Starting phenix.real_space_refine on Fri Jul 3 03:25:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vx1_65405/07_2026/9vx1_65405.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vx1_65405/07_2026/9vx1_65405.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vx1_65405/07_2026/9vx1_65405.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vx1_65405/07_2026/9vx1_65405.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vx1_65405/07_2026/9vx1_65405.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vx1_65405/07_2026/9vx1_65405.map" } resolution = 2.77 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= 0.002 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 2 5.21 5 S 41 5.16 5 C 7304 2.51 5 N 2015 2.21 5 O 2198 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11572 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3819 Classifications: {'peptide': 485} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 26, 'TRANS': 458} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 1846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1846 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 215} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "Z" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 127 Classifications: {'RNA': 6} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 1, 'rna3p_pyr': 3} Link IDs: {'rna2p': 1, 'rna3p': 4} Chain: "D" Number of atoms: 3809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3809 Classifications: {'peptide': 483} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 26, 'TRANS': 456} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "E" Number of atoms: 1842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1842 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 11, 'TRANS': 217} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "a" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 127 Classifications: {'RNA': 6} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 1, 'rna3p_pyr': 3} Link IDs: {'rna2p': 1, 'rna3p': 4} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.84, per 1000 atoms: 0.25 Number of scatterers: 11572 At special positions: 0 Unit cell: (90.35, 125.45, 89.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 41 16.00 P 12 15.00 Mg 2 11.99 O 2198 8.00 N 2015 7.00 C 7304 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 518.8 milliseconds 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2642 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 16 sheets defined 36.0% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 16 through 18 No H-bonds generated for 'chain 'A' and resid 16 through 18' Processing helix chain 'A' and resid 23 through 32 removed outlier: 3.500A pdb=" N LEU A 28 " --> pdb=" O PRO A 24 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU A 30 " --> pdb=" O LEU A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 64 removed outlier: 3.815A pdb=" N GLU A 54 " --> pdb=" O SER A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 114 removed outlier: 3.607A pdb=" N LYS A 111 " --> pdb=" O SER A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 138 removed outlier: 3.615A pdb=" N GLY A 131 " --> pdb=" O ASP A 127 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU A 132 " --> pdb=" O GLU A 128 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA A 135 " --> pdb=" O GLY A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 164 removed outlier: 4.225A pdb=" N ARG A 157 " --> pdb=" O LYS A 153 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS A 162 " --> pdb=" O VAL A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 190 Processing helix chain 'A' and resid 201 through 206 removed outlier: 4.189A pdb=" N ILE A 205 " --> pdb=" O TRP A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 218 Processing helix chain 'A' and resid 225 through 243 removed outlier: 3.691A pdb=" N ASN A 232 " --> pdb=" O GLY A 228 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS A 240 " --> pdb=" O SER A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 328 removed outlier: 3.563A pdb=" N ILE A 316 " --> pdb=" O ALA A 312 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N HIS A 326 " --> pdb=" O ALA A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 358 removed outlier: 3.594A pdb=" N GLY A 349 " --> pdb=" O GLU A 345 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A 352 " --> pdb=" O ASP A 348 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU A 356 " --> pdb=" O ALA A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 440 removed outlier: 4.143A pdb=" N GLU A 437 " --> pdb=" O GLN A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 461 Processing helix chain 'A' and resid 462 through 470 removed outlier: 4.248A pdb=" N VAL A 468 " --> pdb=" O LYS A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 485 Processing helix chain 'B' and resid 185 through 195 removed outlier: 3.952A pdb=" N ILE B 190 " --> pdb=" O PRO B 186 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ALA B 191 " --> pdb=" O ARG B 187 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL B 192 " --> pdb=" O LYS B 188 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE B 193 " --> pdb=" O ALA B 189 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN B 195 " --> pdb=" O ALA B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 220 removed outlier: 3.774A pdb=" N SER B 220 " --> pdb=" O PRO B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 231 Processing helix chain 'B' and resid 236 through 241 removed outlier: 3.645A pdb=" N LEU B 241 " --> pdb=" O LYS B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 263 removed outlier: 3.954A pdb=" N ARG B 250 " --> pdb=" O ASP B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 360 removed outlier: 4.158A pdb=" N LEU B 358 " --> pdb=" O PHE B 354 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ALA B 360 " --> pdb=" O ALA B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 384 Processing helix chain 'D' and resid 16 through 18 No H-bonds generated for 'chain 'D' and resid 16 through 18' Processing helix chain 'D' and resid 23 through 32 removed outlier: 3.518A pdb=" N LEU D 28 " --> pdb=" O PRO D 24 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU D 30 " --> pdb=" O LEU D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 64 removed outlier: 3.811A pdb=" N GLU D 54 " --> pdb=" O SER D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 114 removed outlier: 3.702A pdb=" N LYS D 111 " --> pdb=" O SER D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 138 removed outlier: 3.645A pdb=" N VAL D 122 " --> pdb=" O HIS D 118 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA D 135 " --> pdb=" O GLY D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 164 removed outlier: 4.172A pdb=" N ARG D 157 " --> pdb=" O LYS D 153 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS D 162 " --> pdb=" O VAL D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 190 Processing helix chain 'D' and resid 201 through 206 removed outlier: 4.212A pdb=" N ILE D 205 " --> pdb=" O TRP D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 218 Processing helix chain 'D' and resid 225 through 243 removed outlier: 