Starting phenix.real_space_refine on Thu Aug 6 20:30:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10my_75296/08_2026/10my_75296_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/10my_75296/08_2026/10my_75296.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/10my_75296/08_2026/10my_75296.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10my_75296/08_2026/10my_75296.map" model { file = "/net/cci-nas-00/data/ceres_data/10my_75296/08_2026/10my_75296_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10my_75296/08_2026/10my_75296_neut.cif" } resolution = 3.44 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.013 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 84 5.16 5 C 10314 2.51 5 N 3027 2.21 5 O 3111 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16536 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2754 Classifications: {'peptide': 350} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 341} Chain: "B" Number of atoms: 2758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2758 Classifications: {'peptide': 351} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 342} Chain: "C" Number of atoms: 2754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2754 Classifications: {'peptide': 350} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 341} Chain: "D" Number of atoms: 2758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2758 Classifications: {'peptide': 351} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 342} Chain: "E" Number of atoms: 2754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2754 Classifications: {'peptide': 350} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 341} Chain: "F" Number of atoms: 2758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2758 Classifications: {'peptide': 351} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 342} Time building chain proxies: 3.76, per 1000 atoms: 0.23 Number of scatterers: 16536 At special positions: 0 Unit cell: (136.906, 131.516, 83.006, 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 84 16.00 O 3111 8.00 N 3027 7.00 C 10314 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.42 Conformation dependent library (CDL) restraints added in 703.3 milliseconds 4182 Ramachandran restraints generated. 2091 Oldfield, 0 Emsley, 2091 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3936 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 12 sheets defined 48.0% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 2 through 13 removed outlier: 4.173A pdb=" N TYR A 6 " --> pdb=" O GLU A 2 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU A 11 " --> pdb=" O LEU A 7 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N THR A 12 " --> pdb=" O ASP A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 54 Processing helix chain 'A' and resid 55 through 65 removed outlier: 4.001A pdb=" N GLU A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.895A pdb=" N LEU A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 119 removed outlier: 4.065A pdb=" N ASN A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 147 removed outlier: 3.531A pdb=" N MET A 138 " --> pdb=" O LYS A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 191 removed outlier: 3.539A pdb=" N ALA A 186 " --> pdb=" O SER A 182 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 194 No H-bonds generated for 'chain 'A' and resid 192 through 194' Processing helix chain 'A' and resid 206 through 219 removed outlier: 3.674A pdb=" N GLY A 219 " --> pdb=" O PHE A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 241 removed outlier: 3.559A pdb=" N LEU A 239 " --> pdb=" O LEU A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 257 removed outlier: 3.708A pdb=" N LEU A 252 " --> pdb=" O GLU A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 295 removed outlier: 3.560A pdb=" N LEU A 291 " --> pdb=" O ARG A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 307 removed outlier: 4.062A pdb=" N ALA A 305 " --> pdb=" O LYS A 301 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 325 removed outlier: 3.743A pdb=" N ASP A 325 " --> pdb=" O GLN A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 336 Processing helix chain 'A' and resid 339 through 350 removed outlier: 3.740A pdb=" N LEU A 343 " --> pdb=" O SER A 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 1 through 14 removed outlier: 4.139A pdb=" N GLN B 5 " --> pdb=" O GLY B 1 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 54 Processing helix chain 'B' and resid 58 through 65 Processing helix chain 'B' and resid 103 through 108 Processing helix chain 'B' and resid 110 through 118 removed outlier: 3.979A pdb=" N GLN B 114 " --> pdb=" O PRO B 110 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE B 118 " --> pdb=" O GLN B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 147 Processing helix chain 'B' and resid 182 through 194 removed outlier: 3.707A pdb=" N ALA B 186 " --> pdb=" O SER B 182 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ARG B 192 " --> pdb=" O LYS B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 219 Processing helix chain 'B' and resid 230 through 241 removed outlier: 3.530A pdb=" N LEU B 241 " --> pdb=" O ARG B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 257 removed outlier: 4.094A pdb=" N GLU B 248 " --> pdb=" O LYS B 244 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N GLN B 249 " --> pdb=" O GLU B 245 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU B 252 " --> pdb=" O GLU B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 294 Processing helix chain 'B' and resid 296 through 298 No H-bonds generated for 'chain 'B' and resid 296 through 298' Processing helix chain 'B' and resid 299 through 307 removed outlier: 3.531A pdb=" N SER B 307 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 325 Processing helix chain 'B' and resid 329 through 335 Processing helix chain 'B' and resid 339 through 350 removed outlier: 3.801A pdb=" N LEU B 343 " --> pdb=" O SER B 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 13 removed outlier: 4.171A pdb=" N TYR C 6 " --> pdb=" O GLU C 2 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU C 11 " --> pdb=" O LEU C 7 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N THR C 12 " --> pdb=" O ASP C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 54 removed outlier: 3.513A pdb=" N VAL C 46 " --> pdb=" O SER C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 65 removed outlier: 3.833A pdb=" N GLU C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 119 removed outlier: 4.045A pdb=" N ASN C 115 " --> pdb=" O GLU C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 147 Processing helix chain 'C' and resid 182 through 191 removed outlier: 3.546A pdb=" N ALA C 186 " --> pdb=" O SER C 182 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU C 191 " --> pdb=" O LEU C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 194 No H-bonds generated for 'chain 'C' and resid 192 through 194' Processing helix chain 'C' and resid 206 through 219 removed outlier: 3.638A pdb=" N GLY C 219 " --> pdb=" O PHE C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 241 Processing helix chain 'C' and resid 246 through 257 removed outlier: 3.671A pdb=" N LEU C 252 " --> pdb=" O GLU C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 295 removed outlier: 3.555A pdb=" N LEU C 291 " --> pdb=" O ARG C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 307 removed outlier: 4.031A pdb=" N ALA C 305 " --> pdb=" O LYS C 301 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG C 306 " --> pdb=" O ALA C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 325 removed