Starting phenix.real_space_refine on Thu Sep 18 00:10:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6v0b_20986/09_2025/6v0b_20986.cif Found real_map, /net/cci-nas-00/data/ceres_data/6v0b_20986/09_2025/6v0b_20986.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6v0b_20986/09_2025/6v0b_20986.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6v0b_20986/09_2025/6v0b_20986.map" model { file = "/net/cci-nas-00/data/ceres_data/6v0b_20986/09_2025/6v0b_20986.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6v0b_20986/09_2025/6v0b_20986.cif" } resolution = 4.1 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= 0.001 sd= 0.009 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: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 8135 2.51 5 N 2075 2.21 5 O 2245 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12485 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2497 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 14, 'TRANS': 291} Restraints were copied for chains: B, C, D, E Time building chain proxies: 1.73, per 1000 atoms: 0.14 Number of scatterers: 12485 At special positions: 0 Unit cell: (92.0724, 92.0724, 117.283, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 2245 8.00 N 2075 7.00 C 8135 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: 0.90 Conformation dependent library (CDL) restraints added in 410.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2900 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 20 sheets defined 25.2% alpha, 32.7% 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 62 through 67 removed outlier: 3.594A pdb=" N TRP A 66 " --> pdb=" O GLN A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 207 removed outlier: 3.935A pdb=" N SER A 207 " --> pdb=" O TYR A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 220 removed outlier: 4.135A pdb=" N ILE A 216 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ALA A 217 " --> pdb=" O GLY A 213 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TRP A 220 " --> pdb=" O ILE A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 253 removed outlier: 3.558A pdb=" N THR A 234 " --> pdb=" O GLU A 230 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL A 243 " --> pdb=" O MET A 239 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N SER A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ASN A 251 " --> pdb=" O PHE A 247 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ILE A 252 " --> pdb=" O TYR A 248 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU A 253 " --> pdb=" O THR A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 264 removed outlier: 3.674A pdb=" N GLN A 264 " --> pdb=" O VAL A 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 261 through 264' Processing helix chain 'A' and resid 265 through 285 removed outlier: 4.374A pdb=" N ILE A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU A 278 " --> pdb=" O PHE A 274 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 279 " --> pdb=" O ALA A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 307 Processing helix chain 'B' and resid 62 through 67 removed outlier: 3.592A pdb=" N TRP B 66 " --> pdb=" O GLN B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 207 removed outlier: 3.935A pdb=" N SER B 207 " --> pdb=" O TYR B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 220 removed outlier: 4.136A pdb=" N ILE B 216 " --> pdb=" O LEU B 212 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ALA B 217 " --> pdb=" O GLY B 213 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TRP B 220 " --> pdb=" O ILE B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 253 removed outlier: 3.558A pdb=" N THR B 234 " --> pdb=" O GLU B 230 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL B 243 " --> pdb=" O MET B 239 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N SER B 250 " --> pdb=" O ALA B 246 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ASN B 251 " --> pdb=" O PHE B 247 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ILE B 252 " --> pdb=" O TYR B 248 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU B 253 " --> pdb=" O THR B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 264 removed outlier: 3.674A pdb=" N GLN B 264 " --> pdb=" O VAL B 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 261 through 264' Processing helix chain 'B' and resid 265 through 285 removed outlier: 4.374A pdb=" N ILE B 273 " --> pdb=" O GLY B 269 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU B 278 " --> pdb=" O PHE B 274 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU B 279 " --> pdb=" O ALA B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 307 Processing helix chain 'C' and resid 62 through 67 removed outlier: 3.593A pdb=" N TRP C 66 " --> pdb=" O GLN C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 207 removed outlier: 3.934A pdb=" N SER C 207 " --> pdb=" O TYR C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 220 removed outlier: 4.136A pdb=" N ILE C 216 " --> pdb=" O LEU C 212 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ALA C 217 " --> pdb=" O GLY C 213 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TRP C 220 " --> pdb=" O ILE C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 253 removed outlier: 3.558A pdb=" N THR C 234 " --> pdb=" O GLU C 230 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL C 243 " --> pdb=" O MET C 239 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N SER C 250 " --> pdb=" O ALA C 246 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ASN C 251 " --> pdb=" O PHE C 247 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ILE C 252 " --> pdb=" O TYR C 248 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU C 253 " --> pdb=" O THR C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 264 removed outlier: 3.674A pdb=" N GLN C 264 " --> pdb=" O VAL C 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 261 through 264' Processing helix chain 'C' and resid 265 through 285 removed outlier: 4.373A pdb=" N ILE C 273 " --> pdb=" O GLY C 269 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU C 278 " --> pdb=" O PHE C 274 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU C 279 " --> pdb=" O ALA C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 307 Processing helix chain 'D' and resid 62 through 67 removed outlier: 3.593A pdb=" N TRP D 66 " --> pdb=" O GLN D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 207 removed outlier: 3.934A pdb=" N SER D 207 " --> pdb=" O TYR D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 220 removed outlier: 4.135A pdb=" N ILE D 216 " --> pdb=" O LEU D 212 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ALA D 217 " --> pdb=" O GLY D 213 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TRP D 220 " --> pdb=" O ILE D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 253 removed outlier: 3.558A pdb=" N THR D 234 " --> pdb=" O GLU D 230 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL D 243 " --> pdb=" O MET D 239 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N SER D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ASN D 251 " --> pdb=" O PHE D 247 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ILE D 252 " --> pdb=" O TYR D 248 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU D 253 " --> pdb=" O THR D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 264 removed outlier: 3.674A pdb=" N GLN D 264 " --> pdb=" O VAL D 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 261 through 264' Processing helix chain 'D' and resid 265 through 285 removed outlier: 4.374A pdb=" N ILE D 273 " --> pdb=" O GLY D 269 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU D 278 " --> pdb=" O PHE D 274 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU D 279 " --> pdb=" O ALA D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 307 Processing helix chain 'E' and resid 62 through 67 removed outlier: 3.594A pdb=" N TRP E 66 " --> pdb=" O GLN E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 207 removed outlier: 3.935A pdb=" N SER E 207 " --> pdb=" O TYR E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 220 removed outlier: 4.136A pdb=" N ILE E 216 " --> pdb=" O LEU E 212 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ALA E 217 " --> pdb=" O GLY E 213 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TRP E 220 " --> pdb=" O ILE E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 253 removed outlier: 3.558A pdb=" N THR E 234 " --> pdb=" O GLU E 230 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL E 243 " --> pdb=" O MET E 239 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N SER E 250 " --> pdb=" O ALA E 246 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ASN E 251 " --> pdb=" O PHE E 247 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ILE E 252 " --> pdb=" O TYR E 248 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU E 253 " --> pdb=" O THR E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 264 removed outlier: 3.675A pdb=" N GLN E 264 " --> pdb=" O VAL E 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 261 through 264' Processing helix chain 'E' and resid 265 through 285 removed outlier: 4.374A pdb=" N ILE E 273 " --> pdb=" O GLY E 269 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU E 278 " --> pdb=" O PHE E 274 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU E 279 " --> pdb=" O ALA E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 307 Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 27 removed outlier: 5.530A pdb=" N ILE A 23 " --> pdb=" O ASP A 36 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ASP A 36 " --> pdb=" O ILE A 23 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N GLY A 25 " --> pdb=" O LYS A 34 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LYS A 34 " --> pdb=" O GLY A 25 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL A 35 " --> pdb=" O GLY A 108 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY A 108 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY A 37 " --> pdb=" O PHE A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 22 through 27 removed outlier: 5.530A pdb=" N ILE A 23 " --> pdb=" O ASP A 36 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ASP A 36 " --> pdb=" O ILE A 23 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N GLY A 25 " --> pdb=" O LYS A 34 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LYS A 34 " --> pdb=" O GLY A 25 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N VAL A 14 " --> pdb=" O LEU A 140 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 77 removed outlier: 3.780A pdb=" N GLU A 131 " --> pdb=" O GLU A 77 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N SER A 189 " --> pdb=" O PRO A 132 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG A 194 " --> pdb=" O SER A 167 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER A 167 " --> pdb=" O ARG A 194 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 76 through 77 removed outlier: 3.780A pdb=" N GLU A 131 " --> pdb=" O GLU A 77 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N SER A 189 " --> pdb=" O PRO A 132 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 22 through 27 removed outlier: 5.531A pdb=" N ILE B 23 " --> pdb=" O ASP B 36 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ASP B 36 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N GLY B 25 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS B 34 " --> pdb=" O GLY B 25 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL B 35 " --> pdb=" O GLY B 108 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY B 108 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY B 37 " --> pdb=" O PHE B 106 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 22 through 27 removed outlier: 5.531A pdb=" N ILE B 23 " --> pdb=" O ASP B 36 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ASP B 36 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N GLY B 25 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS B 34 " --> pdb=" O GLY B 25 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N VAL B 14 " --> pdb=" O LEU B 140 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 76 