3.520A pdb=" N TRP D 231 " --> pdb=" O ALA D 227 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN D 232 " --> pdb=" O GLY D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 328 removed outlier: 3.615A pdb=" N ILE D 316 " --> pdb=" O ALA D 312 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N HIS D 326 " --> pdb=" O ALA D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 358 removed outlier: 3.512A pdb=" N ALA D 352 " --> pdb=" O ASP D 348 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA D 353 " --> pdb=" O GLY D 349 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU D 356 " --> pdb=" O ALA D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 440 removed outlier: 3.515A pdb=" N GLU D 436 " --> pdb=" O ALA D 432 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLU D 437 " --> pdb=" O GLN D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 461 Processing helix chain 'D' and resid 462 through 470 removed outlier: 4.292A pdb=" N VAL D 468 " --> pdb=" O LYS D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 481 through 485 Processing helix chain 'E' and resid 185 through 195 removed outlier: 3.768A pdb=" N ILE E 190 " --> pdb=" O PRO E 186 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ALA E 191 " --> pdb=" O ARG E 187 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL E 192 " --> pdb=" O LYS E 188 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE E 193 " --> pdb=" O ALA E 189 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN E 195 " --> pdb=" O ALA E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 220 removed outlier: 3.728A pdb=" N SER E 220 " --> pdb=" O PRO E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 231 removed outlier: 3.512A pdb=" N VAL E 231 " --> pdb=" O ILE E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 241 removed outlier: 3.772A pdb=" N LEU E 241 " --> pdb=" O LYS E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 263 removed outlier: 3.940A pdb=" N ARG E 250 " --> pdb=" O ASP E 246 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN E 257 " --> pdb=" O HIS E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 355 through 361 removed outlier: 3.618A pdb=" N ALA E 360 " --> pdb=" O ALA E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 384 removed outlier: 3.910A pdb=" N LEU E 371 " --> pdb=" O LYS E 367 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7 removed outlier: 4.195A pdb=" N GLU A 4 " --> pdb=" O ASP A 391 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR A 388 " --> pdb=" O TYR A 399 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N CYS A 259 " --> pdb=" O PHE A 335 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N LEU A 337 " --> pdb=" O CYS A 259 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL A 261 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N PHE A 275 " --> pdb=" O ARG A 295 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ARG A 295 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N SER A 277 " --> pdb=" O GLY A 293 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 20 through 21 Processing sheet with id=AA3, first strand: chain 'A' and resid 93 through 103 removed outlier: 4.138A pdb=" N GLU A 97 " --> pdb=" O ILE A 44 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL A 46 " --> pdb=" O GLU A 97 " (cutoff:3.500A) removed outlier: 9.278A pdb=" N GLY A 99 " --> pdb=" O VAL A 46 " (cutoff:3.500A) removed outlier: 12.062A pdb=" N GLY A 48 " --> pdb=" O GLY A 99 " (cutoff:3.500A) removed outlier: 9.465A pdb=" N THR A 101 " --> pdb=" O GLY A 48 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N VAL A 145 " --> pdb=" O VAL A 41 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LYS A 43 " --> pdb=" O VAL A 145 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ILE A 147 " --> pdb=" O LYS A 43 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N GLY A 45 " --> pdb=" O ILE A 147 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ALA A 149 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N VAL A 47 " --> pdb=" O ALA A 149 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 297 through 298 Processing sheet with id=AA5, first strand: chain 'A' and resid 376 through 377 Processing sheet with id=AA6, first strand: chain 'B' and resid 168 through 170 removed outlier: 3.668A pdb=" N THR B 339 " --> pdb=" O SER B 324 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N HIS B 321 " --> pdb=" O PHE B 278 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 168 through 170 removed outlier: 3.668A pdb=" N THR B 339 " --> pdb=" O SER B 324 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N VAL B 302 " --> pdb=" O HIS B 321 " (cutoff:3.500A) removed outlier: 13.578A pdb=" N PHE B 323 " --> pdb=" O ALA B 300 " (cutoff:3.500A) removed outlier: 17.387A pdb=" N ALA B 300 " --> pdb=" O PHE B 323 " (cutoff:3.500A) removed outlier: 26.382A pdb=" N THR B 298 " --> pdb=" O PRO B 325 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N ASP B 299 " --> pdb=" O TYR B 291 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N TYR B 291 " --> pdb=" O ASP B 299 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ASN B 301 " --> pdb=" O PHE B 289 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N PHE B 289 " --> pdb=" O ASN B 301 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL B 303 " --> pdb=" O ARG B 287 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 204 through 206 Processing sheet with id=AA9, first strand: chain 'D' and resid 4 through 7 removed outlier: 4.316A pdb=" N GLU D 4 " --> pdb=" O ASP D 391 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N CYS D 259 " --> pdb=" O PHE D 335 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N LEU D 337 " --> pdb=" O CYS D 259 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL D 261 " --> pdb=" O LEU D 337 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N PHE D 275 " --> pdb=" O ARG D 295 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ARG D 295 " --> pdb=" O PHE D 275 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N SER D 277 " --> pdb=" O GLY D 293 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 20 through 21 Processing sheet with id=AB2, first strand: chain 'D' and resid 93 through 103 removed outlier: 4.136A pdb=" N GLU D 97 " --> pdb=" O ILE D 44 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL D 46 " --> pdb=" O GLU D 97 " (cutoff:3.500A) removed outlier: 9.352A pdb=" N GLY D 99 " --> pdb=" O VAL D 46 " (cutoff:3.500A) removed outlier: 12.097A pdb=" N GLY D 48 " --> pdb=" O GLY D 99 " (cutoff:3.500A) removed outlier: 9.544A pdb=" N THR D 101 " --> pdb=" O GLY D 48 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N VAL D 145 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LYS D 43 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N ILE D 147 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N GLY D 45 " --> pdb=" O ILE D 147 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ALA D 149 " --> pdb=" O GLY D 45 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL D 47 " --> pdb=" O ALA D 149 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 297 through 298 Processing sheet with id=AB4, first strand: chain 'D' and resid 376 through 377 Processing sheet with id=AB5, first strand: chain 'E' and resid 168 through 170 removed outlier: 3.576A pdb=" N THR E 339 " --> pdb=" O SER E 324 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N VAL E 302 " --> pdb=" O HIS E 321 " (cutoff:3.500A) removed outlier: 13.715A pdb=" N PHE E 323 " --> pdb=" O ALA E 300 " (cutoff:3.500A) removed outlier: 17.482A pdb=" N ALA E 300 " --> pdb=" O PHE E 323 " (cutoff:3.500A) removed outlier: 26.225A pdb=" N THR E 298 " --> pdb=" O PRO E 325 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N ASP E 299 " --> pdb=" O TYR E 291 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N TYR E 291 " --> pdb=" O ASP E 299 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N ASN E 301 " --> pdb=" O PHE E 289 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N PHE E 289 " --> pdb=" O ASN E 301 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 204 through 206 Processing sheet with id=AB7, first strand: chain 'E' and resid 267 through 270 451 hydrogen bonds defined for protein. 