065218 restraints weight = 25303.613| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 2.35 r_work: 0.2800 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12100 Z= 0.124 Angle : 0.524 6.308 16428 Z= 0.251 Chirality : 0.045 0.130 1808 Planarity : 0.004 0.044 2092 Dihedral : 6.900 79.089 1672 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.11 % Allowed : 9.00 % Favored : 89.89 % 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: -0.69 (0.22), residues: 1468 helix: -0.86 (0.22), residues: 580 sheet: -0.56 (0.31), residues: 236 loop : 0.24 (0.26), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 290 TYR 0.007 0.001 TYR D 294 PHE 0.007 0.001 PHE D 200 TRP 0.012 0.001 TRP C 340 HIS 0.003 0.001 HIS D 87 Details of bonding type rmsd covalent geometry : bond 0.00295 (12096) covalent geometry : angle 0.52408 (16428) hydrogen bonds : bond 0.02460 ( 421) hydrogen bonds : angle 4.25895 ( 1083) Misc. bond : bond 0.00022 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.461 Fit side-chains REVERT: A 123 MET cc_start: 0.9519 (mmt) cc_final: 0.9234 (mmt) REVERT: A 157 ASP cc_start: 0.8246 (t70) cc_final: 0.7972 (t0) REVERT: A 349 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8094 (mp) REVERT: B 157 ASP cc_start: 0.8208 (t70) cc_final: 0.7650 (t0) REVERT: B 372 ARG cc_start: 0.8437 (ptp-170) cc_final: 0.8086 (ptt-90) REVERT: C 286 ASP cc_start: 0.7403 (t0) cc_final: 0.7146 (t0) REVERT: C 355 MET cc_start: 0.8952 (mmm) cc_final: 0.8667 (mmm) REVERT: D 123 MET cc_start: 0.9389 (mmt) cc_final: 0.9149 (mmt) REVERT: D 313 MET cc_start: 0.9210 (mmm) cc_final: 0.8944 (mmm) outliers start: 14 outliers final: 10 residues processed: 110 average time/residue: 0.0865 time to fit residues: 14.6194 Evaluate side-chains 105 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 349 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 31 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 123 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 chunk 2 optimal weight: 0.2980 chunk 79 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3194 r_free = 0.3194 target = 0.078715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.065584 restraints weight = 25272.099| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 2.33 r_work: 0.2803 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12100 Z= 0.126 Angle : 0.527 6.463 16428 Z= 0.252 Chirality : 0.044 0.129 1808 Planarity : 0.004 0.043 2092 Dihedral : 6.705 75.864 1672 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.35 % Allowed : 8.92 % Favored : 89.73 % 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: -0.42 (0.23), residues: 1468 helix: -0.60 (0.22), residues: 580 sheet: -0.41 (0.31), residues: 236 loop : 0.35 (0.26), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 290 TYR 0.013 0.001 TYR A 143 PHE 0.006 0.001 PHE D 200 TRP 0.011 0.001 TRP B 340 HIS 0.003 0.001 HIS D 87 Details of bonding type rmsd covalent geometry : bond 0.00301 (12096) covalent geometry : angle 0.52676 (16428) hydrogen bonds : bond 0.02506 ( 421) hydrogen bonds : angle 4.21911 ( 1083) Misc. bond : bond 0.00018 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.387 Fit side-chains REVERT: A 123 MET cc_start: 0.9506 (mmt) cc_final: 0.9220 (mmt) REVERT: A 157 ASP cc_start: 0.8298 (t70) cc_final: 0.8055 (t0) REVERT: A 349 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8406 (mp) REVERT: B 157 ASP cc_start: 0.8217 (t70) cc_final: 0.7674 (t0) REVERT: B 372 ARG cc_start: 0.8460 (ptp-170) cc_final: 0.8131 (ptt-90) REVERT: C 355 MET cc_start: 0.8943 (mmm) cc_final: 0.8651 (mmm) REVERT: D 123 MET cc_start: 0.9444 (mmt) cc_final: 0.9213 (mmt) REVERT: D 313 MET cc_start: 0.9163 (mmm) cc_final: 0.8900 (mmm) outliers start: 17 outliers final: 15 residues processed: 110 average time/residue: 0.1010 time to fit residues: 16.8560 Evaluate side-chains 109 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 349 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 144 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 113 optimal weight: 0.0570 chunk 52 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 74 optimal weight: 6.9990 chunk 4 optimal weight: 0.0870 chunk 103 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 overall best weight: 1.0078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.078082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.064966 restraints weight = 25186.037| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 2.32 r_work: 0.2791 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12100 Z= 0.153 Angle : 0.542 6.795 16428 Z= 0.261 Chirality : 0.045 0.131 1808 Planarity : 0.004 0.042 2092 Dihedral : 6.784 77.897 1672 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.75 % Allowed : 8.52 % Favored : 89.73 % 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: -0.36 (0.23), residues: 1468 helix: -0.58 (0.22), residues: 588 sheet: -0.26 (0.32), residues: 