through 77 removed outlier: 3.780A pdb=" N GLU B 131 " --> pdb=" O GLU B 77 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N SER B 189 " --> pdb=" O PRO B 132 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG B 194 " --> pdb=" O SER B 167 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER B 167 " --> pdb=" O ARG B 194 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 76 through 77 removed outlier: 3.780A pdb=" N GLU B 131 " --> pdb=" O GLU B 77 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N SER B 189 " --> pdb=" O PRO B 132 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 22 through 27 removed outlier: 5.531A pdb=" N ILE C 23 " --> pdb=" O ASP C 36 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ASP C 36 " --> pdb=" O ILE C 23 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N GLY C 25 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS C 34 " --> pdb=" O GLY C 25 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL C 35 " --> pdb=" O GLY C 108 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLY C 108 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY C 37 " --> pdb=" O PHE C 106 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 22 through 27 removed outlier: 5.531A pdb=" N ILE C 23 " --> pdb=" O ASP C 36 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ASP C 36 " --> pdb=" O ILE C 23 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N GLY C 25 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS C 34 " --> pdb=" O GLY C 25 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N VAL C 14 " --> pdb=" O LEU C 140 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 76 through 77 removed outlier: 3.779A pdb=" N GLU C 131 " --> pdb=" O GLU C 77 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N SER C 189 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG C 194 " --> pdb=" O SER C 167 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER C 167 " --> pdb=" O ARG C 194 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 76 through 77 removed outlier: 3.779A pdb=" N GLU C 131 " --> pdb=" O GLU C 77 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N SER C 189 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 22 through 27 removed outlier: 5.531A pdb=" N ILE D 23 " --> pdb=" O ASP D 36 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ASP D 36 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N GLY D 25 " --> pdb=" O LYS D 34 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS D 34 " --> pdb=" O GLY D 25 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL D 35 " --> pdb=" O GLY D 108 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY D 108 " --> pdb=" O VAL D 35 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY D 37 " --> pdb=" O PHE D 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 22 through 27 removed outlier: 5.531A pdb=" N ILE D 23 " --> pdb=" O ASP D 36 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ASP D 36 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N GLY D 25 " --> pdb=" O LYS D 34 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS D 34 " --> pdb=" O GLY D 25 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N VAL D 14 " --> pdb=" O LEU D 140 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 76 through 77 removed outlier: 3.779A pdb=" N GLU D 131 " --> pdb=" O GLU D 77 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N SER D 189 " --> pdb=" O PRO D 132 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG D 194 " --> pdb=" O SER D 167 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER D 167 " --> pdb=" O ARG D 194 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 76 through 77 removed outlier: 3.779A pdb=" N GLU D 131 " --> pdb=" O GLU D 77 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N SER D 189 " --> pdb=" O PRO D 132 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 22 through 27 removed outlier: 5.531A pdb=" N ILE E 23 " --> pdb=" O ASP E 36 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N ASP E 36 " --> pdb=" O ILE E 23 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N GLY E 25 " --> pdb=" O LYS E 34 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS E 34 " --> pdb=" O GLY E 25 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL E 35 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY E 108 " --> pdb=" O VAL E 35 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY E 37 " --> pdb=" O PHE E 106 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 22 through 27 removed outlier: 5.531A pdb=" N ILE E 23 " --> pdb=" O ASP E 36 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N ASP E 36 " --> pdb=" O ILE E 23 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N GLY E 25 " --> pdb=" O LYS E 34 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS E 34 " --> pdb=" O GLY E 25 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N VAL E 14 " --> pdb=" O LEU E 140 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 76 through 77 removed outlier: 3.780A pdb=" N GLU E 131 " --> pdb=" O GLU E 77 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N SER E 189 " --> pdb=" O PRO E 132 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG E 194 " --> pdb=" O SER E 167 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER E 167 " --> pdb=" O ARG E 194 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 76 through 77 removed outlier: 3.780A pdb=" N GLU E 131 " --> pdb=" O GLU E 77 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N SER E 189 " --> pdb=" O PRO E 132 " (cutoff:3.500A) 390 hydrogen bonds defined for protein. 