1266 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.96 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2544 1.33 - 1.45: 2742 1.45 - 1.56: 6488 1.56 - 1.68: 22 1.68 - 1.80: 74 Bond restraints: 11870 Sorted by residual: bond pdb=" N PRO E 351 " pdb=" CD PRO E 351 " ideal model delta sigma weight residual 1.473 1.557 -0.084 1.40e-02 5.10e+03 3.58e+01 bond pdb=" N PRO B 351 " pdb=" CD PRO B 351 " ideal model delta sigma weight residual 1.473 1.551 -0.078 1.40e-02 5.10e+03 3.09e+01 bond pdb=" N9 A a 1 " pdb=" C4 A a 1 " ideal model delta sigma weight residual 1.374 1.351 0.023 6.00e-03 2.78e+04 1.47e+01 bond pdb=" N9 A Z 1 " pdb=" C4 A Z 1 " ideal model delta sigma weight residual 1.374 1.351 0.023 6.00e-03 2.78e+04 1.45e+01 bond pdb=" CA MET E 330 " pdb=" CB MET E 330 " ideal model delta sigma weight residual 1.526 1.481 0.045 1.49e-02 4.50e+03 9.14e+00 ... (remaining 11865 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 15366 1.87 - 3.75: 646 3.75 - 5.62: 86 5.62 - 7.49: 16 7.49 - 9.36: 11 Bond angle restraints: 16125 Sorted by residual: angle pdb=" C1' G a 6 " pdb=" N9 G a 6 " pdb=" C4 G a 6 " ideal model delta sigma weight residual 126.50 132.32 -5.82 1.30e+00 5.92e-01 2.00e+01 angle pdb=" C1' G Z 6 " pdb=" N9 G Z 6 " pdb=" C4 G Z 6 " ideal model delta sigma weight residual 126.50 132.28 -5.78 1.30e+00 5.92e-01 1.97e+01 angle pdb=" N9 G Z 6 " pdb=" C4 G Z 6 " pdb=" N3 G Z 6 " ideal model delta sigma weight residual 126.00 128.58 -2.58 6.00e-01 2.78e+00 1.85e+01 angle pdb=" N9 G a 6 " pdb=" C4 G a 6 " pdb=" N3 G a 6 " ideal model delta sigma weight residual 126.00 128.54 -2.54 6.00e-01 2.78e+00 1.80e+01 angle pdb=" C MET E 330 " pdb=" N ALA E 331 " pdb=" CA ALA E 331 " ideal model delta sigma weight residual 121.54 129.63 -8.09 1.91e+00 2.74e-01 1.80e+01 ... (remaining 16120 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 6797 17.67 - 35.34: 228 35.34 - 53.01: 55 53.01 - 70.67: 16 70.67 - 88.34: 7 Dihedral angle restraints: 7103 sinusoidal: 2989 harmonic: 4114 Sorted by residual: dihedral pdb=" CD ARG A 248 " pdb=" NE ARG A 248 " pdb=" CZ ARG A 248 " pdb=" NH1 ARG A 248 " ideal model delta sinusoidal sigma weight residual 0.00 88.34 -88.34 1 1.00e+01 1.00e-02 9.32e+01 dihedral pdb=" CA ASP E 227 " pdb=" C ASP E 227 " pdb=" N ILE E 228 " pdb=" CA ILE E 228 " ideal model delta harmonic sigma weight residual -180.00 -154.87 -25.13 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA THR A 52 " pdb=" C THR A 52 " pdb=" N ILE A 53 " pdb=" CA ILE A 53 " ideal model delta harmonic sigma weight residual 180.00 156.01 23.99 0 5.00e+00 4.00e-02 2.30e+01 ... (remaining 7100 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1182 0.051 - 0.102: 428 0.102 - 0.153: 109 0.153 - 0.204: 25 0.204 - 0.255: 5 Chirality restraints: 1749 Sorted by residual: chirality pdb=" CB ILE D 457 " pdb=" CA ILE D 457 " pdb=" CG1 ILE D 457 " pdb=" CG2 ILE D 457 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CB ILE A 457 " pdb=" CA ILE A 457 " pdb=" CG1 ILE A 457 " pdb=" CG2 ILE A 457 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CG LEU D 291 " pdb=" CB LEU D 291 " pdb=" CD1 LEU D 291 " pdb=" CD2 LEU D 291 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 1746 not shown) Planarity restraints: 2052 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 248 " -1.100 9.50e-02 1.11e+02 4.93e-01 1.46e+02 pdb=" NE ARG A 248 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG A 248 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG A 248 " -0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG A 248 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 366 " 0.019 2.00e-02 2.50e+03 1.77e-02 7.84e+00 pdb=" CG TRP A 366 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP A 366 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP A 366 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 366 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 TRP A 366 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 366 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 366 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 366 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 366 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 366 " -0.020 2.00e-02 2.50e+03 1.69e-02 7.16e+00 pdb=" CG TRP D 366 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP D 366 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP D 366 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 366 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TRP D 366 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 366 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 366 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 366 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 366 " -0.007 2.00e-02 2.50e+03 ... (remaining 2049 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 340 2.70 - 3.25: 10386 3.25 - 3.80: 18234 3.80 - 4.35: 24434 4.35 - 4.90: 40681 Nonbonded interactions: 94075 Sorted by model distance: nonbonded pdb=" OP1 A a 1 " pdb="MG MG D 501 " model vdw 2.150 2.170 nonbonded pdb=" OD1 ASN A 447 " pdb="MG MG A 501 " model vdw 2.201 2.170 nonbonded pdb=" OP1 A Z 1 " pdb="MG MG A 501 " model vdw 2.206 2.170 nonbonded pdb=" OE2 GLU A 284 " pdb=" OH TYR A 323 " model vdw 2.255 3.040 nonbonded pdb=" OE2 GLU D 284 " pdb=" OH TYR D 323 " model vdw 2.270 3.040 ... (remaining 94070 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 70 or resid 73 through 76 or (resid 77 and (name \ N or name CA or name C or name O or name CB )) or resid 78 through 501)) selection = (chain 'D' and (resid 1 through 165 or (resid 166 and (name N or name CA or name \ C or name O or name CB )) or resid 167 through 501)) } ncs_group { reference = (chain 'B' and (resid 161 through 186 or (resid 187 and (name N or name CA or na \ me C or name O or name CB )) or resid 188 through 294 or (resid 295 through 297 \ and (name N or name CA or name C or name O or name CB )) or resid 298 through 36 \ 6 or (resid 367 and (name N or name CA or name C or name O or name CB )) or resi \ d 368 through 413)) selection = (chain 'E' and (resid 161 through 282 or resid 285 through 413)) } ncs_group { reference = chain 'Z' selection = chain 'a' } 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: 4.