outlier: 3.678A pdb=" N ASP C 325 " --> pdb=" O GLN C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 336 Processing helix chain 'C' and resid 339 through 350 removed outlier: 3.716A pdb=" N LEU C 343 " --> pdb=" O SER C 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 1 through 14 removed outlier: 4.156A pdb=" N GLN D 5 " --> pdb=" O GLY D 1 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 52 Processing helix chain 'D' and resid 58 through 65 Processing helix chain 'D' and resid 103 through 108 Processing helix chain 'D' and resid 110 through 118 removed outlier: 3.988A pdb=" N GLN D 114 " --> pdb=" O PRO D 110 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE D 118 " --> pdb=" O GLN D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 147 Processing helix chain 'D' and resid 182 through 194 removed outlier: 3.708A pdb=" N ALA D 186 " --> pdb=" O SER D 182 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU D 191 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ARG D 192 " --> pdb=" O LYS D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 219 Processing helix chain 'D' and resid 230 through 240 Processing helix chain 'D' and resid 243 through 257 removed outlier: 4.090A pdb=" N GLU D 248 " --> pdb=" O LYS D 244 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N GLN D 249 " --> pdb=" O GLU D 245 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU D 252 " --> pdb=" O GLU D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 294 Processing helix chain 'D' and resid 296 through 298 No H-bonds generated for 'chain 'D' and resid 296 through 298' Processing helix chain 'D' and resid 299 through 307 removed outlier: 3.537A pdb=" N SER D 307 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 325 Processing helix chain 'D' and resid 329 through 335 Processing helix chain 'D' and resid 339 through 350 removed outlier: 3.800A pdb=" N LEU D 343 " --> pdb=" O SER D 339 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 13 removed outlier: 4.176A pdb=" N TYR E 6 " --> pdb=" O GLU E 2 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LEU E 11 " --> pdb=" O LEU E 7 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N THR E 12 " --> pdb=" O ASP E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 54 removed outlier: 3.509A pdb=" N VAL E 46 " --> pdb=" O SER E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 65 removed outlier: 3.999A pdb=" N GLU E 61 " --> pdb=" O ALA E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 108 removed outlier: 3.896A pdb=" N LEU E 107 " --> pdb=" O THR E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 119 removed outlier: 4.053A pdb=" N ASN E 115 " --> pdb=" O GLU E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 147 removed outlier: 3.523A pdb=" N MET E 138 " --> pdb=" O LYS E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 191 removed outlier: 3.551A pdb=" N ALA E 186 " --> pdb=" O SER E 182 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU E 191 " --> pdb=" O LEU E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 194 No H-bonds generated for 'chain 'E' and resid 192 through 194' Processing helix chain 'E' and resid 206 through 219 removed outlier: 3.614A pdb=" N GLY E 219 " --> pdb=" O PHE E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 241 removed outlier: 3.551A pdb=" N LEU E 239 " --> pdb=" O LEU E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 256 removed outlier: 3.697A pdb=" N LEU E 252 " --> pdb=" O GLU E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 295 removed outlier: 3.551A pdb=" N LEU E 291 " --> pdb=" O ARG E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 305 removed outlier: 4.146A pdb=" N ALA E 305 " --> pdb=" O LYS E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 325 removed outlier: 3.707A pdb=" N ASP E 325 " --> pdb=" O GLN E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 336 Processing helix chain 'E' and resid 339 through 350 removed outlier: 3.765A pdb=" N LEU E 343 " --> pdb=" O SER E 339 " (cutoff:3.500A) Processing helix chain 'F' and resid 1 through 14 removed outlier: 4.236A pdb=" N GLN F 5 " --> pdb=" O GLY F 1 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 53 Processing helix chain 'F' and resid 58 through 65 Processing helix chain 'F' and resid 103 through 108 Processing helix chain 'F' and resid 110 through 118 removed outlier: 4.001A pdb=" N GLN F 114 " --> pdb=" O PRO F 110 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN F 115 " --> pdb=" O GLU F 111 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE F 118 " --> pdb=" O GLN F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 147 Processing helix chain 'F' and resid 182 through 194 removed outlier: 3.712A pdb=" N ALA F 186 " --> pdb=" O SER F 182 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU F 191 " --> pdb=" O LEU F 187 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ARG F 192 " --> pdb=" O LYS F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 219 Processing helix chain 'F' and resid 230 through 240 Processing helix chain 'F' and resid 243 through 257 removed outlier: 4.088A pdb=" N GLU F 248 " --> pdb=" O LYS F 244 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N GLN F 249 " --> pdb=" O GLU F 245 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU F 252 " --> pdb=" O GLU F 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 285 through 294 Processing helix chain 'F' and resid 296 through 298 No H-bonds generated for 'chain 'F' and resid 296 through 298' Processing helix chain 'F' and resid 299 through 307 removed outlier: 3.514A pdb=" N SER F 307 " --> pdb=" O THR F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 325 Processing helix chain 'F' and resid 329 through 335 Processing helix chain 'F' and resid 339 through 350 removed outlier: 3.797A pdb=" N LEU F 343 " --> pdb=" O SER F 339 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS F 350 " --> pdb=" O MET F 346 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 37 removed outlier: 3.583A pdb=" N LEU A 27 " --> pdb=" O TYR A 19 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP A 17 " --> pdb=" O ARG A 29 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N VAL A 93 " --> pdb=" O SER A 82 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ARG A 78 " --> pdb=" O ILE A 97 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 171 through 175 removed outlier: 3.517A pdb=" N GLU A 157 " --> pdb=" O ARG A 174 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU A 154 " --> pdb=" O MET A 197 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE A 198 " --> pdb=" O MET A 223 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N THR A 225 " --> pdb=" O ILE A 198 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE A 200 " --> pdb=" O THR A 225 " (cutoff:3.500A) removed outlier: 8.830A pdb=" N HIS A 227 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N VAL A 124 " --> pdb=" O ALA A 224 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N LEU A 226 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N VAL A 126 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N LEU A 123 " --> pdb=" O LEU A 258 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 33 through 35 removed outlier: 3.855A pdb=" N ASP B 17 " --> pdb=" O ARG B 29 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA B 68 " --> pdb=" O ALA B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 170 through 175 removed outlier: 6.375A pdb=" N ILE B 153 " --> pdb=" O THR B 172 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ARG B 174 " --> pdb=" O ILE B 153 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N THR B 155 " --> pdb=" O ARG B 174 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE B 198 " --> pdb=" O MET B 223 " (cutoff:3.500A) removed outlier: 8.648A pdb=" N THR B 225 " --> pdb=" O ILE B 198 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N ILE B 200 " --> pdb=" O THR B 225 " (cutoff:3.500A) removed outlier: 10.065A pdb=" N HIS B 227 " --> pdb=" O ILE B 200 " (cutoff:3.500A) removed outlier: 11.292A pdb=" N GLU B 202 " --> pdb=" O HIS B 227 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA B 224 " --> pdb=" O VAL B 124 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU B 226 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LEU B 123 " --> pdb=" O LYS B 259 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL B 261 " --> pdb=" O LEU B 123 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LEU B 125 " --> pdb=" O VAL B 261 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ALA B 263 " --> pdb=" O LEU B 125 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL B 127 " --> pdb=" O ALA B 263 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N GLN B 265 " --> pdb=" O VAL B 127 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 33 through 37 removed outlier: 3.581A pdb=" N LEU C 27 " --> pdb=" O TYR C 19 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP C 17 " --> pdb=" O ARG C 29 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL C 93 " --> pdb=" O SER C 82 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ARG C 78 " --> pdb=" O ILE C 97 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 171 through 175 removed outlier: 3.515A pdb=" N GLU C 157 " --> pdb=" O ARG C 174 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU C 154 " --> pdb=" O MET C 197 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N VAL C 124 " --> pdb=" O ALA C 224 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N LEU C 226 " --> pdb=" O VAL C 124 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N VAL C 126 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N LEU C 123 " --> pdb=" O LEU C 258 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 33 through 35 removed outlier: 3.807A pdb=" N ASP D 17 " --> pdb=" O ARG D 29 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA D 68 " --> pdb=" O ALA D 83 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 170 through 175 removed outlier: 6.372A pdb=" N ILE D 153 " --> pdb=" O THR D 172 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N ARG D 174 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N THR D 155 " --> pdb=" O ARG D 174 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR D 225 " --> pdb=" O ILE D 200 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N GLU D 202 " --> pdb=" O THR D 225 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N HIS D 227 " --> pdb=" O GLU D 202 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA D 224 " --> pdb=" O VAL D 124 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU D 226 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LEU D 123 " --> pdb=" O LYS D 259 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N VAL D 261 " --> pdb=" O LEU D 123 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU D 125 " --> pdb=" O VAL D 261 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N ALA D 263 " --> pdb=" O LEU D 125 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL D 127 " --> pdb=" O ALA D 263 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLN D 265 " --> pdb=" O VAL D 127 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 33 through 37 removed outlier: 3.588A pdb=" N LEU E 27 " --> pdb=" O TYR E 19 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP E 17 " --> pdb=" O ARG E 29 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N VAL E 93 " --> pdb=" O SER E 82 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ARG E 78 " --> pdb=" O ILE E 97 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 171 through 175 removed outlier: 3.501A pdb=" N GLU E 157 " --> pdb=" O ARG E 174 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU E 154 " --> pdb=" O MET E 197 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE E 198 " --> pdb=" O MET E 223 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N THR E 225 " --> pdb=" O ILE E 198 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE E 200 " --> pdb=" O THR E 225 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N HIS E 227 " --> pdb=" O ILE E 200 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N VAL E 124 " --> pdb=" O ALA E 224 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N LEU E 226 " --> pdb=" O VAL E 124 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N VAL E 126 " --> pdb=" O LEU E 226 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N LEU E 123 " --> pdb=" O LEU E 258 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 33 through 35 removed outlier: 3.809A pdb=" N ASP F 17 " --> pdb=" O ARG F 29 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA F 68 " --> pdb=" O ALA F 83 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 170 through 175 removed outlier: 6.393A pdb=" N ILE F 153 " --> pdb=" O THR F 172 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N ARG F 174 " --> pdb=" O ILE F 153 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N THR F 155 " --> pdb=" O ARG F 174 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ILE F 198 " --> pdb=" O MET F 223 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N THR F 225 " --> pdb=" O ILE F 198 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N ILE F 200 " --> pdb=" O THR F 225 " (cutoff:3.500A) removed outlier: 10.115A pdb=" N HIS F 227 " --> pdb=" O ILE F 200 " (cutoff:3.500A) removed outlier: 11.306A pdb=" N GLU F 202 " --> pdb=" O HIS F 227 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA F 224 " --> pdb=" O VAL F 124 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU F 226 " --> pdb=" O VAL F 126 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LEU F 123 " --> pdb=" O LYS F 259 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N VAL F 261 " --> pdb=" O LEU F 123 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU F 125 " --> pdb=" O VAL F 261 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N ALA F 263 " --> pdb=" O LEU F 125 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL F 127 " --> pdb=" O ALA F 263 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLN F 265 " --> pdb=" O VAL F 127 " (cutoff:3.500A) 803 hydrogen bonds defined for protein. 2319 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.59 Time building geometry restraints manager: 1.