1125 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: 1.69 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: 1.22 - 1.34: 3952 1.34 - 1.46: 2919 1.46 - 1.58: 5904 1.58 - 1.69: 0 1.69 - 1.81: 50 Bond restraints: 12825 Sorted by residual: bond pdb=" N CYS B 300 " pdb=" CA CYS B 300 " ideal model delta sigma weight residual 1.456 1.489 -0.034 1.32e-02 5.74e+03 6.55e+00 bond pdb=" N CYS E 300 " pdb=" CA CYS E 300 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.32e-02 5.74e+03 6.36e+00 bond pdb=" N CYS D 300 " pdb=" CA CYS D 300 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.32e-02 5.74e+03 6.34e+00 bond pdb=" N CYS A 300 " pdb=" CA CYS A 300 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.32e-02 5.74e+03 6.25e+00 bond pdb=" N CYS C 300 " pdb=" CA CYS C 300 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.32e-02 5.74e+03 6.24e+00 ... (remaining 12820 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 16337 1.82 - 3.65: 969 3.65 - 5.47: 124 5.47 - 7.29: 40 7.29 - 9.12: 10 Bond angle restraints: 17480 Sorted by residual: angle pdb=" C PRO C 183 " pdb=" N ASN C 184 " pdb=" CA ASN C 184 " ideal model delta sigma weight residual 121.54 130.66 -9.12 1.91e+00 2.74e-01 2.28e+01 angle pdb=" C PRO D 183 " pdb=" N ASN D 184 " pdb=" CA ASN D 184 " ideal model delta sigma weight residual 121.54 130.64 -9.10 1.91e+00 2.74e-01 2.27e+01 angle pdb=" C PRO B 183 " pdb=" N ASN B 184 " pdb=" CA ASN B 184 " ideal model delta sigma weight residual 121.54 130.61 -9.07 1.91e+00 2.74e-01 2.26e+01 angle pdb=" C PRO E 183 " pdb=" N ASN E 184 " pdb=" CA ASN E 184 " ideal model delta sigma weight residual 121.54 130.58 -9.04 1.91e+00 2.74e-01 2.24e+01 angle pdb=" C PRO A 183 " pdb=" N ASN A 184 " pdb=" CA ASN A 184 " ideal model delta sigma weight residual 121.54 130.55 -9.01 1.91e+00 2.74e-01 2.22e+01 ... (remaining 17475 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.11: 6291 14.11 - 28.22: 851 28.22 - 42.33: 272 42.33 - 56.44: 61 56.44 - 70.55: 25 Dihedral angle restraints: 7500 sinusoidal: 3010 harmonic: 4490 Sorted by residual: dihedral pdb=" CA ASN B 289 " pdb=" C ASN B 289 " pdb=" N GLY B 290 " pdb=" CA GLY B 290 " ideal model delta harmonic sigma weight residual 180.00 151.07 28.93 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA ASN E 289 " pdb=" C ASN E 289 " pdb=" N GLY E 290 " pdb=" CA GLY E 290 " ideal model delta harmonic sigma weight residual 180.00 151.11 28.89 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA ASN A 289 " pdb=" C ASN A 289 " pdb=" N GLY A 290 " pdb=" CA GLY A 290 " ideal model delta harmonic sigma weight residual 180.00 151.11 28.89 0 5.00e+00 4.00e-02 3.34e+01 ... (remaining 7497 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1498 0.066 - 0.132: 374 0.132 - 0.198: 61 0.198 - 0.263: 2 0.263 - 0.329: 5 Chirality restraints: 1940 Sorted by residual: chirality pdb=" CG LEU E 214 " pdb=" CB LEU E 214 " pdb=" CD1 LEU E 214 " pdb=" CD2 LEU E 214 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CG LEU A 214 " pdb=" CB LEU A 214 " pdb=" CD1 LEU A 214 " pdb=" CD2 LEU A 214 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.70e+00 chirality pdb=" CG LEU D 214 " pdb=" CB LEU D 214 " pdb=" CD1 LEU D 214 " pdb=" CD2 LEU D 214 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.69e+00 ... (remaining 1937 not shown) Planarity restraints: 2230 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 274 " 0.035 2.00e-02 2.50e+03 3.46e-02 2.09e+01 pdb=" CG PHE A 274 " -0.078 2.00e-02 2.50e+03 pdb=" CD1 PHE A 274 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 PHE A 274 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 274 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 274 " 0.020 2.00e-02 2.50e+03 pdb=" CZ PHE A 274 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 274 " 0.035 2.00e-02 2.50e+03 3.46e-02 2.09e+01 pdb=" CG PHE C 274 " -0.078 2.00e-02 2.50e+03 pdb=" CD1 PHE C 274 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 PHE C 274 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE C 274 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE C 274 " 0.020 2.00e-02 2.50e+03 pdb=" CZ PHE C 274 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 274 " 0.035 2.00e-02 2.50e+03 3.45e-02 2.09e+01 pdb=" CG PHE D 274 " -0.078 2.00e-02 2.50e+03 pdb=" CD1 PHE D 274 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 PHE D 274 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE D 274 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE D 274 " 0.020 2.00e-02 2.50e+03 pdb=" CZ PHE D 274 " 0.000 2.00e-02 2.50e+03 ... (remaining 2227 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 3323 2.80 - 3.32: 11440 3.32 - 3.85: 21011 3.85 - 4.37: 23553 4.37 - 4.90: 39449 Nonbonded interactions: 98776 Sorted by model distance: nonbonded pdb=" OG SER D 143 " pdb=" OG1 THR D 168 " model vdw 2.272 3.040 nonbonded pdb=" OG SER E 143 " pdb=" OG1 THR E 168 " model vdw 2.272 3.040 nonbonded pdb=" OG SER C 143 " pdb=" OG1 THR C 168 " model vdw 2.272 3.040 nonbonded pdb=" OG SER B 143 " pdb=" OG1 THR B 168 " model vdw 2.272 3.040 nonbonded pdb=" OG SER A 143 " pdb=" OG1 THR A 168 " model vdw 2.273 3.040 ... (remaining 98771 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.530 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.850 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 12825 Z= 0.279 Angle : 0.981 9.117 17480 Z= 0.552 Chirality : 0.059 0.329 1940 Planarity : 0.007 0.051 2230 Dihedral : 15.045 70.555 4600 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 0.51 % Allowed : 10.22 % Favored : 89.27 % 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 aren not related in a simple way. whole: -4.96 (0.18), residues: 1520 helix: -4.23 (0.15), residues: 345 sheet: -3.11 (0.22), residues: 395 loop : -2.89 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 199 TYR 0.024 0.003 TYR C 102 PHE 0.078 0.003 PHE D 274 TRP 0.007 0.002 TRP B 160 HIS 0.006 0.003 HIS D 169 Details of bonding type rmsd covalent geometry : bond 0.00572 (12825) covalent geometry : angle 0.98149 (17480) hydrogen bonds : bond 0.18482 ( 335) hydrogen bonds : angle 10.14840 ( 1125) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 215 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 LEU cc_start: 0.9030 (tp) cc_final: 0.8802 (tp) REVERT: A 131 GLU cc_start: 0.8404 (mt-10) cc_final: 0.7906 (mm-30) REVERT: A 154 ASN cc_start: 0.7762 (m-40) cc_final: 0.7513 (t0) REVERT: A 239 MET cc_start: 0.9116 (mmm) cc_final: 0.8802 (mmm) REVERT: B 130 LEU cc_start: 0.9119 (tp) cc_final: 0.8845 (tp) REVERT: B 154 ASN cc_start: 