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.890 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 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 : 0.009 0.093 11870 Z= 0.396 Angle : 0.884 9.364 16125 Z= 0.517 Chirality : 0.057 0.255 1749 Planarity : 0.013 0.493 2052 Dihedral : 10.790 88.344 4461 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.08 (0.18), residues: 1404 helix: -4.39 (0.10), residues: 434 sheet: -1.23 (0.26), residues: 349 loop : -2.13 (0.21), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 483 TYR 0.034 0.003 TYR D 485 PHE 0.033 0.004 PHE E 214 TRP 0.042 0.005 TRP A 366 HIS 0.014 0.003 HIS B 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00898 / 0.40 (11870) covalent geometry : angle 0.88383 / 0.52 (16125) hydrogen bonds : bond 0.27611 / 18.33 ( 438) hydrogen bonds : angle 10.30757 / 7.29 ( 1266) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 354 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.6897 (tt0) cc_final: 0.6641 (tt0) REVERT: A 18 HIS cc_start: 0.7260 (m-70) cc_final: 0.7014 (m-70) REVERT: A 123 GLU cc_start: 0.6636 (mt-10) cc_final: 0.5879 (mt-10) REVERT: A 127 ASP cc_start: 0.7283 (m-30) cc_final: 0.6865 (m-30) REVERT: A 132 GLU cc_start: 0.7406 (mt-10) cc_final: 0.7175 (mt-10) REVERT: A 248 ARG cc_start: 0.7299 (ttt90) cc_final: 0.7043 (ttt90) REVERT: A 250 MET cc_start: 0.6723 (mmm) cc_final: 0.6164 (mmm) REVERT: A 351 ILE cc_start: 0.8029 (mp) cc_final: 0.7792 (mm) REVERT: A 355 ASP cc_start: 0.7563 (m-30) cc_final: 0.7363 (m-30) REVERT: A 363 ASP cc_start: 0.7727 (m-30) cc_final: 0.7516 (m-30) REVERT: A 373 THR cc_start: 0.7622 (p) cc_final: 0.6919 (t) REVERT: A 391 ASP cc_start: 0.7152 (t0) cc_final: 0.6934 (t70) REVERT: A 393 HIS cc_start: 0.6649 (m-70) cc_final: 0.6383 (m-70) REVERT: B 271 LYS cc_start: 0.7513 (mtpp) cc_final: 0.7293 (mtpp) REVERT: B 279 ARG cc_start: 0.8059 (mtt-85) cc_final: 0.7854 (mtt90) REVERT: D 123 GLU cc_start: 0.6718 (mt-10) cc_final: 0.5921 (mt-10) REVERT: D 127 ASP cc_start: 0.7147 (m-30) cc_final: 0.6864 (m-30) REVERT: D 153 LYS cc_start: 0.7796 (mttp) cc_final: 0.7577 (mttp) REVERT: D 164 ASP cc_start: 0.6926 (t70) cc_final: 0.6712 (t0) REVERT: D 213 GLN cc_start: 0.8453 (tp-100) cc_final: 0.8214 (mm-40) REVERT: D 250 MET cc_start: 0.6904 (mmm) cc_final: 0.6415 (mmm) REVERT: D 351 ILE cc_start: 0.7828 (mt) cc_final: 0.7527 (mm) REVERT: D 355 ASP cc_start: 0.7579 (m-30) cc_final: 0.7361 (m-30) REVERT: E 190 ILE cc_start: 0.8699 (mt) cc_final: 0.8447 (mt) REVERT: E 194 LEU cc_start: 0.8533 (mt) cc_final: 0.8240 (mp) outliers start: 0 outliers final: 0 residues processed: 354 average time/residue: 0.7137 time to fit residues: 270.0793 Evaluate side-chains 293 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 293 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.4980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.3980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 181 ASN A 198 GLN A 272 GLN A 280 GLN A 450 GLN B 253 HIS B 257 GLN D 198 GLN D 452 ASN E 352 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.149873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.129994 restraints weight = 14797.621| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 2.17 r_work: 0.3535 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11870 Z= 0.157 Angle : 0.607 7.593 16125 Z= 0.323 Chirality : 0.043 0.136 1749 Planarity : 0.006 0.060 2052 Dihedral : 9.093 73.426 1738 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.34 % Allowed : 12.19 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.66 (0.20), residues: 1404 helix: -2.18 (0.19), residues: 453 sheet: -0.91 (0.27), residues: 343 loop : -1.79 (0.23), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 248 TYR 0.015 0.002 TYR B 343 PHE 0.014 0.002 PHE D 275 TRP 0.025 0.002 TRP D 446 HIS 0.005 0.001 HIS B 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (11870) covalent geometry : angle 0.60703 / 0.32 (16125) hydrogen bonds : bond 0.05250 / 3.56 ( 438) hydrogen bonds : angle 6.19674 / 4.32 ( 1266) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 293 time to evaluate : 0.442 Fit side-chains revert: symmetry clash REVERT: A 4 GLU cc_start: 0.7795 (tp30) cc_final: 0.7593 (mm-30) REVERT: A 43 LYS cc_start: 0.8383 (mtmm) cc_final: 0.8036 (mtpp) REVERT: A 94 PHE cc_start: 0.8155 (m-80) cc_final: 0.7848 (m-80) REVERT: A 119 TYR cc_start: 0.7992 (t80) cc_final: 0.7577 (t80) REVERT: A 123 GLU cc_start: 0.7352 (mt-10) cc_final: 0.7086 (mt-10) REVERT: A 250 MET cc_start: 0.7345 (mmm) cc_final: 0.6790 (mmm) REVERT: A 272 GLN cc_start: 0.7500 (OUTLIER) cc_final: 0.7228 (mm-40) REVERT: A 280 GLN cc_start: 0.8096 (mt0) cc_final: 0.7882 (mp10) REVERT: A 345 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7651 (pt0) REVERT: A 373 THR cc_start: 0.7993 (p) cc_final: 0.7221 (t) REVERT: A 393 HIS cc_start: 0.7448 (m-70) cc_final: 0.7143 (m-70) REVERT: D 62 THR cc_start: 0.7966 (t) cc_final: 0.7739 (p) REVERT: D 67 VAL cc_start: 0.8397 (t) cc_final: 0.8012 (p) REVERT: D 94 PHE cc_start: 0.8115 (m-80) cc_final: 0.7882 (m-80) REVERT: D 123 GLU cc_start: 0.7188 (mt-10) cc_final: 0.6673 (mt-10) REVERT: D 127 ASP cc_start: 0.7672 (m-30) cc_final: 0.7371 (m-30) REVERT: D 213 GLN cc_start: 0.8718 (tp-100) cc_final: 0.8491 (mm-40) REVERT: D 250 MET cc_start: 0.7429 (mmm) cc_final: 0.6873 (mmm) REVERT: D 297 ARG cc_start: 0.7884 (ttm170) cc_final: 0.7645 (ttm170) REVERT: D 355 ASP cc_start: 0.8005 (m-30) cc_final: 0.7760 (m-30) REVERT: D 403 SER cc_start: 0.8815 (m) cc_final: 0.8506 (p) REVERT: D 463 ARG cc_start: 0.7670 (OUTLIER) cc_final: 0.7435 (ttp-170) REVERT: E 163 ASP cc_start: 0.7715 (m-30) cc_final: 0.7456 (m-30) outliers start: 28 outliers final: 12 residues processed: 299 average time/residue: 0.6924 time to fit residues: 221.6138 Evaluate side-chains 296 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 282 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ARG Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 272 GLN Chi-restraints excluded: chain A residue 285 ARG Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain D residue 115 GLU Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 437 GLU Chi-restraints excluded: chain D residue 463 ARG Chi-restraints excluded: chain D residue 478 ILE Chi-restraints excluded: chain E residue 179 ILE Chi-restraints excluded: chain E residue 245 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 112 optimal weight: 0.5980 chunk 123 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 16 optimal weight: 0.0050 chunk 109 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 89 optimal weight: 0.0970 chunk 98 optimal weight: 1.9990 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 20 HIS A 272 GLN A 433 GLN D 21 HIS D 198 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.149313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.129274 restraints weight = 14894.074| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 2.20 r_work: 0.3529 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11870 Z= 0.131 Angle : 0.548 7.565 