Starting phenix.real_space_refine on Sat Jul 4 02:31:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vmm_65191/07_2026/9vmm_65191.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vmm_65191/07_2026/9vmm_65191.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vmm_65191/07_2026/9vmm_65191.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vmm_65191/07_2026/9vmm_65191.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vmm_65191/07_2026/9vmm_65191.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vmm_65191/07_2026/9vmm_65191.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 24 5.49 5 Mg 8 5.21 5 S 92 5.16 5 C 11064 2.51 5 N 2968 2.21 5 O 3300 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 112 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17456 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4304 Classifications: {'peptide': 541} Link IDs: {'PTRANS': 28, 'TRANS': 512} Chain breaks: 2 Chain: "B" Number of atoms: 4304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4304 Classifications: {'peptide': 541} Link IDs: {'PTRANS': 28, 'TRANS': 512} Chain breaks: 2 Chain: "C" Number of atoms: 4304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4304 Classifications: {'peptide': 541} Link IDs: {'PTRANS': 28, 'TRANS': 512} Chain breaks: 2 Chain: "D" Number of atoms: 4304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4304 Classifications: {'peptide': 541} Link IDs: {'PTRANS': 28, 'TRANS': 512} Chain breaks: 2 Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'CTP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'CTP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'CTP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'CTP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 4.14, per 1000 atoms: 0.24 Number of scatterers: 17456 At special positions: 0 Unit cell: (138.58, 82.82, 123.82, 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 92 16.00 P 24 15.00 Mg 8 11.99 O 3300 8.00 N 2968 7.00 C 11064 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.53 Conformation dependent library (CDL) restraints added in 754.1 milliseconds 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4000 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 16 sheets defined 48.8% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 15 through 29 Processing helix chain 'A' and resid 46 through 50 removed outlier: 3.990A pdb=" N THR A 49 " --> pdb=" O ASP A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 79 removed outlier: 4.215A pdb=" N GLY A 72 " --> pdb=" O ASP A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 103 Processing helix chain 'A' and resid 116 through 130 removed outlier: 3.828A pdb=" N GLN A 122 " --> pdb=" O THR A 118 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU A 130 " --> pdb=" O MET A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 155 No H-bonds generated for 'chain 'A' and resid 153 through 155' Processing helix chain 'A' and resid 156 through 170 removed outlier: 4.872A pdb=" N PHE A 168 " --> pdb=" O ARG A 164 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS A 169 " --> pdb=" O GLN A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 173 No H-bonds generated for 'chain 'A' and resid 171 through 173' Processing helix chain 'A' and resid 194 through 207 Processing helix chain 'A' and resid 223 through 235 Processing helix chain 'A' and resid 237 through 239 No H-bonds generated for 'chain 'A' and resid 237 through 239' Processing helix chain 'A' and resid 249 through 251 No H-bonds generated for 'chain 'A' and resid 249 through 251' Processing helix chain 'A' and resid 252 through 260 Processing helix chain 'A' and resid 261 through 270 removed outlier: 4.338A pdb=" N ARG A 268 " --> pdb=" O ASP A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 295 Processing helix chain 'A' and resid 311 through 313 No H-bonds generated for 'chain 'A' and resid 311 through 313' Processing helix chain 'A' and resid 314 through 329 removed outlier: 3.651A pdb=" N ALA A 327 " --> pdb=" O HIS A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 344 through 349 Processing helix chain 'A' and resid 350 through 363 removed outlier: 3.737A pdb=" N TYR A 354 " --> pdb=" O GLU A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 391 Processing helix chain 'A' and resid 399 through 413 removed outlier: 3.740A pdb=" N GLN A 403 " --> pdb=" O CYS A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 468 removed outlier: 3.633A pdb=" N LYS A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 493 removed outlier: 4.017A pdb=" N LYS A 490 " --> pdb=" O PRO A 486 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N CYS A 491 " --> pdb=" O VAL A 487 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU A 493 " --> pdb=" O LYS A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 531 removed outlier: 3.627A pdb=" N PHE A 529 " --> pdb=" O HIS A 526 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU A 530 " --> pdb=" O PRO A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 548 Processing helix chain 'A' and resid 550 through 