0.7727 (m-40) cc_final: 0.7466 (m-40) REVERT: B 239 MET cc_start: 0.9159 (mmm) cc_final: 0.8528 (mpp) REVERT: C 154 ASN cc_start: 0.7940 (m-40) cc_final: 0.7577 (t0) REVERT: C 308 PHE cc_start: 0.5863 (m-80) cc_final: 0.5636 (m-10) REVERT: D 131 GLU cc_start: 0.8359 (mt-10) cc_final: 0.8114 (mt-10) REVERT: D 239 MET cc_start: 0.9106 (mmm) cc_final: 0.8435 (mpp) REVERT: E 239 MET cc_start: 0.9082 (mmm) cc_final: 0.8704 (mmm) outliers start: 7 outliers final: 2 residues processed: 222 average time/residue: 0.0931 time to fit residues: 31.5839 Evaluate side-chains 150 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 148 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 80 ASN A 125 GLN A 138 GLN A 177 HIS ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 ASN B 125 GLN ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 HIS B 264 GLN C 21 ASN C 80 ASN C 125 GLN C 138 GLN C 177 HIS D 62 GLN D 80 ASN D 125 GLN D 138 GLN D 177 HIS E 80 ASN E 125 GLN ** E 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.110346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.088174 restraints weight = 42739.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.090882 restraints weight = 26288.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.092859 restraints weight = 19126.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.094047 restraints weight = 15295.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.094928 restraints weight = 13191.804| |-----------------------------------------------------------------------------| r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12825 Z= 0.152 Angle : 0.674 8.742 17480 Z= 0.359 Chirality : 0.046 0.149 1940 Planarity : 0.005 0.043 2230 Dihedral : 6.762 23.429 1680 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % 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 aren not related in a simple way. whole: -4.27 (0.18), residues: 1520 helix: -3.26 (0.20), residues: 345 sheet: -2.82 (0.21), residues: 410 loop : -2.55 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 199 TYR 0.019 0.002 TYR C 270 PHE 0.027 0.002 PHE E 247 TRP 0.007 0.001 TRP C 161 HIS 0.006 0.001 HIS C 177 Details of bonding type rmsd covalent geometry : bond 0.00329 (12825) covalent geometry : angle 0.67367 (17480) hydrogen bonds : bond 0.04446 ( 335) hydrogen bonds : angle 7.80900 ( 1125) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 GLU cc_start: 0.8424 (mt-10) cc_final: 0.7858 (mt-10) REVERT: B 185 GLN cc_start: 0.2210 (mm-40) cc_final: 0.1945 (mm-40) REVERT: B 199 ARG cc_start: 0.8055 (mtm180) cc_final: 0.7492 (mtm180) REVERT: C 131 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7841 (mm-30) REVERT: D 131 GLU cc_start: 0.8471 (mt-10) cc_final: 0.7827 (mt-10) REVERT: D 199 ARG cc_start: 0.7953 (mtm180) cc_final: 0.7691 (mtm180) REVERT: E 131 GLU cc_start: 0.8393 (mt-10) cc_final: 0.7651 (mt-10) REVERT: E 199 ARG cc_start: 0.8022 (mtm180) cc_final: 0.7692 (mtm180) REVERT: E 239 MET cc_start: 0.8954 (mmm) cc_final: 0.8703 (mmm) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.1021 time to fit residues: 28.7289 Evaluate side-chains 123 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 55 optimal weight: 7.9990 chunk 106 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 43 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 chunk 116 optimal weight: 7.9990 chunk 4 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 GLN C 21 ASN C 264 GLN D 264 GLN E 264 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.105620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.082943 restraints weight = 43821.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.085594 restraints weight = 26817.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.087310 restraints weight = 19537.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.088418 restraints weight = 15889.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.089268 restraints weight = 13887.312| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 12825 Z= 0.285 Angle : 0.778 8.759 17480 Z= 0.413 Chirality : 0.048 0.152 1940 Planarity : 0.006 0.053 2230 Dihedral : 7.099 25.290 1680 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.88 % Favored : 91.12 % Rotamer: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % 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 aren not related in a simple way. whole: -3.90 (0.19), residues: 1520 helix: -2.74 (0.23), residues: 360 sheet: -2.69 (0.22), residues: 410 loop : -2.35 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 255 TYR 0.028 0.003 TYR E 102 PHE 0.032 0.003 PHE E 208 TRP 0.014 0.002 TRP B 72 HIS 0.012 0.003 HIS C 177 Details of bonding type rmsd covalent geometry : bond 0.00608 (12825) covalent geometry : angle 0.77822 (17480) hydrogen bonds : bond 0.04719 ( 335) hydrogen bonds : angle 7.49329 ( 1125) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 VAL cc_start: 0.9192 (t) cc_final: 0.8942 (p) REVERT: A 131 GLU cc_start: 0.8485 (mt-10) cc_final: 0.7768 (mt-10) REVERT: A 247 PHE cc_start: 0.8797 (t80) cc_final: 0.8554 (t80) REVERT: C 127 VAL cc_start: 0.9243 (t) cc_final: 0.8942 (p) REVERT: C 130 LEU cc_start: 0.9075 (tp) cc_final: 0.8377 (tp) REVERT: C 131 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7483 (mm-30) REVERT: C 199 ARG cc_start: 0.8059 (mtm180) cc_final: 0.7342 (mtm180) REVERT: C 247 PHE cc_start: 0.8817 (t80) cc_final: 0.8593 (t80) REVERT: D 131 GLU cc_start: 0.8463 (mt-10) cc_final: 0.7799 (mt-10) REVERT: D 199 ARG cc_start: 0.8086 (mtm180) cc_final: 0.7855 (mtm180) REVERT: D 270 TYR cc_start: 0.8425 (m-80) cc_final: 0.8163 (m-80) REVERT: E 199 ARG cc_start: 0.7971 (mtm180) cc_final: 0.7741 (mtm180) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.0971 time to fit residues: 22.5555 Evaluate side-chains 107 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 121 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 chunk 145 optimal weight: 4.9990 chunk 19 optimal weight: 0.0980 chunk 29 optimal weight: 0.0980 chunk 88 optimal weight: 5.9990 chunk 127 optimal weight: 0.9980 chunk 71 optimal weight: 8.9990 chunk 4 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 chunk 112 optimal weight: 7.