16125 Z= 0.286 Chirality : 0.043 0.211 1749 Planarity : 0.005 0.063 2052 Dihedral : 8.764 73.492 1738 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.42 % Allowed : 13.19 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.21), residues: 1404 helix: -1.03 (0.22), residues: 454 sheet: -0.82 (0.27), residues: 350 loop : -1.51 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 6 TYR 0.013 0.001 TYR B 343 PHE 0.011 0.001 PHE D 275 TRP 0.017 0.001 TRP D 446 HIS 0.008 0.001 HIS A 20 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (11870) covalent geometry : angle 0.54755 / 0.29 (16125) hydrogen bonds : bond 0.04182 / 2.85 ( 438) hydrogen bonds : angle 5.61355 / 3.90 ( 1266) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 285 time to evaluate : 0.457 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4482 (ppp) cc_final: 0.4281 (ppp) REVERT: A 119 TYR cc_start: 0.7948 (t80) cc_final: 0.7295 (t80) REVERT: A 123 GLU cc_start: 0.7328 (mt-10) cc_final: 0.6706 (mt-10) REVERT: A 127 ASP cc_start: 0.7852 (m-30) cc_final: 0.7488 (m-30) REVERT: A 250 MET cc_start: 0.7235 (mmm) cc_final: 0.6647 (mmm) REVERT: A 345 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7600 (mt-10) REVERT: A 373 THR cc_start: 0.8111 (p) cc_final: 0.7350 (t) REVERT: A 378 ARG cc_start: 0.8236 (mtp85) cc_final: 0.7992 (mtp180) REVERT: B 257 GLN cc_start: 0.8100 (OUTLIER) cc_final: 0.7607 (mp10) REVERT: B 359 LEU cc_start: 0.7489 (OUTLIER) cc_final: 0.7270 (mm) REVERT: D 30 GLU cc_start: 0.7460 (mt-10) cc_final: 0.7220 (mt-10) REVERT: D 67 VAL cc_start: 0.8389 (t) cc_final: 0.8005 (p) REVERT: D 123 GLU cc_start: 0.7129 (mt-10) cc_final: 0.6651 (mt-10) REVERT: D 127 ASP cc_start: 0.7573 (m-30) cc_final: 0.7330 (m-30) REVERT: D 213 GLN cc_start: 0.8733 (tp-100) cc_final: 0.8498 (mm-40) REVERT: D 257 SER cc_start: 0.7858 (t) cc_final: 0.7592 (t) REVERT: D 284 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7538 (pm20) REVERT: D 403 SER cc_start: 0.8789 (m) cc_final: 0.8557 (p) REVERT: D 437 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7601 (mt-10) REVERT: D 463 ARG cc_start: 0.7657 (OUTLIER) cc_final: 0.7440 (ttp-170) REVERT: E 163 ASP cc_start: 0.7689 (m-30) cc_final: 0.7449 (m-30) REVERT: E 257 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.7627 (mp10) outliers start: 29 outliers final: 11 residues processed: 292 average time/residue: 0.7101 time to fit residues: 221.6740 Evaluate side-chains 306 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 289 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 120 ARG Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 285 ARG Chi-restraints excluded: chain B residue 257 GLN Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain D residue 115 GLU Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 437 GLU Chi-restraints excluded: chain D residue 463 ARG Chi-restraints excluded: chain D residue 478 ILE Chi-restraints excluded: chain E residue 179 ILE Chi-restraints excluded: chain E residue 257 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 20 optimal weight: 0.0570 chunk 47 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 139 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 127 optimal weight: 0.9990 overall best weight: 0.6902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 326 HIS D 326 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.147288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.127204 restraints weight = 14877.479| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.19 r_work: 0.3510 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 11870 Z= 0.151 Angle : 0.534 7.471 16125 Z= 0.280 Chirality : 0.043 0.151 1749 Planarity : 0.004 0.041 2052 Dihedral : 8.603 73.418 1738 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.50 % Allowed : 14.27 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.22), residues: 1404 helix: -0.47 (0.23), residues: 454 sheet: -0.66 (0.28), residues: 331 loop : -1.34 (0.24), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 93 TYR 0.012 0.001 TYR D 239 PHE 0.014 0.002 PHE E 278 TRP 0.026 0.002 TRP A 446 HIS 0.004 0.001 HIS B 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.15 (11870) covalent geometry : angle 0.53356 / 0.28 (16125) hydrogen bonds : bond 0.03813 / 2.58 ( 438) hydrogen bonds : angle 5.39278 / 3.75 ( 1266) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 281 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 VAL cc_start: 0.8236 (t) cc_final: 0.8002 (p) REVERT: A 119 TYR cc_start: 0.7951 (t80) cc_final: 0.7730 (t80) REVERT: A 127 ASP cc_start: 0.7813 (m-30) cc_final: 0.7444 (m-30) REVERT: A 250 MET cc_start: 0.7287 (mmm) cc_final: 0.6708 (mmm) REVERT: A 326 HIS cc_start: 0.6714 (m90) cc_final: 0.6509 (m90) REVERT: A 345 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7563 (mt-10) REVERT: A 373 THR cc_start: 0.8185 (p) cc_final: 0.7467 (t) REVERT: A 378 ARG cc_start: 0.8211 (mtp85) cc_final: 0.7788 (mtp85) REVERT: A 391 ASP cc_start: 0.7815 (t0) cc_final: 0.7587 (t70) REVERT: B 257 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7595 (mp10) REVERT: B 359 LEU cc_start: 0.7498 (OUTLIER) cc_final: 0.7279 (mm) REVERT: D 30 GLU cc_start: 0.7459 (mt-10) cc_final: 0.7237 (mt-10) REVERT: D 67 VAL cc_start: 0.8383 (t) cc_final: 0.8015 (p) REVERT: D 123 GLU cc_start: 0.7113 (mt-10) cc_final: 0.6592 (mt-10) REVERT: D 127 ASP cc_start: 0.7513 (m-30) cc_final: 0.7276 (m-30) REVERT: D 213 GLN cc_start: 0.8735 (tp-100) cc_final: 0.8505 (mm-40) REVERT: D 257 SER cc_start: 0.7887 (t) cc_final: 0.7625 (t) REVERT: D 284 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7614 (pm20) REVERT: D 403 SER cc_start: 0.8812 (m) cc_final: 0.8539 (p) REVERT: E 163 ASP cc_start: 0.7723 (m-30) cc_final: 0.7508 (m-30) outliers start: 30 outliers final: 14 residues processed: 291 average time/residue: 0.7161 time to fit residues: 222.7110 Evaluate side-chains 301 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 284 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 120 ARG Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain B residue 257 GLN Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain D residue 115 GLU Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 281 MET Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 478 ILE Chi-restraints excluded: chain E residue 281 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 78 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 129 optimal weight: 2.9990 chunk 138 optimal weight: 0.6980 chunk 98 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 433 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.146785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.126874 restraints weight = 14833.943| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.18 r_work: 0.3499 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 11870 Z= 0.169 Angle : 0.540 8.149 16125 Z= 0.282 Chirality : 0.044 0.188 1749 Planarity : 0.004 0.042 2052 Dihedral : 8.506 73.397 1738 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.59 % Allowed : 14.36 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.22), residues: 1404 helix: -0.09 (0.24), residues: 455 sheet: -0.60 (0.28), residues: 331 loop : -1.25 (0.24), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 6 TYR 0.013 0.002 TYR B 343 PHE 0.016 0.002 PHE E 278 TRP 0.028 0.002 TRP D 446 HIS 0.004 0.001 HIS B 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.17 (11870) covalent geometry : angle 0.53991 / 0.28 (16125) hydrogen bonds : bond 0.03747 / 2.53 ( 438) hydrogen bonds : angle 5.28624 / 3.68 ( 1266) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 286 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 TYR cc_start: 0.7950 (t80) cc_final: 0.7724 (t80) REVERT: A 127 ASP cc_start: 0.7811 (m-30) cc_final: 0.7449 (m-30) REVERT: A 250 MET cc_start: 0.7275 (mmm) cc_final: 0.6721 (mmm) REVERT: A 345 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7596 (mt-10) REVERT: A 373 THR cc_start: 0.8214 (p) cc_final: 0.7543 (t) REVERT: A 378 ARG cc_start: 0.8206 (mtp85) cc_final: 0.7958 (mtp180) REVERT: A 391 ASP cc_start: 0.7808 (t0) cc_final: 0.7581 (t70) REVERT: A 483 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.7705 (mtm-85) REVERT: B 257 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7616 (mp10) REVERT: B 359 LEU cc_start: 0.7541 (OUTLIER) cc_final: 0.7321 (mm) REVERT: D 30 GLU cc_start: 0.7449 (mt-10) cc_final: 0.7233 (mt-10) REVERT: D 67 VAL cc_start: 0.8393 (t) cc_final: 0.8026 (p) REVERT: D 123 GLU cc_start: 0.7125 (mt-10) cc_final: 0.6604 (mt-10) REVERT: D 127 ASP cc_start: 0.7518 (m-30) cc_final: 0.7270 (m-30) REVERT: D 213 GLN cc_start: 0.8730 (tp-100) cc_final: 0.8492 (mm-40) REVERT: D 257 SER cc_start: 0.7938 (t) cc_final: 0.7686 (t) REVERT: D 284 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7941 (pm20) REVERT: D 403 SER cc_start: 0.8811 (m) cc_final: 0.8527 (p) REVERT: D 483 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.7790 (mtm-85) outliers start: 31 outliers final: 18 residues processed: 297 average time/residue: 0.7165 time to fit residues: 227.4255 Evaluate side-chains 293 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 270 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 120 ARG Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 483 ARG Chi-restraints excluded: chain B residue 257 GLN Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 115 GLU Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 281 MET Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 452 ASN Chi-restraints excluded: chain D residue 478 ILE Chi-restraints excluded: chain D residue 483 ARG Chi-restraints excluded: chain E residue 281 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 58 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 89 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 GLN A 424 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.147890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.127928 restraints weight = 14795.774| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 2.17 r_work: 0.3505 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 11870 Z= 0.170 Angle : 0.539 8.478 16125 Z= 0.280 Chirality : 0.044 0.166 1749 Planarity : 0.004 0.043 2052 Dihedral : 8.456 73.402 1738 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.59 % Allowed : 15.03 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.22), residues: 1404 helix: 0.14 (0.24), residues: 455 sheet: -0.50 (0.28), residues: 336 loop : -1.19 (0.25), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 6 TYR 0.013 0.001 TYR B 343 PHE 0.016 0.002 PHE D 8 TRP 0.027 0.002 TRP D 446 HIS 0.005 0.001 HIS D 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.17 (11870) covalent geometry : angle 0.53889 / 0.28 (16125) hydrogen bonds : bond 0.03694 / 2.51 ( 438) hydrogen bonds : angle 5.24302 / 3.64 ( 1266) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 281 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 LYS cc_start: 0.8474 (tppp) cc_final: 0.8135 (mmmm) REVERT: A 119 TYR cc_start: 0.7969 (t80) cc_final: 0.7724 (t80) REVERT: A 127 ASP cc_start: 0.7795 (m-30) cc_final: 0.7426 (m-30) REVERT: A 132 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7713 (mt-10) REVERT: A 250 MET cc_start: 0.7236 (mmm) cc_final: 0.6671 (mmm) REVERT: A 345 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7630 (mt-10) REVERT: A 373 THR cc_start: 0.8229 (p) cc_final: 0.7557 (t) REVERT: A 378 ARG cc_start: 0.8213 (mtp85) cc_final: 0.7942 (mtp180) REVERT: A 391 ASP cc_start: 0.7822 (t0) cc_final: 0.7601 (t70) REVERT: A 483 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.8012 (mtt90) REVERT: B 257 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7613 (mp10) REVERT: B 359 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7327 (mm) REVERT: D 30 GLU cc_start: 0.7438 (mt-10) cc_final: 0.7217 (mt-10) REVERT: D 67 VAL cc_start: 0.8402 (t) cc_final: 0.8039 (p) REVERT: D 123 GLU cc_start: 0.7107 (mt-10) cc_final: 0.6583 (mt-10) REVERT: D 127 ASP cc_start: 0.7488 (m-30) cc_final: 0.7248 (m-30) REVERT: D 213 GLN cc_start: 0.8725 (tp-100) cc_final: 0.8483 (mm-40) REVERT: D 257 SER cc_start: 0.7957 (t) cc_final: 0.7662 (t) REVERT: D 284 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7841 (pm20) REVERT: D 403 SER cc_start: 0.8801 (m) cc_final: 0.8512 (p) REVERT: D 428 GLU cc_start: 0.8273 (mt-10) cc_final: 0.8032 (mt-10) REVERT: D 483 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.8008 (mtt90) outliers start: 31 outliers final: 18 residues processed: 291 average time/residue: 0.7293 time to fit residues: 226.6013 Evaluate side-chains 298 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 274 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ARG Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 285 ARG Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 483 ARG Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 257 GLN Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain D residue 12 GLU Chi-restraints excluded: chain D residue 115 GLU Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 281 MET Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 478 ILE Chi-restraints excluded: chain D residue 483 ARG Chi-restraints excluded: chain E residue 281 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 5 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 121 optimal weight: 0.3980 chunk 9 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 131 optimal weight: 7.9990 chunk 94 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.146693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.126782 restraints weight = 14843.500| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.17 r_work: 0.3503 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 11870 Z= 0.170 Angle : 0.536 8.787 16125 Z= 0.279 Chirality : 0.043 0.161 1749 Planarity : 0.004 0.050 2052 Dihedral : 8.412 73.399 1738 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.09 % Allowed : 14.86 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.22), residues: 1404 helix: 0.30 (0.24), residues: 452 sheet: -0.42 (0.28), residues: 336 loop : -1.10 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 93 TYR 0.013 0.001 TYR B 343 PHE 0.016 0.002 PHE E 278 TRP 0.025 0.002 TRP D 446 HIS 0.005 0.001 HIS B 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.17 (11870) covalent geometry : angle 0.53647 / 0.28 (16125) hydrogen