Starting phenix.real_space_refine on Wed Feb 4 16:27:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vx1_65405/02_2026/9vx1_65405.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vx1_65405/02_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_65405/02_2026/9vx1_65405.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vx1_65405/02_2026/9vx1_65405.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vx1_65405/02_2026/9vx1_65405.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vx1_65405/02_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/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: 3.06, per 1000 atoms: 0.26 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: 0.94 Conformation dependent library (CDL) restraints added in 494.4 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: 0.44 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: 1.77 Time building geometry restraints manager: 1.24 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=" 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 bond pdb=" N LEU B 239 " pdb=" CA LEU B 239 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.19e-02 7.06e+03 8.85e+00 bond pdb=" CB VAL A 158 " pdb=" CG1 VAL A 158 " ideal model delta sigma weight residual 1.521 1.431 0.090 3.30e-02 9.18e+02 7.44e+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=" 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 angle pdb=" C MET B 330 " pdb=" N ALA B 331 " pdb=" CA ALA B 331 " ideal model delta sigma weight residual 121.54 129.61 -8.07 1.91e+00 2.74e-01 1.79e+01 angle pdb=" C ALA D 165 " pdb=" N ARG D 166 " pdb=" CA ARG D 166 " ideal model delta sigma weight residual 121.54 129.16 -7.62 1.91e+00 2.74e-01 1.59e+01 angle pdb=" C LYS E 296 " pdb=" N LYS E 297 " pdb=" CA LYS E 297 " ideal model delta sigma weight residual 120.71 126.32 -5.61 1.42e+00 4.96e-01 1.56e+01 angle pdb=" CA TRP E 212 " pdb=" CB TRP E 212 " pdb=" CG TRP E 212 " ideal model delta sigma weight residual 113.60 120.97 -7.37 1.90e+00 2.77e-01 1.51e+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: 5.320 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: 0.290 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.820 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 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= 0.376 Angle : 0.884 9.364 16125 Z= 0.491 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 covalent geometry : bond 0.00898 (11870) covalent geometry : angle 0.88381 (16125) hydrogen bonds : bond 0.27611 ( 438) hydrogen bonds : angle 10.30757 ( 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 : 0.466 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: 0.6808 time to fit residues: 256.6235 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 : 0.433 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 326 HIS D 452 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.149600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.130358 restraints weight = 14815.286| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 2.13 r_work: 0.3544 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 11870 Z= 0.144 Angle : 0.575 7.654 16125 Z= 0.304 Chirality : 0.043 0.133 1749 Planarity : 0.005 0.061 2052 Dihedral : 8.917 73.517 1738 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.00 % Allowed : 12.35 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.62 (0.20), residues: 1404 helix: -2.19 (0.19), residues: 453 sheet: -0.91 (0.27), residues: 343 loop : -1.71 (0.23), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 6 TYR 0.015 0.002 TYR B 343 PHE 0.012 0.002 PHE D 275 TRP 0.023 0.002 TRP D 446 HIS 0.004 0.001 HIS E 320 Details of bonding type rmsd covalent geometry : bond 0.00341 (11870) covalent geometry : angle 0.57465 (16125) hydrogen bonds : bond 0.04283 ( 438) hydrogen bonds : angle 5.92478 ( 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 307 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 283 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.7800 (tp30) cc_final: 0.7586 (mm-30) REVERT: A 43 LYS cc_start: 0.8386 (mtmm) cc_final: 0.8054 (mtpp) REVERT: A 119 TYR cc_start: 0.7920 (t80) cc_final: 0.7455 (t80) REVERT: A 123 GLU cc_start: 0.7322 (mt-10) cc_final: 0.7032 (mt-10) REVERT: A 250 MET cc_start: 0.7342 (mmm) cc_final: 0.6778 (mmm) REVERT: A 373 THR cc_start: 0.8042 (p) cc_final: 0.7304 (t) REVERT: D 4 GLU cc_start: 0.7420 (tp30) cc_final: 0.7218 (tp30) REVERT: D 30 GLU cc_start: 0.7509 (mt-10) cc_final: 0.7271 (mt-10) REVERT: D 62 THR cc_start: 