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.109814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.087277 restraints weight = 42500.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.090199 restraints weight = 25296.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.092122 restraints weight = 17977.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.093446 restraints weight = 14327.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.094288 restraints weight = 12256.878| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12825 Z= 0.145 Angle : 0.657 8.416 17480 Z= 0.340 Chirality : 0.046 0.143 1940 Planarity : 0.004 0.044 2230 Dihedral : 6.471 22.191 1680 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % 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 aren not related in a simple way. whole: -3.64 (0.19), residues: 1520 helix: -2.31 (0.24), residues: 345 sheet: -2.40 (0.22), residues: 430 loop : -2.40 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 301 TYR 0.022 0.002 TYR A 270 PHE 0.030 0.002 PHE D 247 TRP 0.008 0.001 TRP B 220 HIS 0.003 0.001 HIS D 177 Details of bonding type rmsd covalent geometry : bond 0.00318 (12825) covalent geometry : angle 0.65657 (17480) hydrogen bonds : bond 0.03697 ( 335) hydrogen bonds : angle 6.99418 ( 1125) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 GLU cc_start: 0.8453 (mt-10) cc_final: 0.7838 (mt-10) REVERT: B 131 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7898 (mt-10) REVERT: C 130 LEU cc_start: 0.8818 (tp) cc_final: 0.8204 (tp) REVERT: C 131 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7463 (mm-30) REVERT: D 128 LEU cc_start: 0.8694 (tt) cc_final: 0.8168 (mp) REVERT: D 131 GLU cc_start: 0.8330 (mt-10) cc_final: 0.7970 (mt-10) REVERT: D 199 ARG cc_start: 0.8092 (mtm180) cc_final: 0.7724 (mtm180) REVERT: D 270 TYR cc_start: 0.8356 (m-80) cc_final: 0.8142 (m-80) REVERT: E 128 LEU cc_start: 0.8634 (tt) cc_final: 0.8025 (mp) REVERT: E 199 ARG cc_start: 0.8070 (mtm180) cc_final: 0.7800 (mtm180) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.1048 time to fit residues: 23.0192 Evaluate side-chains 110 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 148 optimal weight: 20.0000 chunk 89 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 147 optimal weight: 20.0000 chunk 70 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 64 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.112135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.089604 restraints weight = 42353.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.092607 restraints weight = 25385.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.094601 restraints weight = 18060.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.095811 restraints weight = 14373.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.096779 restraints weight = 12346.142| |-----------------------------------------------------------------------------| r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12825 Z= 0.125 Angle : 0.640 8.572 17480 Z= 0.328 Chirality : 0.046 0.141 1940 Planarity : 0.004 0.043 2230 Dihedral : 6.133 20.495 1680 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.36 (0.19), residues: 1520 helix: -1.80 (0.25), residues: 345 sheet: -2.15 (0.22), residues: 430 loop : -2.43 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 91 TYR 0.021 0.002 TYR A 270 PHE 0.026 0.002 PHE C 247 TRP 0.010 0.001 TRP B 161 HIS 0.002 0.001 HIS D 177 Details of bonding type rmsd covalent geometry : bond 0.00280 (12825) covalent geometry : angle 0.63956 (17480) hydrogen bonds : bond 0.03426 ( 335) hydrogen bonds : angle 6.61759 ( 1125) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 GLU cc_start: 0.8299 (mt-10) cc_final: 0.8052 (mm-30) REVERT: B 131 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7871 (mt-10) REVERT: B 199 ARG cc_start: 0.8040 (mtm180) cc_final: 0.7277 (mtm180) REVERT: C 131 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7665 (mm-30) REVERT: C 199 ARG cc_start: 0.8012 (mtm180) cc_final: 0.7272 (mtm180) REVERT: D 128 LEU cc_start: 0.8633 (tt) cc_final: 0.8115 (mp) REVERT: D 131 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7899 (mt-10) REVERT: D 199 ARG cc_start: 0.8121 (mtm180) cc_final: 0.7166 (mtm180) REVERT: D 270 TYR cc_start: 0.8353 (m-80) cc_final: 0.8050 (m-80) REVERT: E 128 LEU cc_start: 0.8542 (tt) cc_final: 0.7935 (mp) REVERT: E 131 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7577 (mm-30) REVERT: E 199 ARG cc_start: 0.8057 (mtm180) cc_final: 0.7792 (mtm180) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.0990 time to fit residues: 22.8601 Evaluate side-chains 117 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 93 optimal weight: 0.9980 chunk 29 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 62 optimal weight: 9.9990 chunk 142 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 143 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 chunk 137 optimal weight: 10.0000 chunk 103 optimal weight: 7.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.108271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.085696 restraints weight = 43131.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.088444 restraints weight = 26255.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.090178 restraints weight = 19043.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.091456 restraints weight = 15450.