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5784 1.34 - 1.46: 2623 1.46 - 1.58: 8195 1.58 - 1.69: 0 1.69 - 1.81: 156 Bond restraints: 16758 Sorted by residual: bond pdb=" N LYS F 108 " pdb=" CA LYS F 108 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.29e-02 6.01e+03 1.12e+00 bond pdb=" N LYS D 108 " pdb=" CA LYS D 108 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.29e-02 6.01e+03 1.10e+00 bond pdb=" N LYS B 108 " pdb=" CA LYS B 108 " ideal model delta sigma weight residual 1.457 1.471 -0.013 1.29e-02 6.01e+03 1.07e+00 bond pdb=" CA ILE F 328 " pdb=" CB ILE F 328 " ideal model delta sigma weight residual 1.550 1.541 0.010 1.03e-02 9.43e+03 9.41e-01 bond pdb=" CA ILE B 26 " pdb=" CB ILE B 26 " ideal model delta sigma weight residual 1.530 1.540 -0.010 1.05e-02 9.07e+03 9.04e-01 ... (remaining 16753 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.22: 21857 1.22 - 2.45: 598 2.45 - 3.67: 109 3.67 - 4.89: 15 4.89 - 6.12: 8 Bond angle restraints: 22587 Sorted by residual: angle pdb=" N VAL F 310 " pdb=" CA VAL F 310 " pdb=" C VAL F 310 " ideal model delta sigma weight residual 112.98 109.46 3.52 1.25e+00 6.40e-01 7.92e+00 angle pdb=" N VAL B 310 " pdb=" CA VAL B 310 " pdb=" C VAL B 310 " ideal model delta sigma weight residual 112.98 109.54 3.44 1.25e+00 6.40e-01 7.57e+00 angle pdb=" N VAL D 310 " pdb=" CA VAL D 310 " pdb=" C VAL D 310 " ideal model delta sigma weight residual 112.98 109.55 3.43 1.25e+00 6.40e-01 7.51e+00 angle pdb=" C GLY E 272 " pdb=" N LYS E 273 " pdb=" CA LYS E 273 " ideal model delta sigma weight residual 121.54 126.62 -5.08 1.91e+00 2.74e-01 7.07e+00 angle pdb=" C GLY A 272 " pdb=" N LYS A 273 " pdb=" CA LYS A 273 " ideal model delta sigma weight residual 121.54 126.59 -5.05 1.91e+00 2.74e-01 7.00e+00 ... (remaining 22582 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.95: 8998 16.95 - 33.90: 1015 33.90 - 50.84: 258 50.84 - 67.79: 31 67.79 - 84.74: 15 Dihedral angle restraints: 10317 sinusoidal: 4242 harmonic: 6075 Sorted by residual: dihedral pdb=" CA ASP E 75 " pdb=" C ASP E 75 " pdb=" N SER E 76 " pdb=" CA SER E 76 " ideal model delta harmonic sigma weight residual 180.00 162.93 17.07 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA ASP C 75 " pdb=" C ASP C 75 " pdb=" N SER C 76 " pdb=" CA SER C 76 " ideal model delta harmonic sigma weight residual 180.00 163.02 16.98 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA ASP A 75 " pdb=" C ASP A 75 " pdb=" N SER A 76 " pdb=" CA SER A 76 " ideal model delta harmonic sigma weight residual 180.00 163.07 16.93 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 10314 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1973 0.037 - 0.073: 435 0.073 - 0.110: 133 0.110 - 0.147: 60 0.147 - 0.183: 3 Chirality restraints: 2604 Sorted by residual: chirality pdb=" CB ILE A 203 " pdb=" CA ILE A 203 " pdb=" CG1 ILE A 203 " pdb=" CG2 ILE A 203 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.40e-01 chirality pdb=" CB ILE E 203 " pdb=" CA ILE E 203 " pdb=" CG1 ILE E 203 " pdb=" CG2 ILE E 203 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 7.07e-01 chirality pdb=" CB ILE C 203 " pdb=" CA ILE C 203 " pdb=" CG1 ILE C 203 " pdb=" CG2 ILE C 203 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 6.95e-01 ... (remaining 2601 not shown) Planarity restraints: 2961 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL F 242 " -0.023 5.00e-02 4.00e+02 3.51e-02 1.97e+00 pdb=" N PRO F 243 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO F 243 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO F 243 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 242 " 0.023 5.00e-02 4.00e+02 3.50e-02 1.96e+00 pdb=" N PRO B 243 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 243 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 243 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 242 " 0.023 5.00e-02 4.00e+02 3.49e-02 1.95e+00 pdb=" N PRO D 243 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO D 243 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 243 " 0.019 5.00e-02 4.00e+02 ... (remaining 2958 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1592 2.75 - 3.29: 16037 3.29 - 3.82: 26683 3.82 - 4.36: 31229 4.36 - 4.90: 54291 Nonbonded interactions: 129832 Sorted by model distance: nonbonded pdb=" O THR C 214 " pdb=" OG1 THR C 218 " model vdw 2.210 3.040 nonbonded pdb=" O THR E 214 " pdb=" OG1 THR E 218 " model vdw 2.212 3.040 nonbonded pdb=" O GLY F 201 " pdb=" OG1 THR F 225 " model vdw 2.217 3.040 nonbonded pdb=" OG SER A 82 " pdb=" OE1 GLN F 193 " model vdw 2.228 3.040 nonbonded pdb=" OE1 GLN D 193 " pdb=" OG SER E 82 " model vdw 2.235 3.040 ... (remaining 129827 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 1 through 350) selection = chain 'C' selection = (chain 'D' and resid 1 through 350) selection = chain 'E' selection = (chain 'F' and resid 1 through 350) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.780 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: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 15.370 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.040 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16758 Z= 0.101 Angle : 0.494 6.117 22587 Z= 0.286 Chirality : 0.038 0.183 2604 Planarity : 0.003 0.035 2961 Dihedral : 15.103 84.739 6381 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.17 % Allowed : 4.48 % Favored : 95.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.19), residues: 2091 helix: 0.53 (0.17), residues: 948 sheet: 0.81 (0.25), residues: 465 loop : -1.41 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 204 TYR 0.005 0.001 TYR D 28 PHE 0.008 0.001 PHE B 62 HIS 0.005 0.000 HIS B 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00180 / 0.10 (16758) covalent geometry : angle 0.49416 / 0.29 (22587) hydrogen bonds : bond 0.17059 / 11.32 ( 803) hydrogen bonds : angle 5.64961 / 3.97 ( 2319) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4182 Ramachandran restraints generated. 2091 Oldfield, 0 Emsley, 2091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4182 Ramachandran restraints generated. 2091 Oldfield, 0 Emsley, 2091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 138 time to evaluate : 0.660 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 MET cc_start: 0.9338 (mmp) cc_final: 0.8694 (mmm) REVERT: B 320 TYR cc_start: 0.9400 (t80) cc_final: 0.8778 (t80) REVERT: B 346 MET cc_start: 0.9406 (ptp) cc_final: 0.9052 (ptp) REVERT: D 320 TYR cc_start: 0.9410 (t80) cc_final: 0.8818 (t80) REVERT: D 346 MET cc_start: 0.9402 (ptp) cc_final: 0.9061 (ptp) REVERT: E 304 MET cc_start: 0.9123 (mmp) cc_final: 0.8565 (mmm) REVERT: F 320 TYR cc_start: 0.9713 (t80) cc_final: 0.9165 (t80) REVERT: F 346 MET cc_start: 0.9683 (ppp) cc_final: 0.9208 (ppp) outliers start: 3 outliers final: 3 residues processed: 141 average time/residue: 0.1449 time to fit residues: 29.5690 Evaluate side-chains 116 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 113 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain C residue 217 GLU Chi-restraints excluded: chain E residue 217 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 7.9990 chunk 200 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 HIS B 148 HIS C 148 HIS D 148 HIS E 148 HIS F 148 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.065800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.045346 restraints weight = 66031.237| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 4.42 r_work: 0.2658 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16758 Z= 0.193 Angle : 0.550 7.469 22587 Z= 0.291 Chirality : 0.040 0.143 2604 Planarity : 0.004 0.054 2961 Dihedral : 4.085 33.560 2316 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 1.47 % Allowed : 10.37 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.19), residues: 2091 helix: 0.78 (0.18), residues: 978 sheet: 1.00 (0.25), residues: 474 loop : -1.43 (0.23), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 206 TYR 0.014 0.002 TYR F 19 PHE 0.010 0.001 PHE F 85 HIS 0.007 0.001 HIS A 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.19 (16758) covalent geometry : angle 0.54971 / 0.29 (22587) hydrogen bonds : bond 0.03716 / 2.52 ( 803) hydrogen bonds : angle 4.35689 / 3.05 ( 2319) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4182 Ramachandran restraints generated. 2091 Oldfield, 0 Emsley, 2091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4182 Ramachandran restraints generated. 