0.7991 (t) cc_final: 0.7785 (p) REVERT: D 67 VAL cc_start: 0.8392 (t) cc_final: 0.8013 (p) REVERT: D 94 PHE cc_start: 0.8085 (m-80) cc_final: 0.7847 (m-80) REVERT: D 123 GLU cc_start: 0.7169 (mt-10) cc_final: 0.6548 (mt-10) REVERT: D 127 ASP cc_start: 0.7589 (m-30) cc_final: 0.7279 (m-30) REVERT: D 164 ASP cc_start: 0.7497 (t70) cc_final: 0.7263 (t0) REVERT: D 213 GLN cc_start: 0.8701 (tp-100) cc_final: 0.8476 (mm-40) REVERT: D 250 MET cc_start: 0.7418 (mmm) cc_final: 0.6876 (mmm) REVERT: D 257 SER cc_start: 0.7873 (t) cc_final: 0.7665 (t) REVERT: D 355 ASP cc_start: 0.7999 (m-30) cc_final: 0.7774 (m-30) REVERT: D 403 SER cc_start: 0.8821 (m) cc_final: 0.8543 (p) REVERT: D 463 ARG cc_start: 0.7685 (OUTLIER) cc_final: 0.7422 (ttp-170) REVERT: E 163 ASP cc_start: 0.7686 (m-30) cc_final: 0.7425 (m-30) REVERT: E 194 LEU cc_start: 0.8596 (mt) cc_final: 0.8394 (mp) outliers start: 24 outliers final: 9 residues processed: 288 average time/residue: 0.6560 time to fit residues: 201.7169 Evaluate side-chains 289 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 279 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 285 ARG Chi-restraints excluded: chain B residue 245 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 463 ARG Chi-restraints excluded: chain D residue 478 ILE Chi-restraints excluded: chain E residue 179 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: 1.9990 chunk 16 optimal weight: 0.0020 chunk 109 optimal weight: 1.9990 chunk 50 optimal weight: 0.0870 chunk 20 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 overall best weight: 0.9370 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 GLN A 326 HIS A 433 GLN D 198 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.146405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.126356 restraints weight = 14881.323| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.19 r_work: 0.3490 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 11870 Z= 0.189 Angle : 0.562 7.595 16125 Z= 0.294 Chirality : 0.044 0.158 1749 Planarity : 0.005 0.048 2052 Dihedral : 8.616 73.367 1738 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.84 % Allowed : 12.69 % Favored : 84.47 % 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: -1.79 (0.21), residues: 1404 helix: -1.05 (0.22), residues: 454 sheet: -0.71 (0.27), residues: 338 loop : -1.44 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 483 TYR 0.016 0.002 TYR A 482 PHE 0.017 0.002 PHE E 278 TRP 0.025 0.002 TRP A 446 HIS 0.005 0.001 HIS E 379 Details of bonding type rmsd covalent geometry : bond 0.00467 (11870) covalent geometry : angle 0.56186 (16125) hydrogen bonds : bond 0.04129 ( 438) hydrogen bonds : angle 5.47891 ( 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 316 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 282 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 TYR cc_start: 0.7961 (t80) cc_final: 0.7717 (t80) REVERT: A 127 ASP cc_start: 0.7825 (m-30) cc_final: 0.7469 (m-30) REVERT: A 250 MET cc_start: 0.7286 (mmm) cc_final: 0.6708 (mmm) REVERT: A 373 THR cc_start: 0.8232 (p) cc_final: 0.7588 (t) REVERT: B 359 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.7236 (mm) REVERT: D 4 GLU cc_start: 0.7548 (tp30) cc_final: 0.7324 (tp30) REVERT: D 30 GLU cc_start: 0.7478 (mt-10) cc_final: 0.7246 (mt-10) REVERT: D 67 VAL cc_start: 0.8379 (t) cc_final: 0.8002 (p) REVERT: D 123 GLU cc_start: 0.7141 (mt-10) cc_final: 0.6601 (mt-10) REVERT: D 127 ASP cc_start: 0.7531 (m-30) cc_final: 0.7304 (m-30) REVERT: D 153 LYS cc_start: 0.8234 (mttp) cc_final: 0.7983 (mttp) REVERT: D 164 ASP cc_start: 0.7501 (t70) cc_final: 0.7232 (t0) REVERT: D 213 GLN cc_start: 0.8679 (tp-100) cc_final: 0.8452 (mm-40) REVERT: D 250 MET cc_start: 0.7404 (mmm) cc_final: 0.6956 (mmm) REVERT: D 257 SER cc_start: 0.7953 (t) cc_final: 0.7687 (t) REVERT: D 284 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7448 (pm20) REVERT: D 403 SER cc_start: 0.8835 (m) cc_final: 0.8488 (p) REVERT: D 463 ARG cc_start: 0.7689 (OUTLIER) cc_final: 0.7446 (ttp-170) REVERT: D 483 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.7762 (mtm-85) REVERT: E 194 LEU cc_start: 0.8564 (mt) cc_final: 0.8360 (mp) outliers start: 34 outliers final: 14 residues processed: 290 average time/residue: 0.6384 time to fit residues: 197.2200 Evaluate side-chains 291 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 273 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET 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 179 ILE Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain D residue 7 ILE 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 339 THR Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 463 ARG Chi-restraints excluded: chain D residue 478 ILE Chi-restraints excluded: chain D residue 483 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 20 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 GLN A 424 HIS D 21 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.146364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.126507 restraints weight = 14832.075| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.16 r_work: 0.3502 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 11870 Z= 0.190 Angle : 0.550 7.565 16125 Z= 0.288 Chirality : 0.044 0.162 1749 Planarity : 0.004 0.046 2052 Dihedral : 8.514 73.367 1738 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.92 % Allowed : 13.94 % Favored : 83.14 % 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: -1.31 (0.22), residues: 1404 helix: -0.41 (0.23), residues: 455 sheet: -0.64 (0.27), residues: 338 loop : -1.23 (0.25), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 483 TYR 0.015 0.002 TYR B 343 PHE 0.017 0.002 PHE E 278 TRP 0.030 0.002 TRP D 446 HIS 0.005 0.001 HIS B 379 Details of bonding type rmsd covalent geometry : bond 0.00469 (11870) covalent geometry : angle 0.55011 (16125) hydrogen bonds : bond 0.03811 ( 438) hydrogen bonds : angle 5.32271 ( 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 318 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 283 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.8109 (mmmm) REVERT: A 119 TYR cc_start: 0.7976 (t80) cc_final: 0.7728 (t80) REVERT: A 127 ASP cc_start: 0.7824 (m-30) cc_final: 0.7465 (m-30) REVERT: A 250 MET cc_start: 0.7274 (mmm) cc_final: 0.6707 (mmm) REVERT: A 373 THR cc_start: 0.8247 (p) cc_final: 0.7597 (t) REVERT: A 470 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.8169 (ptmm) REVERT: B 359 LEU cc_start: 0.7505 (OUTLIER) cc_final: 0.7272 (mm) REVERT: D 4 GLU cc_start: 0.7533 (tp30) cc_final: 0.7320 (tp30) REVERT: D 30 GLU cc_start: 0.7491 (mt-10) cc_final: 0.7247 (mt-10) REVERT: D 67 VAL cc_start: 0.8390 (t) cc_final: 0.8018 (p) REVERT: D 123 GLU cc_start: 0.7150 (mt-10) cc_final: 0.6588 (mt-10) REVERT: D 127 ASP cc_start: 0.7496 (m-30) cc_final: 0.7234 (m-30) REVERT: D 130 ILE cc_start: 0.8373 (mm) cc_final: 0.8156 (mp) REVERT: D 153 LYS cc_start: 0.8250 (mttp) cc_final: 0.7996 (mttp) REVERT: D 164 ASP cc_start: 0.7507 (t70) cc_final: 0.7239 (t0) REVERT: D 198 GLN cc_start: 0.8656 (tp40) cc_final: 0.8456 (tp40) REVERT: D 213 GLN cc_start: 0.8711 (tp-100) cc_final: 0.8439 (mm-40) REVERT: D 257 SER cc_start: 0.7993 (t) cc_final: 0.7634 (t) REVERT: D 284 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7660 (pm20) REVERT: D 403 SER cc_start: 0.8833 (m) cc_final: 0.8481 (p) REVERT: D 463 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.7428 (ttp-170) REVERT: D 483 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.7809 (mtm-85) outliers start: 35 outliers final: 16 residues processed: 294 average time/residue: 0.6436 time to fit residues: 201.7032 Evaluate side-chains 298 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 276 time to evaluate : 0.337 ------------------------------------------------------------------------------- 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 171 LYS Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 285 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 B residue 341 THR Chi-restraints excluded: chain B residue 359 LEU 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 463 ARG 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 78 optimal weight: 0.3980 chunk 35 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 129 optimal weight: 0.0060 chunk 138 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 HIS A 272 GLN D 224 GLN D 272 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.146446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.127006 restraints weight = 14813.517| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.11 r_work: 0.3524 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11870 Z= 0.131 Angle : 0.519 7.568 16125 Z= 0.269 Chirality : 0.042 0.149 1749 Planarity : 0.004 0.039 2052 Dihedral : 8.312 73.475 1738 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.75 % Allowed : 15.11 % Favored : 82.14 % 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: -0.87 (0.22), residues: 1404 helix: 0.19 (0.24), residues: 453 sheet: -0.59 (0.27), residues: 333 loop : -1.05 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 483 TYR 0.012 0.001 TYR B 343 PHE 0.013 0.001 PHE E 211 TRP 0.030 0.002 TRP A 446 HIS 0.009 0.001 HIS A 20 Details of bonding type rmsd covalent geometry : bond 0.00315 (11870) covalent geometry : angle 0.51864 (16125) hydrogen bonds : bond 0.03376 ( 438) hydrogen bonds : angle 5.13521 ( 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 308 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 275 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8111 (mmmm) REVERT: A 127 ASP cc_start: 0.7808 (m-30) cc_final: 0.7445 (m-30) REVERT: A 132 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7694 (mt-10) REVERT: A 250 MET cc_start: 0.7143 (mmm) cc_final: 0.6626 (mmm) REVERT: A 373 THR cc_start: 0.8229 (p) cc_final: 0.7535 (t) REVERT: A 391 ASP cc_start: 0.7788 (t0) cc_final: 0.7588 (t0) REVERT: A 470 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.8154 (ptmm) REVERT: A 483 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.7980 (mtt90) REVERT: B 359 LEU cc_start: 0.7558 (OUTLIER) cc_final: 0.7312 (mm) REVERT: D 4 GLU cc_start: 0.7587 (tp30) cc_final: 0.7384 (tp30) REVERT: D 12 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7074 (mp0) REVERT: D 30 GLU cc_start: 0.7447 (mt-10) cc_final: 0.7213 (mt-10) REVERT: D 123 GLU cc_start: 0.7064 (mt-10) cc_final: 0.6455 (mt-10) REVERT: D 127 ASP cc_start: 0.7459 (m-30) cc_final: 0.7196 (m-30) REVERT: D 130 ILE cc_start: 0.8354 (mm) cc_final: 0.8109 (mp) REVERT: D 153 LYS cc_start: 0.8225 (mttp) cc_final: 0.7980 (mttp) REVERT: D 164 ASP cc_start: 0.7482 (t70) cc_final: 0.7233 (t0) REVERT: D 213 GLN cc_start: 0.8668 (tp-100) cc_final: 0.8401 (mm-40) REVERT: D 284 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7921 (pm20) REVERT: D 403 SER cc_start: 0.8807 (m) cc_final: 0.8498 (p) REVERT: D 463 ARG cc_start: 0.7606 (OUTLIER) cc_final: 0.7398 (ttp-170) REVERT: D 483 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.7787 (mtm-85) outliers start: 33 outliers final: 14 residues processed: 285 average time/residue: 0.7171 time to fit residues: 217.4047 Evaluate side-chains 288 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 266 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LYS 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 236 SER Chi-restraints excluded: chain A residue 285 ARG Chi-restraints excluded: chain A residue 295 ARG Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 483 ARG 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 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 339 THR Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 463 ARG 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: 1.9990 chunk 18 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 89 optimal weight: 0.0870 chunk 30 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 overall best weight: 1.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.145650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.125927 restraints weight = 14784.745| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.13 r_work: 0.3487 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 11870 Z= 0.232 Angle : 0.580 7.939 16125 Z= 0.300 Chirality : 0.045 0.187 1749 Planarity : 0.004 0.054 2052 Dihedral : 8.449 73.272 1738 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.09 % Allowed : 16.03 % Favored : 80.88 % 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: -0.81 (0.22), residues: 1404 helix: 0.16 (0.24), residues: 455 sheet: -0.38 (0.28), residues: 347 loop : -1.07 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 483 TYR 0.016 0.002 TYR B 343 PHE 0.018 0.002 PHE E 278 TRP 0.025 0.002 TRP A 446 HIS 0.006 0.001 HIS A 424 Details of bonding type rmsd covalent geometry : bond 0.00576 (11870) covalent geometry : angle 0.58026 (16125) hydrogen bonds : bond 0.03979 ( 438) hydrogen bonds : angle 5.30908 ( 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 311 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 274 time to evaluate : 0.447 Fit side-chains revert: symmetry clash REVERT: A 108 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.8101 (mmmm) REVERT: A 119 TYR cc_start: 0.8015 (t80) cc_final: 0.7183 (t80) REVERT: A 123 GLU cc_start: 0.7378 (mt-10) cc_final: 0.6558 (mt-10) REVERT: A 127 ASP cc_start: 0.7797 (m-30) cc_final: 0.7433 (m-30) REVERT: A 132 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7725 (mt-10) REVERT: A 250 MET cc_start: 0.7116 (mmm) cc_final: 0.6636 (mmm) REVERT: A 373 THR cc_start: 0.8239 (p) cc_final: 0.7600 (t) REVERT: A 391 ASP cc_start: 0.7849 (t0) cc_final: 0.7628 (t70) REVERT: A 470 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.8170 (ptmm) REVERT: A 483 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.8167 (mtt90) REVERT: B 359 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.7297 (mm) REVERT: D 4 GLU cc_start: 0.7675 (tp30) cc_final: 0.7451 (tp30) REVERT: D 12 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7175 (mp0) REVERT: D 30 GLU cc_start: 0.7445 (mt-10) cc_final: 0.7213 (mt-10) REVERT: D 123 GLU cc_start: 0.7108 (mt-10) cc_final: 0.6529 (mt-10) REVERT: D 127 ASP cc_start: 0.7514 (m-30) cc_final: 0.7240 (m-30) REVERT: D 164 ASP cc_start: 0.7505 (t70) cc_final: 0.7245 (t0) REVERT: D 213 GLN cc_start: 0.8665 (tp-100) cc_final: 0.8398 (mm-40) REVERT: D 284 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7963 (pm20) REVERT: D 355 ASP cc_start: 0.7998 (m-30) cc_final: 0.7743 (m-30) REVERT: D 403 SER cc_start: 0.8833 (m) cc_final: 0.8471 (p) REVERT: D 483 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.7797 (mtm-85) outliers start: 37 outliers final: 22 residues processed: 287 average time/residue: 0.7032 time to fit residues: 214.9689 Evaluate side-chains 300 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 270 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 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 168 THR Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 236 SER 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 470 LYS Chi-restraints excluded: chain A residue 483 ARG 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 155 LEU 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 339 THR Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 385 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 5 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 121 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 87 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 131 optimal weight: 7.9990 chunk 94 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 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 = 0.3895 r_free = 0.3895 target = 0.148512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.128640 restraints weight = 14757.987| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.14 r_work: 0.3509 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11870 Z= 0.154 Angle : 0.538 8.378 16125 Z= 0.277 Chirality : 0.043 0.164 1749 Planarity : 0.004 0.041 2052 Dihedral : 8.328 73.429 1738 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.17 % Allowed : 16.44 % Favored : 80.38 % 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: -0.62 (0.22), residues: 1404 helix: 0.47 (0.25), residues: 452 sheet: -0.40 (0.27), residues: 332 loop : -0.99 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 483 TYR 0.013 0.001 TYR B 343 PHE 0.013 0.002 PHE E 278 TRP 0.024 0.002 TRP A 446 HIS 0.005 0.001 HIS D 425 Details of bonding type rmsd covalent geometry : bond 0.00377 (11870) covalent geometry : angle 0.53826 (16125) hydrogen bonds : bond 0.03534 ( 438) hydrogen bonds : angle 5.18584 ( 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 317 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 279 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.8097 (mmmm) REVERT: A 119 TYR cc_start: 0.7962 (t80) cc_final: 0.7707 (t80) REVERT: A 127 ASP cc_start: 0.7781 (m-30) cc_final: 0.7424 (m-30) REVERT: A 132 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7696 (mt-10) REVERT: A 250 MET cc_start: 0.7083 (mmm) cc_final: 0.6637 (mmm) REVERT: A 373 THR cc_start: 0.8223 (p) cc_final: 0.7555 (t) REVERT: A 391 ASP cc_start: 0.7823 (t0) cc_final: 0.7616 (t70) REVERT: A 470 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8175 (ptmm) REVERT: A 483 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.8148 (mtt90) REVERT: B 359 LEU cc_start: 0.7542 (OUTLIER) cc_final: 0.7255 (mm) REVERT: D 4 GLU cc_start: 0.7630 (tp30) cc_final: 0.7417 (tp30) REVERT: D 12 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7157 (mp0) REVERT: D 30 GLU cc_start: 0.7468 (mt-10) cc_final: 0.7247 (mt-10) REVERT: D 123 GLU cc_start: 0.7062 (mt-10) cc_final: 0.6426 (mt-10) REVERT: D 127 ASP cc_start: 0.7483 (m-30) cc_final: 0.7210 (m-30) REVERT: D 164 ASP cc_start: 0.7508 (t70) cc_final: 0.7251 (t0) REVERT: D 213 GLN cc_start: 0.8622 (tp-100) cc_final: 0.8354 (mm-40) REVERT: D 284 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7887 (pm20) REVERT: D 355 ASP