555 Processing helix chain 'B' and resid 15 through 29 Processing helix chain 'B' and resid 46 through 50 removed outlier: 3.990A pdb=" N THR B 49 " --> pdb=" O ASP B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 79 removed outlier: 4.215A pdb=" N GLY B 72 " --> pdb=" O ASP B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 103 Processing helix chain 'B' and resid 116 through 130 removed outlier: 3.828A pdb=" N GLN B 122 " --> pdb=" O THR B 118 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU B 130 " --> pdb=" O MET B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 155 No H-bonds generated for 'chain 'B' and resid 153 through 155' Processing helix chain 'B' and resid 156 through 170 removed outlier: 4.872A pdb=" N PHE B 168 " --> pdb=" O ARG B 164 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS B 169 " --> pdb=" O GLN B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 173 No H-bonds generated for 'chain 'B' and resid 171 through 173' Processing helix chain 'B' and resid 194 through 207 Processing helix chain 'B' and resid 223 through 235 Processing helix chain 'B' and resid 237 through 239 No H-bonds generated for 'chain 'B' and resid 237 through 239' Processing helix chain 'B' and resid 249 through 251 No H-bonds generated for 'chain 'B' and resid 249 through 251' Processing helix chain 'B' and resid 252 through 260 Processing helix chain 'B' and resid 261 through 270 removed outlier: 4.338A pdb=" N ARG B 268 " --> pdb=" O ASP B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 295 Processing helix chain 'B' and resid 311 through 313 No H-bonds generated for 'chain 'B' and resid 311 through 313' Processing helix chain 'B' and resid 314 through 329 removed outlier: 3.651A pdb=" N ALA B 327 " --> pdb=" O HIS B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 344 through 349 Processing helix chain 'B' and resid 350 through 363 removed outlier: 3.737A pdb=" N TYR B 354 " --> pdb=" O GLU B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 391 Processing helix chain 'B' and resid 399 through 413 removed outlier: 3.740A pdb=" N GLN B 403 " --> pdb=" O CYS B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 468 removed outlier: 3.633A pdb=" N LYS B 466 " --> pdb=" O SER B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 493 removed outlier: 4.017A pdb=" N LYS B 490 " --> pdb=" O PRO B 486 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N CYS B 491 " --> pdb=" O VAL B 487 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU B 493 " --> pdb=" O LYS B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 531 removed outlier: 3.627A pdb=" N PHE B 529 " --> pdb=" O HIS B 526 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU B 530 " --> pdb=" O PRO B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 548 Processing helix chain 'B' and resid 550 through 555 Processing helix chain 'C' and resid 15 through 29 Processing helix chain 'C' and resid 46 through 50 removed outlier: 3.990A pdb=" N THR C 49 " --> pdb=" O ASP C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 79 removed outlier: 4.215A pdb=" N GLY C 72 " --> pdb=" O ASP C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 103 Processing helix chain 'C' and resid 116 through 130 removed outlier: 3.828A pdb=" N GLN C 122 " --> pdb=" O THR C 118 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU C 130 " --> pdb=" O MET C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 155 No H-bonds generated for 'chain 'C' and resid 153 through 155' Processing helix chain 'C' and resid 156 through 170 removed outlier: 4.872A pdb=" N PHE C 168 " --> pdb=" O ARG C 164 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS C 169 " --> pdb=" O GLN C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 173 No H-bonds generated for 'chain 'C' and resid 171 through 173' Processing helix chain 'C' and resid 194 through 207 Processing helix chain 'C' and resid 223 through 235 Processing helix chain 'C' and resid 237 through 239 No H-bonds generated for 'chain 'C' and resid 237 through 239' Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 252 through 260 Processing helix chain 'C' and resid 261 through 270 removed outlier: 4.338A pdb=" N ARG C 268 " --> pdb=" O ASP C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 295 Processing helix chain 'C' and resid 311 through 313 No H-bonds generated for 'chain 'C' and resid 311 through 313' Processing helix chain 'C' and resid 314 through 329 removed outlier: 3.651A pdb=" N ALA C 327 " --> pdb=" O HIS C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 344 through 349 Processing helix chain 'C' and resid 350 through 363 removed outlier: 3.737A pdb=" N TYR C 354 " --> pdb=" O GLU C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 391 Processing helix chain 'C' and resid 399 through 413 removed outlier: 3.740A pdb=" N GLN C 403 " --> pdb=" O CYS C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 468 removed outlier: 3.633A pdb=" N LYS C 466 " --> pdb=" O SER C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 485 through 493 removed outlier: 4.017A