2091 Oldfield, 0 Emsley, 2091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 0.660 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 213 MET cc_start: 0.9322 (tpp) cc_final: 0.9036 (tpp) REVERT: A 304 MET cc_start: 0.9337 (mmp) cc_final: 0.8782 (mmp) REVERT: B 320 TYR cc_start: 0.9370 (t80) cc_final: 0.8809 (t80) REVERT: B 346 MET cc_start: 0.9363 (ptp) cc_final: 0.9022 (ptp) REVERT: C 61 GLU cc_start: 0.9471 (pt0) cc_final: 0.9236 (pp20) REVERT: C 314 THR cc_start: 0.8633 (OUTLIER) cc_final: 0.8360 (p) REVERT: D 312 MET cc_start: 0.8319 (ttm) cc_final: 0.8110 (ttm) REVERT: D 320 TYR cc_start: 0.9405 (t80) cc_final: 0.8845 (t80) REVERT: D 346 MET cc_start: 0.9379 (ptp) cc_final: 0.9037 (ptp) REVERT: E 213 MET cc_start: 0.9107 (tpp) cc_final: 0.8740 (tpp) REVERT: E 334 LEU cc_start: 0.9553 (OUTLIER) cc_final: 0.9352 (mm) REVERT: F 320 TYR cc_start: 0.9740 (t80) cc_final: 0.9075 (t80) REVERT: F 346 MET cc_start: 0.9702 (ppp) cc_final: 0.9217 (ppp) outliers start: 26 outliers final: 9 residues processed: 126 average time/residue: 0.1313 time to fit residues: 25.4826 Evaluate side-chains 111 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 298 HIS Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 268 ARG Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain D residue 298 HIS Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 334 LEU Chi-restraints excluded: chain F residue 223 MET Chi-restraints excluded: chain F residue 227 HIS Chi-restraints excluded: chain F residue 298 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 178 optimal weight: 3.9990 chunk 142 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 184 optimal weight: 0.7980 chunk 141 optimal weight: 0.9990 chunk 166 optimal weight: 5.9990 chunk 134 optimal weight: 0.0770 chunk 164 optimal weight: 0.7980 chunk 116 optimal weight: 2.9990 chunk 197 optimal weight: 3.9990 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 257 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.066042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.045688 restraints weight = 65888.769| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 4.44 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16758 Z= 0.115 Angle : 0.502 13.116 22587 Z= 0.260 Chirality : 0.039 0.137 2604 Planarity : 0.003 0.058 2961 Dihedral : 3.748 18.936 2307 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 1.70 % Allowed : 13.10 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.19), residues: 2091 helix: 0.95 (0.17), residues: 981 sheet: 0.96 (0.25), residues: 468 loop : -1.49 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 206 TYR 0.007 0.001 TYR A 28 PHE 0.007 0.001 PHE B 85 HIS 0.006 0.001 HIS A 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (16758) covalent geometry : angle 0.50186 / 0.26 (22587) hydrogen bonds : bond 0.03052 / 2.09 ( 803) hydrogen bonds : angle 3.98644 / 2.81 ( 2319) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4182 Ramachandran restraints generated. 2091 Oldfield, 0 Emsley, 2091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4182 Ramachandran restraints generated. 2091 Oldfield, 0 Emsley, 2091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 107 time to evaluate : 0.662 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: symmetry clash REVERT: A 138 MET cc_start: 0.8987 (mmp) cc_final: 0.8674 (mmm) REVERT: A 197 MET cc_start: 0.8730 (tmm) cc_final: 0.8444 (tmm) REVERT: A 213 MET cc_start: 0.9054 (tpp) cc_final: 0.8732 (tpp) REVERT: A 312 MET cc_start: 0.8024 (mmp) cc_final: 0.7658 (mmp) REVERT: A 314 THR cc_start: 0.8217 (OUTLIER) cc_final: 0.7853 (p) REVERT: B 320 TYR cc_start: 0.9349 (t80) cc_final: 0.8732 (t80) REVERT: B 346 MET cc_start: 0.9324 (ptp) cc_final: 0.8937 (ptp) REVERT: C 197 MET cc_start: 0.8785 (tmm) cc_final: 0.8358 (tmm) REVERT: C 314 THR cc_start: 0.8509 (OUTLIER) cc_final: 0.8212 (p) REVERT: D 193 GLN cc_start: 0.8600 (OUTLIER) cc_final: 0.7934 (mp10) REVERT: E 304 MET cc_start: 0.9093 (mmp) cc_final: 0.8611 (mmm) REVERT: F 56 ASP cc_start: 0.9074 (m-30) cc_final: 0.8533 (m-30) REVERT: F 193 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.8022 (mp10) REVERT: F 320 TYR cc_start: 0.9722 (t80) cc_final: 0.9200 (t80) outliers start: 30 outliers final: 12 residues processed: 130 average time/residue: 0.1233 time to fit residues: 25.2721 Evaluate side-chains 117 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain B residue 193 GLN Chi-restraints excluded: chain B residue 298 HIS Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 223 MET Chi-restraints excluded: chain D residue 298 HIS Chi-restraints excluded: chain F residue 193 GLN Chi-restraints excluded: chain F residue 223 MET Chi-restraints excluded: chain F residue 227 HIS Chi-restraints excluded: chain F residue 298 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 126 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 186 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 166 optimal weight: 6.9990 chunk 152 optimal weight: 0.7980 chunk 119 optimal weight: 0.7980 chunk 207 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 146 ASN A 193 GLN C 193 GLN E 146 ASN E 193 GLN F 166 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.063270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.042767 restraints weight = 66921.961| |-----------------------------------------------------------------------------| r_work (start): 0.2774 rms_B_bonded: 4.41 r_work: 0.2606 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 16758 Z= 0.237 Angle : 0.580 10.649 22587 Z= 0.304 Chirality : 0.040 0.141 2604 Planarity : 0.004 0.051 2961 Dihedral : 4.058 18.713 2307 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 2.10 % Allowed : 13.32 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.19), residues: 2091 helix: 0.90 (0.17), residues: 996 sheet: 0.84 (0.25), residues: 474 loop : -1.66 (0.23), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 145 TYR 0.017 0.002 TYR F 19 PHE 0.012 0.002 PHE C 279 HIS 0.005 0.001 HIS A 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.24 (16758) covalent geometry : angle 0.58010 / 0.30 (22587) hydrogen bonds : bond 0.03647 / 2.48 ( 803) hydrogen bonds : angle 4.30500 / 3.01 ( 2319) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4182 Ramachandran restraints generated. 2091 Oldfield, 0 Emsley, 2091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4182 Ramachandran restraints generated. 2091 Oldfield, 0 Emsley, 2091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 101 time to evaluate : 0.678 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 MET cc_start: 0.9297 (mmp) cc_final: 0.9087 (mmm) REVERT: A 213 MET cc_start: 0.9233 (tpp) cc_final: 0.8962 (tpp) REVERT: A 304 MET cc_start: 0.9157 (mmp) cc_final: 0.8707 (mmp) REVERT: A 314 THR cc_start: 0.8402 (OUTLIER) cc_final: 0.7974 (p) REVERT: B 193 GLN cc_start: 0.9128 (OUTLIER) cc_final: 0.8310 (mp10) REVERT: B 320 TYR cc_start: 0.9350 (t80) cc_final: 0.8772 (t80) REVERT: B 346 MET cc_start: 0.9319 (ptp) cc_final: 0.8949 (ptp) REVERT: C 197 MET cc_start: 0.9316 (tmm) cc_final: 0.8900 (tmm) REVERT: E 213 MET cc_start: 0.8988 (tpp) cc_final: 0.8675 (tpp) REVERT: F 320 TYR cc_start: 0.9734 (t80) cc_final: 0.9236 (t80) outliers start: 37 outliers final: 18 residues processed: 125 average time/residue: 0.1278 time to fit residues: 24.8363 Evaluate side-chains 118 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain B residue 193 GLN Chi-restraints excluded: chain B residue 298 HIS Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 85 PHE Chi-restraints excluded: chain C residue 268 ARG Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 298 HIS Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 193 GLN Chi-restraints excluded: chain F residue 223 MET Chi-restraints excluded: chain F residue 298 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 129 optimal weight: 6.9990 chunk 