cc_start: 0.7985 (m-30) cc_final: 0.7729 (m-30) REVERT: D 403 SER cc_start: 0.8836 (m) cc_final: 0.8502 (p) REVERT: D 463 ARG cc_start: 0.7801 (tpp-160) cc_final: 0.7568 (ttp-110) REVERT: D 483 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.7775 (mtm-85) outliers start: 38 outliers final: 17 residues processed: 294 average time/residue: 0.6796 time to fit residues: 212.8453 Evaluate side-chains 295 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 270 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 168 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 236 SER 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 470 LYS Chi-restraints excluded: chain A residue 483 ARG 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 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 339 THR 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: 1.9990 chunk 46 optimal weight: 0.8980 chunk 34 optimal weight: 0.3980 chunk 33 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 104 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 45 optimal weight: 0.4980 chunk 85 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN A 272 GLN D 224 GLN D 425 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.149109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.129321 restraints weight = 14789.954| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 2.14 r_work: 0.3526 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11870 Z= 0.140 Angle : 0.534 8.581 16125 Z= 0.274 Chirality : 0.042 0.155 1749 Planarity : 0.004 0.040 2052 Dihedral : 8.178 73.428 1738 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.92 % Allowed : 17.20 % Favored : 79.88 % 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: -0.44 (0.22), residues: 1404 helix: 0.67 (0.25), residues: 451 sheet: -0.29 (0.27), residues: 330 loop : -0.93 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 93 TYR 0.012 0.001 TYR B 343 PHE 0.013 0.002 PHE E 211 TRP 0.023 0.002 TRP A 446 HIS 0.004 0.001 HIS D 425 Details of bonding type rmsd covalent geometry : bond 0.00338 (11870) covalent geometry : angle 0.53392 (16125) hydrogen bonds : bond 0.03401 ( 438) hydrogen bonds : angle 5.10068 ( 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 308 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 273 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.8123 (mmmm) REVERT: A 127 ASP cc_start: 0.7767 (m-30) cc_final: 0.7404 (m-30) REVERT: A 132 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7692 (mt-10) REVERT: A 250 MET cc_start: 0.7045 (mmm) cc_final: 0.6623 (mmm) REVERT: A 373 THR cc_start: 0.8219 (p) cc_final: 0.7536 (t) REVERT: A 378 ARG cc_start: 0.7929 (mtp180) cc_final: 0.7709 (mtp85) REVERT: A 391 ASP cc_start: 0.7827 (t0) cc_final: 0.7613 (t70) REVERT: A 470 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.8161 (ptmm) REVERT: A 483 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.8145 (mtt90) REVERT: B 257 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7741 (mp10) REVERT: B 359 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7174 (mm) REVERT: D 4 GLU cc_start: 0.7641 (tp30) cc_final: 0.7435 (tp30) REVERT: D 12 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7174 (mp0) REVERT: D 30 GLU cc_start: 0.7463 (mt-10) cc_final: 0.7255 (mt-10) REVERT: D 67 VAL cc_start: 0.8404 (t) cc_final: 0.8053 (p) REVERT: D 123 GLU cc_start: 0.6991 (mt-10) cc_final: 0.6374 (mt-10) REVERT: D 127 ASP cc_start: 0.7469 (m-30) cc_final: 0.7207 (m-30) REVERT: D 132 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7490 (mt-10) REVERT: D 164 ASP cc_start: 0.7493 (t70) cc_final: 0.7246 (t0) REVERT: D 213 GLN cc_start: 0.8572 (tp-100) cc_final: 0.8291 (mm-40) REVERT: D 284 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7772 (pm20) REVERT: D 355 ASP cc_start: 0.7971 (m-30) cc_final: 0.7747 (m-30) REVERT: D 403 SER cc_start: 0.8797 (m) cc_final: 0.8514 (p) REVERT: D 428 GLU cc_start: 0.8251 (mt-10) cc_final: 0.7987 (mt-10) REVERT: D 483 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.7821 (mtm-85) outliers start: 35 outliers final: 20 residues processed: 283 average time/residue: 0.6879 time to fit residues: 207.4457 Evaluate side-chains 298 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 269 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 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 168 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 281 MET 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 360 GLU 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 