pdb=" N LYS C 490 " --> pdb=" O PRO C 486 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N CYS C 491 " --> pdb=" O VAL C 487 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU C 493 " --> pdb=" O LYS C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 531 removed outlier: 3.627A pdb=" N PHE C 529 " --> pdb=" O HIS C 526 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU C 530 " --> pdb=" O PRO C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 548 Processing helix chain 'C' and resid 550 through 555 Processing helix chain 'D' and resid 15 through 29 Processing helix chain 'D' and resid 46 through 50 removed outlier: 3.990A pdb=" N THR D 49 " --> pdb=" O ASP D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 79 removed outlier: 4.215A pdb=" N GLY D 72 " --> pdb=" O ASP D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 103 Processing helix chain 'D' and resid 116 through 130 removed outlier: 3.828A pdb=" N GLN D 122 " --> pdb=" O THR D 118 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU D 130 " --> pdb=" O MET D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 155 No H-bonds generated for 'chain 'D' and resid 153 through 155' Processing helix chain 'D' and resid 156 through 170 removed outlier: 4.872A pdb=" N PHE D 168 " --> pdb=" O ARG D 164 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS D 169 " --> pdb=" O GLN D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 173 No H-bonds generated for 'chain 'D' and resid 171 through 173' Processing helix chain 'D' and resid 194 through 207 Processing helix chain 'D' and resid 223 through 235 Processing helix chain 'D' and resid 237 through 239 No H-bonds generated for 'chain 'D' and resid 237 through 239' Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 252 through 260 Processing helix chain 'D' and resid 261 through 270 removed outlier: 4.338A pdb=" N ARG D 268 " --> pdb=" O ASP D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 295 Processing helix chain 'D' and resid 311 through 313 No H-bonds generated for 'chain 'D' and resid 311 through 313' Processing helix chain 'D' and resid 314 through 329 removed outlier: 3.651A pdb=" N ALA D 327 " --> pdb=" O HIS D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 343 Processing helix chain 'D' and resid 344 through 349 Processing helix chain 'D' and resid 350 through 363 removed outlier: 3.737A pdb=" N TYR D 354 " --> pdb=" O GLU D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 391 Processing helix chain 'D' and resid 399 through 413 removed outlier: 3.740A pdb=" N GLN D 403 " --> pdb=" O CYS D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 468 removed outlier: 3.633A pdb=" N LYS D 466 " --> pdb=" O SER D 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 493 removed outlier: 4.017A pdb=" N LYS D 490 " --> pdb=" O PRO D 486 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N CYS D 491 " --> pdb=" O VAL D 487 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU D 493 " --> pdb=" O LYS D 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 526 through 531 removed outlier: 3.627A pdb=" N PHE D 529 " --> pdb=" O HIS D 526 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU D 530 " --> pdb=" O PRO D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 548 Processing helix chain 'D' and resid 550 through 555 Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 89 removed outlier: 8.262A pdb=" N LEU A 88 " --> pdb=" O SER A 36 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N LYS A 38 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LYS A 2 " --> pdb=" O CYS A 143 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N ILE A 145 " --> pdb=" O LYS A 2 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ILE A 4 " --> pdb=" O ILE A 145 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N LEU A 147 " --> pdb=" O ILE A 4 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL A 6 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TYR A 3 " --> pdb=" O CYS A 176 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ILE A 178 " --> pdb=" O TYR A 3 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU A 5 " --> pdb=" O ILE A 178 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N VAL A 180 " --> pdb=" O LEU A 5 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N THR A 7 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N LEU A 182 " --> pdb=" O THR A 7 " (cutoff:3.500A) removed outlier: 9.612A pdb=" N LEU A 213 " --> pdb=" O PHE A 175 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ASN A 177 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N VAL A 215 " --> pdb=" O ASN A 177 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N HIS A 179 " --> pdb=" O VAL A 215 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N ARG A 217 " --> pdb=" O HIS A 179 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N SER A 181 " --> pdb=" O ARG A 217 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 60 Processing sheet with id=AA3, first strand: chain 'A' and resid 331 through 337 removed outlier: 6.673A pdb=" N CYS A 299 " --> pdb=" O GLU A 333 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N LYS A 335 " --> pdb=" O CYS A 299 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE A 301 " --> pdb=" O LYS A 335 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ILE A 337 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU A 303 " --> pdb=" O ILE A 337 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N LEU A 368 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ALA A 302 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N PHE A 395 " --> pdb=" O VAL A 521 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N VAL A 523 " --> pdb=" O PHE A 395 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N GLY A 397 " --> pdb=" O VAL A 523 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N PHE A 520 " --> pdb=" O LEU A 514 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N MET A 509 " --> pdb=" O GLN A 502 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N GLN A 502 " --> pdb=" O MET A 509 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE A 511 " --> pdb=" O VAL A 500 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 433 through 435 Processing sheet with id=AA5, first strand: chain 'B' and resid 87 through 89 removed outlier: 8.262A pdb=" N LEU B 88 " --> pdb=" O SER B 36 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N LYS B 38 " --> pdb=" O LEU B 88 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LYS B 2 " --> pdb=" O CYS B 143 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N ILE B 145 " --> pdb=" O LYS B 2 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ILE B 4 " --> pdb=" O ILE B 145 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N LEU B 147 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL B 6 " --> pdb=" O LEU B 147 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TYR B 3 " --> pdb=" O CYS B 176 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ILE B 178 " --> pdb=" O TYR B 3 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU B 5 " --> pdb=" O ILE B 178 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N VAL B 180 " --> pdb=" O LEU B 5 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N THR B 7 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N LEU B 182 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 9.612A pdb=" N LEU B 213 " --> pdb=" O PHE B 175 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ASN B 177 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N VAL B 215 " --> pdb=" O ASN B 177 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N HIS B 179 " --> pdb=" O VAL B 215 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N ARG B 217 " --> pdb=" O HIS B 179 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N SER B 181 " --> pdb=" O ARG B 217 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 59 through 60 Processing sheet with id=AA7, first strand: chain 'B' and resid 331 through 337 removed outlier: 6.673A pdb=" N CYS B 299 " --> pdb=" O GLU B 333 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N LYS B 335 " --> pdb=" O CYS B 299 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE B 301 " --> pdb=" O LYS B 335 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ILE B 337 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU B 303 " --> pdb=" O ILE B 337 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N LEU B 368 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ALA B 302 " --> pdb=" O LEU B 368 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N PHE B 395 " --> pdb=" O VAL B 521 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N VAL B 523 " --> pdb=" O PHE B 395 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N GLY B 397 " --> pdb=" O VAL B 523 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N PHE B 520 " --> pdb=" O LEU B 514 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N MET B 509 " --> pdb=" O GLN B 502 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N GLN B 502 " --> pdb=" O MET B 509 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE B 511 " --> pdb=" O VAL B 500 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 433 through 435 Processing sheet with id=AA9, first strand: chain 'C' and resid 87 through 89 removed outlier: 8.262A pdb=" N LEU C 88 " --> pdb=" O SER C 36 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N LYS C 38 " --> pdb=" O LEU C 88 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LYS C 2 " --> pdb=" O CYS C 143 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N ILE C 145 " --> pdb=" O LYS C 2 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ILE C 4 " --> pdb=" O ILE C 145 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N LEU C 147 " --> pdb=" O ILE C 4 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL C 6 " --> pdb=" O LEU C 147 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TYR C 3 " --> pdb=" O CYS C 176 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ILE C 178 " --> pdb=" O TYR C 3 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU C 5 " --> pdb=" O ILE C 178 