139 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 183 optimal weight: 1.9990 chunk 197 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 132 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 chunk 128 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 195 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 37 GLN F 166 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.064004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.043712 restraints weight = 66021.638| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 4.39 r_work: 0.2620 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16758 Z= 0.133 Angle : 0.534 11.903 22587 Z= 0.274 Chirality : 0.040 0.146 2604 Planarity : 0.003 0.045 2961 Dihedral : 3.889 19.142 2307 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.76 % Allowed : 15.02 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.19), residues: 2091 helix: 0.97 (0.17), residues: 999 sheet: 0.84 (0.25), residues: 468 loop : -1.66 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 145 TYR 0.008 0.001 TYR F 19 PHE 0.006 0.001 PHE A 279 HIS 0.005 0.001 HIS A 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (16758) covalent geometry : angle 0.53441 / 0.27 (22587) hydrogen bonds : bond 0.03040 / 2.08 ( 803) hydrogen bonds : angle 4.02069 / 2.83 ( 2319) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4182 Ramachandran restraints generated. 2091 Oldfield, 0 Emsley, 2091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4182 Ramachandran restraints generated. 2091 Oldfield, 0 Emsley, 2091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 103 time to evaluate : 0.793 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: symmetry clash REVERT: A 138 MET cc_start: 0.9254 (mmp) cc_final: 0.9023 (mmm) REVERT: A 197 MET cc_start: 0.9447 (tmm) cc_final: 0.8910 (tmm) REVERT: A 213 MET cc_start: 0.9235 (tpp) cc_final: 0.8992 (tpp) REVERT: A 304 MET cc_start: 0.9257 (mmp) cc_final: 0.8672 (mmp) REVERT: A 312 MET cc_start: 0.7724 (mmp) cc_final: 0.7416 (mmp) REVERT: A 314 THR cc_start: 0.8164 (OUTLIER) cc_final: 0.7754 (p) REVERT: B 320 TYR cc_start: 0.9330 (t80) cc_final: 0.8768 (t80) REVERT: B 346 MET cc_start: 0.9304 (ptp) cc_final: 0.8945 (ptp) REVERT: C 197 MET cc_start: 0.9337 (tmm) cc_final: 0.8954 (tmm) REVERT: C 240 HIS cc_start: 0.9556 (m90) cc_final: 0.9310 (m-70) REVERT: D 320 TYR cc_start: 0.9619 (t80) cc_final: 0.9343 (t80) REVERT: D 346 MET cc_start: 0.9412 (ptp) cc_final: 0.9196 (ptp) REVERT: E 213 MET cc_start: 0.8941 (tpp) cc_final: 0.8688 (tpp) REVERT: E 314 THR cc_start: 0.8231 (OUTLIER) cc_final: 0.7885 (p) REVERT: F 320 TYR cc_start: 0.9738 (t80) cc_final: 0.9045 (t80) REVERT: F 346 MET cc_start: 0.9706 (ppp) cc_final: 0.9067 (ppp) outliers start: 31 outliers final: 17 residues processed: 128 average time/residue: 0.1403 time to fit residues: 27.5311 Evaluate side-chains 116 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain B residue 193 GLN Chi-restraints excluded: chain B residue 298 HIS Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 85 PHE Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 268 ARG Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 223 MET Chi-restraints excluded: chain D residue 298 HIS Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 85 PHE Chi-restraints excluded: chain E residue 204 ARG Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain F residue 193 GLN Chi-restraints excluded: chain F residue 223 MET Chi-restraints excluded: chain F residue 298 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 135 optimal weight: 0.8980 chunk 169 optimal weight: 6.9990 chunk 185 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 172 optimal weight: 0.0040 chunk 69 optimal weight: 0.0870 chunk 91 optimal weight: 0.6980 chunk 84 optimal weight: 0.9990 chunk 108 optimal weight: 0.2980 chunk 143 optimal weight: 1.9990 overall best weight: 0.3970 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.064973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.044689 restraints weight = 65828.025| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 4.44 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 16758 Z= 0.098 Angle : 0.523 12.452 22587 Z= 0.267 Chirality : 0.040 0.300 2604 Planarity : 0.003 0.038 2961 Dihedral : 3.770 18.893 2307 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 1.36 % Allowed : 16.10 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.19), residues: 2091 helix: 1.11 (0.17), residues: 978 sheet: 0.84 (0.25), residues: 468 loop : -1.54 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 268 TYR 0.005 0.001 TYR F 19 PHE 0.006 0.001 PHE A 279 HIS 0.004 0.000 HIS A 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 (16758) covalent geometry : angle 0.52334 / 0.27 (22587) hydrogen bonds : bond 0.02712 / 1.86 ( 803) hydrogen bonds : angle 3.88805 / 2.74 ( 2319) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4182 Ramachandran restraints generated. 2091 Oldfield, 0 Emsley, 2091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4182 Ramachandran restraints generated. 2091 Oldfield, 0 Emsley, 2091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 104 time to evaluate : 0.759 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 138 MET cc_start: 0.9015 (mmp) cc_final: 0.8748 (mmm) REVERT: A 197 MET cc_start: 0.9120 (tmm) cc_final: 0.8870 (tmm) REVERT: A 213 MET cc_start: 0.8984 (tpp) cc_final: 0.8680 (tpp) REVERT: A 304 MET cc_start: 0.9290 (mmp) cc_final: 0.8827 (mmp) REVERT: A 312 MET cc_start: 0.7849 (mmp) cc_final: 0.7470 (mmp) REVERT: A 314 THR cc_start: 0.8173 (OUTLIER) cc_final: 0.7772 (p) REVERT: B 320 TYR cc_start: 0.9311 (t80) cc_final: 0.8693 (t80) REVERT: B 346 MET cc_start: 0.9276 (ptp) cc_final: 0.8847 (ptp) REVERT: C 197 MET cc_start: 0.8751 (tmm) cc_final: 0.8432 (tmm) REVERT: C 240 HIS cc_start: 0.9411 (m90) cc_final: 0.9197 (m-70) REVERT: D 56 ASP cc_start: 0.9050 (m-30) cc_final: 0.8622 (m-30) REVERT: D 320 TYR cc_start: 0.9570 (t80) cc_final: 0.9295 (t80) REVERT: E 197 MET cc_start: 0.9171 (tmm) cc_final: 0.8831 (tmm) REVERT: E 213 MET cc_start: 0.8555 (tpp) cc_final: 0.8282 (tpp) REVERT: E 314 THR cc_start: 0.8148 (OUTLIER) cc_final: 0.7787 (p) REVERT: F 320 TYR cc_start: 0.9745 (t80) cc_final: 0.9070 (t80) REVERT: F 346 MET cc_start: 0.9701 (ppp) cc_final: 0.9027 (ppp) outliers start: 24 outliers final: 16 residues processed: 121 average time/residue: 0.1265 time to fit residues: 24.2743 Evaluate side-chains 118 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain B residue 193 GLN Chi-restraints excluded: chain B residue 298 HIS Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 85 PHE Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 223 MET Chi-restraints excluded: chain D residue 298 HIS Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 85 PHE Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain F residue 193 GLN Chi-restraints excluded: chain F residue 223 MET Chi-restraints excluded: chain F residue 298 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 187 optimal weight: 3.9990 chunk 166 optimal weight: 6.9990 chunk 154 optimal weight: 0.9990 chunk 102 optimal weight: 0.6980 chunk 68 optimal weight: 5.9990 chunk 201 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 131 optimal weight: 5.9990 chunk 170 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 166 HIS F 166 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.064203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.044006 restraints weight = 65432.123| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 4.39 r_work: 0.2631 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16758 Z= 0.136 Angle : 0.562 14.876 22587 Z= 0.281 Chirality : 0.040 0.173 2604 Planarity : 0.003 0.035 2961 Dihedral : 3.800 18.663 2307 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.59 % Allowed : 16.50 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.19), residues: 2091 helix: 1.11 (0.18), residues: 978 sheet: 0.83 (0.25), residues: 468 loop : -1.49 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 145 TYR 0.009 0.001 TYR F 19 PHE 0.007 0.001 PHE A 279 HIS 0.004 0.000 HIS A 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (16758) covalent geometry : angle 0.56211 / 0.28 (22587) hydrogen bonds : bond 0.02949 / 2.03 ( 803) hydrogen bonds : angle 3.98300 / 2.79 ( 2319) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4182 Ramachandran restraints generated. 