12 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 339 THR 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: 0.8980 chunk 72 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 114 optimal weight: 0.5980 chunk 90 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN A 272 GLN D 224 GLN D 425 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 = 0.145672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.126299 restraints weight = 14668.340| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.10 r_work: 0.3513 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11870 Z= 0.169 Angle : 0.557 8.476 16125 Z= 0.285 Chirality : 0.043 0.165 1749 Planarity : 0.004 0.040 2052 Dihedral : 8.217 73.395 1738 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.92 % Allowed : 17.53 % Favored : 79.55 % 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: -0.39 (0.22), residues: 1404 helix: 0.70 (0.25), residues: 451 sheet: -0.21 (0.28), residues: 334 loop : -0.93 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 483 TYR 0.013 0.001 TYR B 343 PHE 0.016 0.002 PHE E 278 TRP 0.032 0.002 TRP D 446 HIS 0.005 0.001 HIS A 424 Details of bonding type rmsd covalent geometry : bond 0.00415 (11870) covalent geometry : angle 0.55651 (16125) hydrogen bonds : bond 0.03563 ( 438) hydrogen bonds : angle 5.16285 ( 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 306 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 271 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.8109 (mmmm) REVERT: A 127 ASP cc_start: 0.7777 (m-30) cc_final: 0.7426 (m-30) REVERT: A 132 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7692 (mt-10) REVERT: A 250 MET cc_start: 0.7083 (mmm) cc_final: 0.6594 (mmm) REVERT: A 373 THR cc_start: 0.8230 (p) cc_final: 0.7552 (t) REVERT: A 391 ASP cc_start: 0.7849 (t0) cc_final: 0.7621 (t70) REVERT: A 470 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.8158 (ptmm) REVERT: A 483 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.8166 (mtt90) REVERT: B 330 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.6947 (mpt) REVERT: B 359 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.7164 (mm) REVERT: D 4 GLU cc_start: 0.7671 (tp30) cc_final: 0.7446 (tp30) REVERT: D 12 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7211 (mp0) REVERT: D 30 GLU cc_start: 0.7447 (mt-10) cc_final: 0.7246 (mt-10) REVERT: D 120 ARG cc_start: 0.7486 (mtp180) cc_final: 0.7254 (mtp180) REVERT: D 123 GLU cc_start: 0.7020 (mt-10) cc_final: 0.6369 (mt-10) REVERT: D 127 ASP cc_start: 0.7474 (m-30) cc_final: 0.7210 (m-30) REVERT: D 164 ASP cc_start: 0.7508 (t70) cc_final: 0.7255 (t0) REVERT: D 213 GLN cc_start: 0.8555 (tp-100) cc_final: 0.8270 (mm-40) REVERT: D 284 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7787 (pm20) REVERT: D 355 ASP cc_start: 0.7968 (m-30) cc_final: 0.7705 (m-30) REVERT: D 403 SER cc_start: 0.8793 (m) cc_final: 0.8487 (p) REVERT: D 428 GLU cc_start: 0.8263 (mt-10) cc_final: 0.8034 (mt-10) REVERT: D 483 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.7783 (mtm-85) outliers start: 35 outliers final: 21 residues processed: 285 average time/residue: 0.7131 time to fit residues: 216.3848 Evaluate side-chains 292 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 262 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 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 168 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 245 ILE 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 360 GLU 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 330 MET 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 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 339 THR Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 385 LEU 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: 0.3980 chunk 19 optimal weight: 0.1980 chunk 63 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 114 optimal weight: 0.1980 chunk 15 optimal weight: 0.1980 chunk 133 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 54 optimal weight: 0.2980 chunk 121 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 overall best weight: 0.2580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN A 272 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 = 0.3926 r_free = 0.3926 target = 0.149337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.129821 restraints weight = 14711.244| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 2.13 r_work: 0.3548 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11870 