236 loop : 0.38 (0.27), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 290 TYR 0.012 0.001 TYR A 143 PHE 0.008 0.001 PHE A 124 TRP 0.011 0.001 TRP B 340 HIS 0.003 0.001 HIS D 87 Details of bonding type rmsd covalent geometry : bond 0.00364 (12096) covalent geometry : angle 0.54203 (16428) hydrogen bonds : bond 0.02583 ( 421) hydrogen bonds : angle 4.24488 ( 1083) Misc. bond : bond 0.00018 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.470 Fit side-chains REVERT: A 123 MET cc_start: 0.9496 (mmt) cc_final: 0.9213 (mmt) REVERT: A 157 ASP cc_start: 0.8339 (t70) cc_final: 0.8084 (t0) REVERT: A 349 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8296 (mp) REVERT: B 157 ASP cc_start: 0.8188 (t70) cc_final: 0.7672 (t0) REVERT: B 372 ARG cc_start: 0.8463 (ptp-170) cc_final: 0.8136 (ptt-90) REVERT: C 355 MET cc_start: 0.8952 (mmm) cc_final: 0.8643 (mmm) REVERT: D 123 MET cc_start: 0.9426 (mmt) cc_final: 0.9190 (mmt) REVERT: D 313 MET cc_start: 0.9181 (mmm) cc_final: 0.8906 (mmm) outliers start: 22 outliers final: 18 residues processed: 112 average time/residue: 0.0927 time to fit residues: 15.6197 Evaluate side-chains 112 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 349 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 142 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 137 optimal weight: 0.0070 chunk 144 optimal weight: 1.9990 overall best weight: 1.1402 ------------------------------------------------------------------------------- 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 = 0.3177 r_free = 0.3177 target = 0.077749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.064584 restraints weight = 25628.797| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 2.34 r_work: 0.2781 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12100 Z= 0.169 Angle : 0.554 6.934 16428 Z= 0.267 Chirality : 0.045 0.132 1808 Planarity : 0.004 0.041 2092 Dihedral : 6.851 79.734 1672 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.67 % Allowed : 8.60 % Favored : 89.73 % 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: -0.29 (0.23), residues: 1468 helix: -0.51 (0.22), residues: 588 sheet: -0.20 (0.33), residues: 236 loop : 0.40 (0.27), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 372 TYR 0.012 0.001 TYR A 143 PHE 0.008 0.001 PHE C 124 TRP 0.011 0.001 TRP B 340 HIS 0.003 0.001 HIS D 87 Details of bonding type rmsd covalent geometry : bond 0.00401 (12096) covalent geometry : angle 0.55389 (16428) hydrogen bonds : bond 0.02636 ( 421) hydrogen bonds : angle 4.28567 ( 1083) Misc. bond : bond 0.00019 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 0.321 Fit side-chains REVERT: A 123 MET cc_start: 0.9498 (mmt) cc_final: 0.9268 (mmt) REVERT: A 157 ASP cc_start: 0.8346 (t70) cc_final: 0.8107 (t0) REVERT: A 305 MET cc_start: 0.9066 (mmt) cc_final: 0.8496 (mmt) REVERT: A 349 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8296 (mp) REVERT: B 157 ASP cc_start: 0.8184 (t70) cc_final: 0.7675 (t0) REVERT: B 372 ARG cc_start: 0.8469 (ptp-170) cc_final: 0.8140 (ptt-90) REVERT: C 355 MET cc_start: 0.8963 (mmm) cc_final: 0.8643 (mmm) REVERT: D 123 MET cc_start: 0.9429 (mmt) cc_final: 0.9185 (mmt) REVERT: D 313 MET cc_start: 0.9184 (mmm) cc_final: 0.8911 (mmm) outliers start: 21 outliers final: 18 residues processed: 110 average time/residue: 0.0921 time to fit residues: 15.4537 Evaluate side-chains 112 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 349 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 0.8980 chunk 111 optimal weight: 5.9990 chunk 110 optimal weight: 0.7980 chunk 120 optimal weight: 5.9990 chunk 54 optimal weight: 0.0020 chunk 28 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 96 optimal weight: 0.0030 chunk 81 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.079446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.066453 restraints weight = 25369.271| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 2.35 r_work: 0.2827 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12100 Z= 0.099 Angle : 0.517 7.051 16428 Z= 0.247 Chirality : 0.044 0.130 1808 Planarity : 0.003 0.043 2092 Dihedral : 6.344 70.713 1672 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.27 % Allowed : 9.16 % Favored : 89.57 % 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: -0.20 (0.23), residues: 1468 helix: -0.31 (0.22), residues: 600 sheet: -0.15 (0.33), residues: 236 loop : 0.33 (0.27), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 372 TYR 0.010 0.001 TYR A 143 PHE 0.006 0.001 PHE C 124 TRP 0.012 0.001 TRP C 340 HIS 0.005 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00237 (12096) covalent geometry : angle 0.51702 (16428) hydrogen bonds : bond 0.02301 ( 421) hydrogen bonds : angle 4.07248 ( 1083) Misc. bond : bond 0.00021 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2375.64 seconds wall clock time: 41 minutes 33.29 seconds (2493.29 seconds total)