2091 Oldfield, 0 Emsley, 2091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4182 Ramachandran restraints generated. 2091 Oldfield, 0 Emsley, 2091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 102 time to evaluate : 0.653 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: symmetry clash revert: symmetry clash REVERT: A 138 MET cc_start: 0.9282 (mmp) cc_final: 0.9067 (mmm) REVERT: A 213 MET cc_start: 0.9193 (tpp) cc_final: 0.8955 (tpp) REVERT: A 304 MET cc_start: 0.9184 (mmp) cc_final: 0.8930 (mmp) REVERT: A 312 MET cc_start: 0.8040 (mmp) cc_final: 0.7493 (mmp) REVERT: A 314 THR cc_start: 0.8269 (OUTLIER) cc_final: 0.7883 (p) REVERT: B 320 TYR cc_start: 0.9367 (t80) cc_final: 0.8781 (t80) REVERT: B 346 MET cc_start: 0.9290 (ptp) cc_final: 0.8890 (ptp) REVERT: C 197 MET cc_start: 0.9315 (tmm) cc_final: 0.8920 (tmm) REVERT: C 202 GLU cc_start: 0.8183 (tp30) cc_final: 0.7980 (tp30) REVERT: C 240 HIS cc_start: 0.9550 (m90) cc_final: 0.9306 (m-70) REVERT: C 304 MET cc_start: 0.9130 (mmt) cc_final: 0.8490 (mmt) REVERT: E 61 GLU cc_start: 0.9086 (OUTLIER) cc_final: 0.8816 (pm20) REVERT: E 197 MET cc_start: 0.9422 (tmm) cc_final: 0.9121 (tmm) REVERT: E 314 THR cc_start: 0.8196 (OUTLIER) cc_final: 0.7857 (p) REVERT: E 320 TYR cc_start: 0.9390 (t80) cc_final: 0.8896 (t80) REVERT: F 320 TYR cc_start: 0.9763 (t80) cc_final: 0.9108 (t80) REVERT: F 346 MET cc_start: 0.9706 (ppp) cc_final: 0.9089 (ppp) outliers start: 28 outliers final: 19 residues processed: 123 average time/residue: 0.1256 time to fit residues: 24.0064 Evaluate side-chains 122 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain B residue 193 GLN Chi-restraints excluded: chain B residue 298 HIS Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 85 PHE Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 268 ARG Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 223 MET Chi-restraints excluded: chain D residue 298 HIS Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 85 PHE Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain F residue 193 GLN Chi-restraints excluded: chain F residue 223 MET Chi-restraints excluded: chain F residue 298 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 199 optimal weight: 4.9990 chunk 77 optimal weight: 0.0770 chunk 150 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 194 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 169 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 chunk 208 optimal weight: 9.9990 chunk 70 optimal weight: 2.9990 chunk 68 optimal weight: 9.9990 overall best weight: 1.0940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 284 ASN D 37 GLN F 166 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.063507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.043328 restraints weight = 65869.015| |-----------------------------------------------------------------------------| r_work (start): 0.2782 rms_B_bonded: 4.39 r_work: 0.2611 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 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 : 0.004 0.040 16758 Z= 0.161 Angle : 0.589 13.115 22587 Z= 0.294 Chirality : 0.040 0.196 2604 Planarity : 0.003 0.035 2961 Dihedral : 3.909 18.612 2307 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.36 % Allowed : 17.46 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.19), residues: 2091 helix: 1.04 (0.17), residues: 993 sheet: 0.80 (0.25), residues: 468 loop : -1.58 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 293 TYR 0.010 0.001 TYR F 19 PHE 0.008 0.001 PHE A 279 HIS 0.004 0.001 HIS A 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (16758) covalent geometry : angle 0.58895 / 0.29 (22587) hydrogen bonds : bond 0.03109 / 2.14 ( 803) hydrogen bonds : angle 4.10215 / 2.88 ( 2319) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4182 Ramachandran restraints generated. 2091 Oldfield, 0 Emsley, 2091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4182 Ramachandran restraints generated. 2091 Oldfield, 0 Emsley, 2091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 0.635 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: symmetry clash REVERT: A 138 MET cc_start: 0.9283 (mmp) cc_final: 0.9081 (mmm) REVERT: A 213 MET cc_start: 0.9148 (tpp) cc_final: 0.8902 (tpp) REVERT: A 304 MET cc_start: 0.9204 (mmp) cc_final: 0.8920 (mmp) REVERT: A 312 MET cc_start: 0.8138 (mmp) cc_final: 0.7690 (mmp) REVERT: A 314 THR cc_start: 0.8305 (OUTLIER) cc_final: 0.7916 (p) REVERT: A 335 HIS cc_start: 0.9360 (m90) cc_final: 0.9024 (m-70) REVERT: B 320 TYR cc_start: 0.9343 (t80) cc_final: 0.8740 (t80) REVERT: B 346 MET cc_start: 0.9262 (ptp) cc_final: 0.8853 (ptp) REVERT: C 197 MET cc_start: 0.9310 (tmm) cc_final: 0.8998 (tmm) REVERT: C 240 HIS cc_start: 0.9544 (m90) cc_final: 0.9300 (m-70) REVERT: C 304 MET cc_start: 0.9144 (mmt) cc_final: 0.8539 (mmt) REVERT: D 346 MET cc_start: 0.9174 (ptt) cc_final: 0.8770 (ptt) REVERT: E 197 MET cc_start: 0.9437 (tmm) cc_final: 0.9113 (tmm) REVERT: E 213 MET cc_start: 0.8778 (tpp) cc_final: 0.8412 (tpp) REVERT: E 304 MET cc_start: 0.9195 (mmp) cc_final: 0.8765 (mmp) REVERT: E 314 THR cc_start: 0.8317 (OUTLIER) cc_final: 0.7898 (p) REVERT: F 320 TYR cc_start: 0.9760 (t80) cc_final: 0.9095 (t80) REVERT: F 346 MET cc_start: 0.9709 (ppp) cc_final: 0.9066 (ppp) outliers start: 24 outliers final: 18 residues processed: 120 average time/residue: 0.1197 time to fit residues: 22.1897 Evaluate side-chains 121 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain B residue 193 GLN Chi-restraints excluded: chain B residue 298 HIS Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 85 PHE Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 268 ARG Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 298 HIS Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 85 PHE Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain F residue 193 GLN Chi-restraints excluded: chain F residue 223 MET Chi-restraints excluded: chain F residue 298 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 12 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 170 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 181 optimal weight: 0.6980 chunk 79 optimal weight: 0.4980 chunk 139 optimal weight: 7.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 37 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.063911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.043711 restraints weight = 65692.292| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 4.42 r_work: 0.2640 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16758 Z= 0.128 Angle : 0.585 13.544 22587 Z= 0.290 Chirality : 0.040 0.187 2604 Planarity : 0.003 0.031 2961 Dihedral : 3.860 18.940 2307 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.36 % Allowed : 17.80 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.19), residues: 2091 helix: 1.08 (0.17), residues: 978 sheet: 0.79 (0.25), residues: 468 loop : -1.46 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 344 TYR 0.008 0.001 TYR D 320 PHE 0.006 0.001 PHE A 279 HIS 0.004 0.000 HIS A 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (16758) covalent geometry : angle 0.58526 / 0.29 (22587) hydrogen bonds : bond 0.02951 / 2.03 ( 803) hydrogen bonds : angle 4.04860 / 2.84 ( 2319) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4182 Ramachandran restraints generated. 