bonds : bond 0.03638 / 2.47 ( 438) hydrogen bonds : angle 5.20151 / 3.62 ( 1266) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 274 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8132 (mmmm) REVERT: A 119 TYR cc_start: 0.7970 (t80) cc_final: 0.7754 (t80) REVERT: A 127 ASP cc_start: 0.7795 (m-30) cc_final: 0.7424 (m-30) REVERT: A 132 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7696 (mt-10) REVERT: A 250 MET cc_start: 0.7236 (mmm) cc_final: 0.6655 (mmm) REVERT: A 345 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7595 (mt-10) REVERT: A 373 THR cc_start: 0.8237 (p) cc_final: 0.7562 (t) REVERT: A 378 ARG cc_start: 0.8195 (mtp85) cc_final: 0.7957 (mtp180) REVERT: A 391 ASP cc_start: 0.7821 (t0) cc_final: 0.7590 (t70) REVERT: A 483 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.8046 (mtt90) REVERT: B 257 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.7614 (mp10) REVERT: B 359 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.7322 (mm) REVERT: D 30 GLU cc_start: 0.7440 (mt-10) cc_final: 0.7220 (mt-10) REVERT: D 123 GLU cc_start: 0.7092 (mt-10) cc_final: 0.6557 (mt-10) REVERT: D 127 ASP cc_start: 0.7482 (m-30) cc_final: 0.7244 (m-30) REVERT: D 213 GLN cc_start: 0.8704 (tp-100) cc_final: 0.8462 (mm-40) REVERT: D 257 SER cc_start: 0.7974 (t) cc_final: 0.7665 (t) REVERT: D 284 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7835 (pm20) REVERT: D 403 SER cc_start: 0.8799 (m) cc_final: 0.8498 (p) REVERT: D 428 GLU cc_start: 0.8299 (mt-10) cc_final: 0.8069 (mt-10) REVERT: D 483 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.8038 (mtt90) outliers start: 37 outliers final: 19 residues processed: 288 average time/residue: 0.7236 time to fit residues: 222.7992 Evaluate side-chains 294 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 268 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 108 LYS Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 285 ARG Chi-restraints excluded: chain A residue 295 ARG Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 483 ARG Chi-restraints excluded: chain B residue 257 GLN Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain D residue 12 GLU Chi-restraints excluded: chain D residue 115 GLU Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 281 MET Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 478 ILE Chi-restraints excluded: chain D residue 483 ARG Chi-restraints excluded: chain E residue 281 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 0.1980 chunk 46 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 GLN D 224 GLN D 272 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.148843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.128710 restraints weight = 14823.398| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.18 r_work: 0.3511 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11870 Z= 0.142 Angle : 0.529 9.244 16125 Z= 0.273 Chirality : 0.042 0.153 1749 Planarity : 0.004 0.061 2052 Dihedral : 8.338 73.453 1738 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.75 % Allowed : 15.53 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.22), residues: 1404 helix: 0.50 (0.25), residues: 452 sheet: -0.39 (0.28), residues: 331 loop : -1.07 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 93 TYR 0.012 0.001 TYR B 343 PHE 0.014 0.002 PHE E 211 TRP 0.034 0.002 TRP A 446 HIS 0.004 0.001 HIS D 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.14 (11870) covalent geometry : angle 0.52885 / 0.27 (16125) hydrogen bonds : bond 0.03460 / 2.35 ( 438) hydrogen bonds : angle 5.16216 / 3.59 ( 1266) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 274 time to evaluate : 0.564 Fit side-chains revert: symmetry clash REVERT: A 108 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.8138 (mmmm) REVERT: A 119 TYR cc_start: 0.7949 (t80) cc_final: 0.7702 (t80) REVERT: A 127 ASP cc_start: 0.7776 (m-30) cc_final: 0.7406 (m-30) REVERT: A 132 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7660 (mt-10) REVERT: A 250 MET cc_start: 0.7185 (mmm) cc_final: 0.6639 (mmm) REVERT: A 345 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7580 (mt-10) REVERT: A 373 THR cc_start: 0.8232 (p) cc_final: 0.7573 (t) REVERT: A 378 ARG cc_start: 0.8180 (mtp85) cc_final: 0.7935 (mtp180) REVERT: A 391 ASP cc_start: 0.7819 (t0) cc_final: 0.7615 (t70) REVERT: A 470 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.8145 (ptmm) REVERT: A 483 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.8053 (mtt90) REVERT: B 257 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7616 (mp10) REVERT: B 359 LEU cc_start: 0.7536 (OUTLIER) cc_final: 0.7282 (mm) REVERT: D 30 GLU cc_start: 0.7473 (mt-10) cc_final: 0.7251 (mt-10) REVERT: D 123 GLU cc_start: 0.7048 (mt-10) cc_final: 0.6488 (mt-10) REVERT: D 127 ASP cc_start: 0.7502 (m-30) cc_final: 0.7262 (m-30) REVERT: D 213 GLN cc_start: 0.8684 (tp-100) cc_final: 0.8441 (mm-40) REVERT: D 257 SER cc_start: 0.7965 (t) cc_final: 0.7644 (t) REVERT: D 284 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7766 (pm20) REVERT: D 403 SER cc_start: 0.8782 (m) cc_final: 0.8499 (p) REVERT: D 428 GLU cc_start: 0.8292 (mt-10) cc_final: 0.8081 (mt-10) REVERT: D 483 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.8048 (mtt90) outliers start: 33 outliers final: 17 residues processed: 286 average time/residue: 0.7204 time to fit residues: 220.2605 Evaluate side-chains 299 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 274 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 108 LYS Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 483 ARG Chi-restraints excluded: chain B residue 257 GLN Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 12 GLU Chi-restraints excluded: chain D residue 115 GLU Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 281 MET Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 478 ILE Chi-restraints excluded: chain D residue 483 ARG Chi-restraints excluded: chain E residue 281 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 128 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 GLN A 369 GLN D 224 GLN D 424 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.147720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.127629 restraints weight = 14605.874| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.17 r_work: 0.3496 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 11870 Z= 0.218 Angle : 0.581 9.051 16125 Z= 0.300 Chirality : 0.045 0.179 1749 Planarity : 0.005 0.064 2052 Dihedral : 8.395 73.341 1738 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.67 % Allowed : 16.19 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.22), residues: 1404 helix: 0.38 (0.24), residues: 452 sheet: -0.30 (0.28), residues: 340 loop : -1.03 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 93 TYR 0.015 0.002 TYR D 90 PHE 0.021 0.002 PHE E 278 TRP 0.036 0.002 TRP A 446 HIS 0.007 0.001 HIS A 424 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.22 (11870) covalent geometry : angle 0.58070 / 0.30 (16125) hydrogen bonds : bond 0.03893 / 2.64 ( 438) hydrogen bonds : angle 5.27470 / 3.68 ( 1266) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 268 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.8123 (mmmm) REVERT: A 127 ASP cc_start: 0.7767 (m-30) cc_final: 0.7412 (m-30) REVERT: A 132 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7669 (mt-10) REVERT: A 250 MET cc_start: 0.7185 (mmm) cc_final: 0.6597 (mmm) REVERT: A 345 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7587 (mt-10) REVERT: A 378 ARG cc_start: 0.8192 (mtp85) cc_final: 0.7917 (mtp180) REVERT: A 391 ASP cc_start: 0.7822 (t0) cc_final: 0.7589 (t70) REVERT: A 470 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8146 (ptmm) REVERT: A 483 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.8100 (mtt90) REVERT: B 257 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7617 (mp10) REVERT: B 359 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.7310 (mm) REVERT: D 30 GLU cc_start: 0.7462 (mt-10) cc_final: 0.7229 (mt-10) REVERT: D 123 GLU cc_start: 0.7102 (mt-10) cc_final: 0.6571 (mt-10) REVERT: D 127 ASP cc_start: 0.7510 (m-30) cc_final: 0.7268 (m-30) REVERT: D 213 GLN cc_start: 0.8664 (tp-100) cc_final: 0.8368 (mm-40) REVERT: D 284 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7821 (pm20) REVERT: D 403 SER cc_start: 0.8802 (m) cc_final: 0.8471 (p) REVERT: D 428 GLU cc_start: 0.8308 (mt-10) cc_final: 0.8052 (mt-10) REVERT: D 483 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.8101 (mtt90) outliers start: 32 outliers final: 18 residues processed: 281 average time/residue: 0.7274 time to fit residues: 218.3165 Evaluate side-chains 291 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 265 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 108 LYS Chi-restraints excluded: chain A residue 120 ARG Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 295 ARG Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 483 ARG Chi-restraints excluded: chain B residue 257 GLN Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 12 GLU Chi-restraints excluded: chain D residue 115 GLU Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 281 MET Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 478 ILE Chi-restraints excluded: chain D residue 483 ARG Chi-restraints excluded: chain E residue 281 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 115 optimal weight: 1.9990 chunk 19 optimal weight: 0.4980 chunk 63 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 114 optimal weight: 0.7980 chunk 15 optimal weight: 0.4980 chunk 133 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.149064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.129118 restraints weight = 14683.120| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 2.15 r_work: 0.3515 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11870 Z= 0.142 Angle : 0.538 9.561 16125 Z= 0.278 Chirality : 0.043 0.154 1749 Planarity : 0.004 0.059 2052 Dihedral : 8.312 73.463 1738 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.25 % Allowed : 16.53 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.22), residues: 1404 helix: 0.66 (0.25), residues: 452 sheet: -0.27 (0.28), residues: 336 loop : -1.00 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 93 TYR 0.012 0.001 TYR B 343 PHE 0.013 0.002 PHE E 211 TRP 0.038 0.002 TRP A 446 HIS 0.004 0.001 HIS D 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.14 (11870) covalent geometry : angle 0.53787 / 0.28 (16125) hydrogen bonds : bond 0.03431 / 2.33 ( 438) hydrogen bonds : angle 5.18572 / 3.61 ( 1266) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 267 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8154 (mmmm) REVERT: A 127 ASP cc_start: 0.7751 (m-30) cc_final: 0.7400 (m-30) REVERT: A 132 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7645 (mt-10) REVERT: A 250 MET cc_start: 0.7167 (mmm) cc_final: 0.6629 (mmm) REVERT: A 345 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7549 (mt-10) REVERT: A 378 ARG cc_start: 0.8154 (mtp85) cc_final: 0.7912 (mtp180) REVERT: A 391 ASP cc_start: 0.7780 (t0) cc_final: 0.7562 (t70) REVERT: A 470 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.8137 (ptmm) REVERT: A 483 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.7976 (mtt90) REVERT: B 257 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7611 (mp10) REVERT: B 359 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.7313 (mm) REVERT: D 30 GLU cc_start: 0.7432 (mt-10) cc_final: 0.7231 (mt-10) REVERT: D 123 GLU cc_start: 0.7048 (mt-10) cc_final: 0.6479 (mt-10) REVERT: D 127 ASP cc_start: 0.7465 (m-30) cc_final: 0.7226 (m-30) REVERT: D 132 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7525 (mt-10) REVERT: D 213 GLN cc_start: 0.8597 (tp-100) cc_final: 0.8370 (mm-40) REVERT: D 284 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7717 (pm20) REVERT: D 403 SER cc_start: 0.8793 (m) cc_final: 0.8504 (p) REVERT: D 428 GLU cc_start: 0.8300 (mt-10) cc_final: 0.8045 (mt-10) REVERT: D 483 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.7758 (mtm-85) outliers start: 27 outliers final: 18 residues processed: 276 average time/residue: 0.7248 time to fit residues: 213.7705 Evaluate side-chains 289 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 263 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 108 LYS Chi-restraints excluded: chain A residue 120 ARG Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 295 ARG Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 483 ARG Chi-restraints excluded: chain B residue 257 GLN Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 12 GLU Chi-restraints excluded: chain D residue 115 GLU Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 281 MET Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 478 ILE Chi-restraints excluded: chain D residue 483 ARG Chi-restraints excluded: chain E residue 281 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 47 optimal weight: 0.7980 chunk 106 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 131 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 110 optimal weight: 0.1980 chunk 11 optimal weight: 0.0870 chunk 84 optimal weight: 0.5980 chunk 138 optimal weight: 0.5980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 GLN D 224 GLN D 425 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.148839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.129109 restraints weight = 14787.326| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.16 r_work: 0.3518 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11870 Z= 0.119 Angle : 0.534 9.505 16125 Z= 0.276 Chirality : 0.042 0.141 1749 Planarity : 0.004 0.057 2052 Dihedral : 8.208 73.518 1738 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.84 % Allowed : 16.36 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.23), residues: 1404 helix: 0.81 (0.25), residues: 453 sheet: -0.23 (0.28), residues: 334 loop : -0.94 (0.25), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 93 TYR 0.011 0.001 TYR B 343 PHE 0.014 0.001 PHE E 211 TRP 0.037 0.002 TRP A 446 HIS 0.004 0.001 HIS D 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (11870) covalent geometry : angle 0.53416 / 0.28 (16125) hydrogen bonds : bond 0.03284 / 2.23 ( 438) hydrogen bonds : angle 5.09551 / 3.54 ( 1266) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5444.53 seconds wall clock time: 93 minutes 34.09 seconds (5614.09 seconds total)