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N VAL C 180 " --> pdb=" O LEU C 5 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N THR C 7 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N LEU C 182 " --> pdb=" O THR C 7 " (cutoff:3.500A) removed outlier: 9.612A pdb=" N LEU C 213 " --> pdb=" O PHE C 175 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ASN C 177 " --> pdb=" O LEU C 213 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N VAL C 215 " --> pdb=" O ASN C 177 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N HIS C 179 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N ARG C 217 " --> pdb=" O HIS C 179 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N SER C 181 " --> pdb=" O ARG C 217 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 59 through 60 Processing sheet with id=AB2, first strand: chain 'C' and resid 331 through 337 removed outlier: 6.673A pdb=" N CYS C 299 " --> pdb=" O GLU C 333 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N LYS C 335 " --> pdb=" O CYS C 299 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE C 301 " --> pdb=" O LYS C 335 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ILE C 337 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU C 303 " --> pdb=" O ILE C 337 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N LEU C 368 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ALA C 302 " --> pdb=" O LEU C 368 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N PHE C 395 " --> pdb=" O VAL C 521 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N VAL C 523 " --> pdb=" O PHE C 395 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N GLY C 397 " --> pdb=" O VAL C 523 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N PHE C 520 " --> pdb=" O LEU C 514 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N MET C 509 " --> pdb=" O GLN C 502 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N GLN C 502 " --> pdb=" O MET C 509 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE C 511 " --> pdb=" O VAL C 500 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 433 through 435 Processing sheet with id=AB4, first strand: chain 'D' and resid 87 through 89 removed outlier: 8.262A pdb=" N LEU D 88 " --> pdb=" O SER D 36 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N LYS D 38 " --> pdb=" O LEU D 88 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LYS D 2 " --> pdb=" O CYS D 143 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N ILE D 145 " --> pdb=" O LYS D 2 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ILE D 4 " --> pdb=" O ILE D 145 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N LEU D 147 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL D 6 " --> pdb=" O LEU D 147 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TYR D 3 " --> pdb=" O CYS D 176 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ILE D 178 " --> pdb=" O TYR D 3 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU D 5 " --> pdb=" O ILE D 178 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N VAL D 180 " --> pdb=" O LEU D 5 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N THR D 7 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N LEU D 182 " --> pdb=" O THR D 7 " (cutoff:3.500A) removed outlier: 9.612A pdb=" N LEU D 213 " --> pdb=" O PHE D 175 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ASN D 177 " --> pdb=" O LEU D 213 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N VAL D 215 " --> pdb=" O ASN D 177 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N HIS D 179 " --> pdb=" O VAL D 215 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N ARG D 217 " --> pdb=" O HIS D 179 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N SER D 181 " --> pdb=" O ARG D 217 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 59 through 60 Processing sheet with id=AB6, first strand: chain 'D' and resid 331 through 337 removed outlier: 6.673A pdb=" N CYS D 299 " --> pdb=" O GLU D 333 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N LYS D 335 " --> pdb=" O CYS D 299 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE D 301 " --> pdb=" O LYS D 335 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ILE D 337 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU D 303 " --> pdb=" O ILE D 337 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N LEU D 368 " --> pdb=" O SER D 300 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ALA D 302 " --> pdb=" O LEU D 368 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N PHE D 395 " --> pdb=" O VAL D 521 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N VAL D 523 " --> pdb=" O PHE D 395 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N GLY D 397 " --> pdb=" O VAL D 523 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N PHE D 520 " --> pdb=" O LEU D 514 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N MET D 509 " --> pdb=" O GLN D 502 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N GLN D 502 " --> pdb=" O MET D 509 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE D 511 " --> pdb=" O VAL D 500 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 433 through 435 716 hydrogen bonds defined for protein. 