2091 Oldfield, 0 Emsley, 2091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4182 Ramachandran restraints generated. 2091 Oldfield, 0 Emsley, 2091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 0.571 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 MET cc_start: 0.9273 (mmp) cc_final: 0.9065 (mmm) REVERT: A 213 MET cc_start: 0.9151 (tpp) cc_final: 0.8907 (tpp) REVERT: A 304 MET cc_start: 0.9197 (mmp) cc_final: 0.8914 (mmp) REVERT: A 312 MET cc_start: 0.8199 (mmp) cc_final: 0.7742 (mmp) REVERT: A 314 THR cc_start: 0.8301 (OUTLIER) cc_final: 0.7910 (p) REVERT: A 320 TYR cc_start: 0.9362 (t80) cc_final: 0.8992 (t80) REVERT: A 335 HIS cc_start: 0.9342 (m90) cc_final: 0.9004 (m-70) REVERT: B 320 TYR cc_start: 0.9351 (t80) cc_final: 0.8752 (t80) REVERT: B 346 MET cc_start: 0.9256 (ptp) cc_final: 0.8814 (ptp) REVERT: C 197 MET cc_start: 0.9312 (tmm) cc_final: 0.9028 (tmm) REVERT: C 240 HIS cc_start: 0.9556 (m90) cc_final: 0.9291 (m-70) REVERT: C 304 MET cc_start: 0.9140 (mmt) cc_final: 0.8511 (mmt) REVERT: E 213 MET cc_start: 0.8739 (tpp) cc_final: 0.8407 (tpp) REVERT: E 314 THR cc_start: 0.8231 (OUTLIER) cc_final: 0.7877 (p) REVERT: E 320 TYR cc_start: 0.9575 (t80) cc_final: 0.9097 (t80) REVERT: F 320 TYR cc_start: 0.9769 (t80) cc_final: 0.9134 (t80) REVERT: F 346 MET cc_start: 0.9700 (ppp) cc_final: 0.8977 (ppp) outliers start: 24 outliers final: 19 residues processed: 121 average time/residue: 0.1399 time to fit residues: 25.3728 Evaluate side-chains 122 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain B residue 193 GLN Chi-restraints excluded: chain B residue 298 HIS Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 85 PHE Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 268 ARG Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 298 HIS Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 85 PHE Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 204 ARG Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain F residue 193 GLN Chi-restraints excluded: chain F residue 223 MET Chi-restraints excluded: chain F residue 298 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 180 optimal weight: 0.0670 chunk 189 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 18 optimal weight: 0.2980 chunk 28 optimal weight: 0.8980 chunk 170 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 185 optimal weight: 1.9990 chunk 158 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 166 HIS F 166 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.064339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.044074 restraints weight = 65381.889| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 4.45 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16758 Z= 0.115 Angle : 0.592 13.587 22587 Z= 0.291 Chirality : 0.040 0.197 2604 Planarity : 0.003 0.030 2961 Dihedral : 3.806 18.845 2307 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.25 % Allowed : 17.86 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.19), residues: 2091 helix: 1.00 (0.17), residues: 990 sheet: 0.78 (0.25), residues: 468 loop : -1.59 (0.23), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 145 TYR 0.009 0.001 TYR D 320 PHE 0.005 0.001 PHE A 279 HIS 0.004 0.000 HIS A 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (16758) covalent geometry : angle 0.59183 / 0.29 (22587) hydrogen bonds : bond 0.02848 / 1.96 ( 803) hydrogen bonds : angle 4.04501 / 2.84 ( 2319) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4182 Ramachandran restraints generated. 2091 Oldfield, 0 Emsley, 2091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4182 Ramachandran restraints generated. 2091 Oldfield, 0 Emsley, 2091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.626 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: symmetry clash revert: symmetry clash REVERT: A 138 MET cc_start: 0.9019 (mmp) cc_final: 0.8748 (mmm) REVERT: A 197 MET cc_start: 0.9060 (tmm) cc_final: 0.8608 (tmm) REVERT: A 213 MET cc_start: 0.8902 (tpp) cc_final: 0.8642 (tpp) REVERT: A 304 MET cc_start: 0.9252 (mmp) cc_final: 0.9017 (mmp) REVERT: A 312 MET cc_start: 0.8157 (mmp) cc_final: 0.7735 (mmp) REVERT: A 314 THR cc_start: 0.8324 (OUTLIER) cc_final: 0.7929 (p) REVERT: A 320 TYR cc_start: 0.9211 (t80) cc_final: 0.8814 (t80) REVERT: B 320 TYR cc_start: 0.9304 (t80) cc_final: 0.8757 (t80) REVERT: B 346 MET cc_start: 0.9229 (ptp) cc_final: 0.8850 (ptp) REVERT: C 197 MET cc_start: 0.8714 (tmm) cc_final: 0.8413 (tmm) REVERT: C 240 HIS cc_start: 0.9383 (m90) cc_final: 0.9150 (m-70) REVERT: C 304 MET cc_start: 0.9161 (mmt) cc_final: 0.8573 (mmt) REVERT: D 346 MET cc_start: 0.9163 (ptt) cc_final: 0.8820 (ptt) REVERT: E 213 MET cc_start: 0.8315 (tpp) cc_final: 0.7980 (tpp) REVERT: E 314 THR cc_start: 0.8269 (OUTLIER) cc_final: 0.7892 (p) REVERT: E 320 TYR cc_start: 0.9472 (t80) cc_final: 0.9016 (t80) REVERT: F 320 TYR cc_start: 0.9747 (t80) cc_final: 0.9120 (t80) REVERT: F 346 MET cc_start: 0.9713 (ppp) cc_final: 0.9053 (ppp) outliers start: 22 outliers final: 17 residues processed: 119 average time/residue: 0.1262 time to fit residues: 22.9286 Evaluate side-chains 122 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain B residue 193 GLN Chi-restraints excluded: chain B residue 298 HIS Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 85 PHE Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 268 ARG Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 298 HIS Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 85 PHE Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain F residue 193 GLN Chi-restraints excluded: chain F residue 223 MET Chi-restraints excluded: chain F residue 298 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 29 optimal weight: 5.9990 chunk 168 optimal weight: 2.9990 chunk 195 optimal weight: 3.9990 chunk 188 optimal weight: 0.5980 chunk 177 optimal weight: 2.9990 chunk 169 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 162 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 335 HIS F 166 HIS F 284 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.062553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.042219 restraints weight = 66386.170| |-----------------------------------------------------------------------------| r_work (start): 0.2745 rms_B_bonded: 4.41 r_work: 0.2576 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 16758 Z= 0.233 Angle : 0.663 13.601 22587 Z= 0.332 Chirality : 0.041 0.181 2604 Planarity : 0.003 0.035 2961 Dihedral : 4.084 18.110 2307 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.19 % Allowed : 17.91 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.19), residues: 2091 helix: 0.84 (0.17), residues: 1005 sheet: 0.84 (0.26), residues: 432 loop : -1.82 (0.22), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 344 TYR 0.014 0.002 TYR F 19 PHE 0.009 0.001 PHE A 279 HIS 0.014 0.001 HIS E 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.23 (16758) covalent geometry : angle 0.66349 / 0.33 (22587) hydrogen bonds : bond 0.03437 / 2.35 ( 803) hydrogen bonds : angle 4.39198 / 3.07 ( 2319) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3179.73 seconds wall clock time: 55 minutes 30.10 seconds (3330.10 seconds total)