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.092152 restraints weight = 13327.532| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 12825 Z= 0.222 Angle : 0.709 8.120 17480 Z= 0.370 Chirality : 0.047 0.149 1940 Planarity : 0.005 0.044 2230 Dihedral : 6.402 21.901 1680 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % 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 aren not related in a simple way. whole: -3.24 (0.20), residues: 1520 helix: -1.72 (0.25), residues: 360 sheet: -2.19 (0.22), residues: 430 loop : -2.26 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 199 TYR 0.021 0.002 TYR D 102 PHE 0.030 0.002 PHE E 274 TRP 0.011 0.001 TRP B 220 HIS 0.007 0.002 HIS D 177 Details of bonding type rmsd covalent geometry : bond 0.00485 (12825) covalent geometry : angle 0.70884 (17480) hydrogen bonds : bond 0.03940 ( 335) hydrogen bonds : angle 6.66906 ( 1125) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 131 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7996 (mt-10) REVERT: C 131 GLU cc_start: 0.8310 (mm-30) cc_final: 0.7700 (mm-30) REVERT: D 131 GLU cc_start: 0.8389 (mt-10) cc_final: 0.7965 (mt-10) REVERT: D 270 TYR cc_start: 0.8534 (m-80) cc_final: 0.8256 (m-80) REVERT: E 131 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7853 (mm-30) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.0967 time to fit residues: 21.3081 Evaluate side-chains 111 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 71 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 chunk 142 optimal weight: 5.9990 chunk 91 optimal weight: 8.9990 chunk 72 optimal weight: 0.8980 chunk 110 optimal weight: 0.7980 chunk 130 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 36 optimal weight: 0.0270 chunk 53 optimal weight: 4.9990 overall best weight: 1.5442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** 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 = 0.4033 r_free = 0.4033 target = 0.111461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.088638 restraints weight = 42333.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.091622 restraints weight = 25168.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.093649 restraints weight = 17866.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.094910 restraints weight = 14184.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.095736 restraints weight = 12164.267| |-----------------------------------------------------------------------------| r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12825 Z= 0.134 Angle : 0.645 8.261 17480 Z= 0.331 Chirality : 0.046 0.140 1940 Planarity : 0.004 0.040 2230 Dihedral : 6.074 20.912 1680 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % 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 aren not related in a simple way. whole: -2.97 (0.20), residues: 1520 helix: -1.12 (0.28), residues: 330 sheet: -2.06 (0.22), residues: 430 loop : -2.27 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 199 TYR 0.022 0.001 TYR A 270 PHE 0.036 0.002 PHE A 274 TRP 0.015 0.001 TRP B 161 HIS 0.003 0.001 HIS B 177 Details of bonding type rmsd covalent geometry : bond 0.00302 (12825) covalent geometry : angle 0.64544 (17480) hydrogen bonds : bond 0.03332 ( 335) hydrogen bonds : angle 6.45318 ( 1125) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7648 (mt-10) REVERT: A 239 MET cc_start: 0.8894 (mmm) cc_final: 0.8687 (mmm) REVERT: C 131 GLU cc_start: 0.8310 (mm-30) cc_final: 0.7696 (mm-30) REVERT: C 199 ARG cc_start: 0.8000 (mtm180) cc_final: 0.7728 (mtm180) REVERT: D 131 GLU cc_start: 0.8318 (mt-10) cc_final: 0.7874 (mt-10) REVERT: D 270 TYR cc_start: 0.8583 (m-80) cc_final: 0.8329 (m-80) REVERT: E 128 LEU cc_start: 0.8632 (tt) cc_final: 0.8023 (mp) REVERT: E 131 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7765 (mm-30) REVERT: E 270 TYR cc_start: 0.8682 (m-80) cc_final: 0.8457 (m-80) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.1017 time to fit residues: 23.6712 Evaluate side-chains 119 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 77 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 chunk 13 optimal weight: 0.3980 chunk 52 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 67 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 146 optimal weight: 6.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 146 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.113163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.090437 restraints weight = 41540.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.093421 restraints weight = 24983.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.095482 restraints weight = 17807.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.096811 restraints weight = 14083.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.097715 restraints weight = 12026.448| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12825 Z= 0.122 Angle : 0.639 8.129 17480 Z= 0.326 Chirality : 0.046 0.137 1940 Planarity : 0.004 0.039 2230 Dihedral : 5.855 20.678 1680 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % 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 aren not related in a simple way. whole: -2.76 (0.20), residues: 1520 helix: -0.99 (0.28), residues: 355 sheet: -1.95 (0.22), residues: 430 loop : -2.12 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 286 TYR 0.028 0.002 TYR E 270 PHE 0.041 0.002 PHE E 274 TRP 0.009 0.001 TRP B 220 HIS 0.013 0.001 HIS D 177 Details of bonding type rmsd covalent geometry : bond 0.00281 (12825) covalent geometry : angle 0.63871 (17480) hydrogen bonds : bond 0.03184 ( 335) hydrogen bonds : angle 6.22653 ( 1125) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7737 (mt-10) REVERT: B 131 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7299 (mt-10) REVERT: C 131 GLU cc_start: 0.8282 (mm-30) cc_final: 0.7641 (mm-30) REVERT: D 131 GLU cc_start: 0.8313 (mt-10) cc_final: 0.8025 (mt-10) REVERT: D 199 ARG cc_start: 0.7829 (mtm180) cc_final: 0.7523 (mtm180) REVERT: D 270 TYR cc_start: 0.8467 (m-80) cc_final: 0.8203 (m-80) REVERT: E 49 LYS cc_start: 0.8018 (pptt) cc_final: 0.7688 (tptt) REVERT: E 128 LEU cc_start: 0.8556 (tt) cc_final: 0.7933 (mp) REVERT: E 131 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7526 (mm-30) REVERT: E 239 MET cc_start: 0.8701 (mmm) cc_final: 0.8498 (mmm) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.1015 time to fit residues: 23.5768 Evaluate side-chains 120 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 71 optimal weight: 5.9990 chunk 109 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 59 optimal weight: 6.9990 chunk 90 optimal weight: 10.0000 chunk 104 optimal weight: 9.9990 chunk 127 optimal weight: 9.9990 chunk 119 optimal weight: 0.5980 chunk 54 optimal weight: 0.9980 overall best weight: 4.3186 ------------------------------------------------------------------------------- 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 = 0.3982 r_free = 0.3982 target = 0.108510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.085583 restraints weight = 42945.