Z= 0.099 Angle : 0.519 8.871 16125 Z= 0.265 Chirality : 0.041 0.132 1749 Planarity : 0.004 0.057 2052 Dihedral : 7.989 73.481 1738 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.00 % Allowed : 18.61 % Favored : 79.38 % 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: -0.13 (0.23), residues: 1404 helix: 1.06 (0.25), residues: 451 sheet: 0.02 (0.28), residues: 341 loop : -0.98 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 93 TYR 0.008 0.001 TYR B 343 PHE 0.014 0.001 PHE E 211 TRP 0.038 0.002 TRP D 446 HIS 0.004 0.000 HIS D 425 Details of bonding type rmsd covalent geometry : bond 0.00229 (11870) covalent geometry : angle 0.51929 (16125) hydrogen bonds : bond 0.03055 ( 438) hydrogen bonds : angle 4.96190 ( 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 286 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 262 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 ARG cc_start: 0.7631 (mpp80) cc_final: 0.7346 (mtp180) REVERT: A 57 ARG cc_start: 0.8060 (mtp-110) cc_final: 0.7751 (mtp180) REVERT: A 108 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.8121 (mmmm) REVERT: A 127 ASP cc_start: 0.7732 (m-30) cc_final: 0.7368 (m-30) REVERT: A 132 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7659 (mt-10) REVERT: A 250 MET cc_start: 0.7068 (mmm) cc_final: 0.6563 (mmm) REVERT: A 345 GLU cc_start: 0.7501 (mt-10) cc_final: 0.7098 (mp0) REVERT: A 373 THR cc_start: 0.8200 (p) cc_final: 0.7468 (t) REVERT: A 391 ASP cc_start: 0.7778 (t0) cc_final: 0.7577 (t70) REVERT: A 483 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.8106 (mtt90) REVERT: B 330 MET cc_start: 0.8520 (OUTLIER) cc_final: 0.8302 (mpm) REVERT: B 359 LEU cc_start: 0.7514 (OUTLIER) cc_final: 0.7113 (mm) REVERT: D 12 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7155 (mp0) REVERT: D 67 VAL cc_start: 0.8400 (t) cc_final: 0.8063 (p) REVERT: D 123 GLU cc_start: 0.6915 (mt-10) cc_final: 0.6212 (mt-10) REVERT: D 127 ASP cc_start: 0.7467 (m-30) cc_final: 0.7198 (m-30) REVERT: D 164 ASP cc_start: 0.7454 (t70) cc_final: 0.7225 (t0) REVERT: D 213 GLN cc_start: 0.8496 (tp-100) cc_final: 0.8216 (mm-40) REVERT: D 284 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7460 (pm20) REVERT: D 355 ASP cc_start: 0.7983 (m-30) cc_final: 0.7753 (m-30) REVERT: D 403 SER cc_start: 0.8739 (m) cc_final: 0.8488 (p) REVERT: D 483 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.7806 (mtm-85) outliers start: 24 outliers final: 10 residues processed: 272 average time/residue: 0.7895 time to fit residues: 227.8630 Evaluate side-chains 278 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 261 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 108 LYS Chi-restraints excluded: chain A residue 120 ARG Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 483 ARG Chi-restraints excluded: chain B residue 330 MET 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 163 VAL Chi-restraints excluded: chain D residue 281 MET Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 339 THR 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: 0.0670 chunk 106 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 50 optimal weight: 0.3980 chunk 131 optimal weight: 0.0020 chunk 31 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 138 optimal weight: 0.6980 overall best weight: 0.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN A 272 GLN D 224 GLN D 425 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.148673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.129034 restraints weight = 14809.578| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.15 r_work: 0.3544 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11870 Z= 0.114 Angle : 0.531 8.829 16125 Z= 0.271 Chirality : 0.041 0.134 1749 Planarity : 0.004 0.061 2052 Dihedral : 7.983 73.439 1738 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.67 % Allowed : 19.45 % Favored : 78.88 % 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: 0.01 (0.23), residues: 1404 helix: 1.19 (0.25), residues: 450 sheet: 0.09 (0.28), residues: 329 loop : -0.87 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 93 TYR 0.014 0.001 TYR A 382 PHE 0.013 0.001 PHE E 211 TRP 0.039 0.002 TRP D 446 HIS 0.008 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00274 (11870) covalent geometry : angle 0.53125 (16125) hydrogen bonds : bond 0.03165 ( 438) hydrogen bonds : angle 4.95181 ( 1266) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5035.19 seconds wall clock time: 86 minutes 18.09 seconds (5178.09 seconds total)