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.088334 restraints weight = 26185.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.090199 restraints weight = 19042.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.091289 restraints weight = 15375.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.092134 restraints weight = 13411.357| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12825 Z= 0.242 Angle : 0.741 7.746 17480 Z= 0.386 Chirality : 0.047 0.152 1940 Planarity : 0.005 0.046 2230 Dihedral : 6.299 22.188 1680 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 17.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % 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 aren not related in a simple way. whole: -2.86 (0.20), residues: 1520 helix: -1.21 (0.28), residues: 330 sheet: -2.01 (0.22), residues: 430 loop : -2.09 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 255 TYR 0.024 0.002 TYR B 270 PHE 0.022 0.002 PHE C 208 TRP 0.013 0.002 TRP B 220 HIS 0.012 0.002 HIS D 177 Details of bonding type rmsd covalent geometry : bond 0.00533 (12825) covalent geometry : angle 0.74145 (17480) hydrogen bonds : bond 0.03871 ( 335) hydrogen bonds : angle 6.58167 ( 1125) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7756 (mt-10) REVERT: B 131 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7370 (mt-10) REVERT: C 131 GLU cc_start: 0.8444 (mm-30) cc_final: 0.7781 (mm-30) REVERT: D 131 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8058 (mt-10) REVERT: E 131 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7513 (mm-30) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.1043 time to fit residues: 21.9208 Evaluate side-chains 113 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 88 optimal weight: 0.0170 chunk 96 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 68 optimal weight: 6.9990 chunk 105 optimal weight: 9.9990 chunk 92 optimal weight: 8.9990 chunk 43 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 79 optimal weight: 9.9990 chunk 140 optimal weight: 7.9990 chunk 50 optimal weight: 0.7980 overall best weight: 2.3624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 151 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.110621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.087949 restraints weight = 42284.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.090818 restraints weight = 25475.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.092742 restraints weight = 18348.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.093999 restraints weight = 14667.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.094887 restraints weight = 12582.783| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12825 Z= 0.162 Angle : 0.685 7.977 17480 Z= 0.351 Chirality : 0.047 0.155 1940 Planarity : 0.004 0.043 2230 Dihedral : 6.103 21.509 1680 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.80 (0.20), residues: 1520 helix: -1.04 (0.28), residues: 330 sheet: -1.95 (0.22), residues: 425 loop : -2.13 (0.22), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 255 TYR 0.023 0.002 TYR A 270 PHE 0.046 0.002 PHE C 274 TRP 0.012 0.001 TRP B 161 HIS 0.011 0.002 HIS D 177 Details of bonding type rmsd covalent geometry : bond 0.00363 (12825) covalent geometry : angle 0.68457 (17480) hydrogen bonds : bond 0.03449 ( 335) hydrogen bonds : angle 6.49132 ( 1125) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7683 (mt-10) REVERT: B 131 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7366 (mt-10) REVERT: C 131 GLU cc_start: 0.8467 (mm-30) cc_final: 0.8009 (mm-30) REVERT: D 131 GLU cc_start: 0.8376 (mt-10) cc_final: 0.7998 (mt-10) REVERT: E 128 LEU cc_start: 0.8556 (tt) cc_final: 0.7961 (mp) REVERT: E 131 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7553 (mm-30) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.1014 time to fit residues: 21.8587 Evaluate side-chains 118 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 102 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 67 optimal weight: 8.9990 chunk 57 optimal weight: 9.9990 chunk 119 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 130 optimal weight: 0.3980 chunk 56 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 105 optimal weight: 9.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.109418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.086755 restraints weight = 42579.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.089556 restraints weight = 25852.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.091404 restraints weight = 18634.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.092613 restraints weight = 14980.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.093482 restraints weight = 12933.072| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12825 Z= 0.198 Angle : 0.718 10.024 17480 Z= 0.369 Chirality : 0.047 0.145 1940 Planarity : 0.004 0.043 2230 Dihedral : 6.197 21.529 1680 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % 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 aren not related in a simple way. whole: -2.66 (0.21), residues: 1520 helix: -0.85 (0.29), residues: 325 sheet: -1.98 (0.22), residues: 425 loop : -2.00 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 255 TYR 0.020 0.002 TYR C 270 PHE 0.022 0.002 PHE C 247 TRP 0.011 0.001 TRP B 220 HIS 0.011 0.002 HIS D 177 Details of bonding type rmsd covalent geometry : bond 0.00442 (12825) covalent geometry : angle 0.71795 (17480) hydrogen bonds : bond 0.03630 ( 335) hydrogen bonds : angle 6.53124 ( 1125) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1990.05 seconds wall clock time: 35 minutes 17.23 seconds (2117.23 seconds total)