2064 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: 3.31 Time building geometry restraints manager: 2.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4676 1.34 - 1.46: 2960 1.46 - 1.58: 10052 1.58 - 1.70: 8 1.70 - 1.82: 140 Bond restraints: 17836 Sorted by residual: bond pdb=" O3B CTP B 603 " pdb=" PG CTP B 603 " ideal model delta sigma weight residual 1.751 1.531 0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" O3B CTP A 602 " pdb=" PG CTP A 602 " ideal model delta sigma weight residual 1.751 1.531 0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" O3B CTP C 602 " pdb=" PG CTP C 602 " ideal model delta sigma weight residual 1.751 1.531 0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" O3B CTP D 603 " pdb=" PG CTP D 603 " ideal model delta sigma weight residual 1.751 1.531 0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" O3B CTP B 602 " pdb=" PG CTP B 602 " ideal model delta sigma weight residual 1.751 1.537 0.214 2.00e-02 2.50e+03 1.15e+02 ... (remaining 17831 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 20920 2.74 - 5.49: 3064 5.49 - 8.23: 156 8.23 - 10.98: 24 10.98 - 13.72: 20 Bond angle restraints: 24184 Sorted by residual: angle pdb=" CA ASP C 271 " pdb=" CB ASP C 271 " pdb=" CG ASP C 271 " ideal model delta sigma weight residual 112.60 119.81 -7.21 1.00e+00 1.00e+00 5.20e+01 angle pdb=" CA ASP A 271 " pdb=" CB ASP A 271 " pdb=" CG ASP A 271 " ideal model delta sigma weight residual 112.60 119.81 -7.21 1.00e+00 1.00e+00 5.20e+01 angle pdb=" CA ASP D 271 " pdb=" CB ASP D 271 " pdb=" CG ASP D 271 " ideal model delta sigma weight residual 112.60 119.81 -7.21 1.00e+00 1.00e+00 5.20e+01 angle pdb=" CA ASP B 271 " pdb=" CB ASP B 271 " pdb=" CG ASP B 271 " ideal model delta sigma weight residual 112.60 119.81 -7.21 1.00e+00 1.00e+00 5.20e+01 angle pdb=" N PRO A 538 " pdb=" CA PRO A 538 " pdb=" C PRO A 538 " ideal model delta sigma weight residual 110.70 117.30 -6.60 1.22e+00 6.72e-01 2.93e+01 ... (remaining 24179 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.11: 9744 16.11 - 32.22: 832 32.22 - 48.33: 244 48.33 - 64.44: 68 64.44 - 80.55: 24 Dihedral angle restraints: 10912 sinusoidal: 4684 harmonic: 6228 Sorted by residual: dihedral pdb=" C ASP D 271 " pdb=" N ASP D 271 " pdb=" CA ASP D 271 " pdb=" CB ASP D 271 " ideal model delta harmonic sigma weight residual -122.60 -138.31 15.71 0 2.50e+00 1.60e-01 3.95e+01 dihedral pdb=" C ASP B 271 " pdb=" N ASP B 271 " pdb=" CA ASP B 271 " pdb=" CB ASP B 271 " ideal model delta harmonic sigma weight residual -122.60 -138.31 15.71 0 2.50e+00 1.60e-01 3.95e+01 dihedral pdb=" C ASP C 271 " pdb=" N ASP C 271 " pdb=" CA ASP C 271 " pdb=" CB ASP C 271 " ideal model delta harmonic sigma weight residual -122.60 -138.31 15.71 0 2.50e+00 1.60e-01 3.95e+01 ... (remaining 10909 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 2072 0.114 - 0.229: 528 0.229 - 0.343: 56 0.343 - 0.457: 12 0.457 - 0.571: 4 Chirality restraints: 2672 Sorted by residual: chirality pdb=" CA ASP D 271 " pdb=" N ASP D 271 " pdb=" C ASP D 271 " pdb=" CB ASP D 271 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.16e+00 chirality pdb=" CA ASP B 271 " pdb=" N ASP B 271 " pdb=" C ASP B 271 " pdb=" CB ASP B 271 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.16e+00 chirality pdb=" CA ASP C 271 " pdb=" N ASP C 271 " pdb=" C ASP C 271 " pdb=" CB ASP C 271 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.16e+00 ... (remaining 2669 not shown) Planarity restraints: 3076 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 124 " -0.088 2.00e-02 2.50e+03 4.87e-02 5.93e+01 pdb=" CG TRP D 124 " 0.009 2.00e-02 2.50e+03 pdb=" CD1 TRP D 124 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP D 124 " 0.039 2.00e-02 2.50e+03 pdb=" NE1 TRP D 124 " 0.043 2.00e-02 2.50e+03 pdb=" CE2 TRP D 124 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP D 124 " 0.051 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 124 " -0.078 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 124 " 0.037 2.00e-02 2.50e+03 pdb=" CH2 TRP D 124 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 124 " 0.088 2.00e-02 2.50e+03 4.87e-02 5.93e+01 pdb=" CG TRP B 124 " -0.009 2.00e-02 2.50e+03 pdb=" CD1 TRP B 124 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP B 124 " -0.039 2.00e-02 2.50e+03 pdb=" NE1 TRP B 124 " -0.043 2.00e-02 2.50e+03 pdb=" CE2 TRP B 124 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 124 " -0.051 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 124 " 0.078 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 124 " -0.037 2.00e-02 2.50e+03 pdb=" CH2 TRP B 124 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 124 " 0.088 2.00e-02 2.50e+03 4.87e-02 5.93e+01 pdb=" CG TRP C 124 " -0.009 2.00e-02 2.50e+03 pdb=" CD1 TRP C 124 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP C 124 " -0.039 2.00e-02 2.50e+03 pdb=" NE1 TRP C 124 " -0.043 2.00e-02 2.50e+03 pdb=" CE2 TRP C 124 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 124 " -0.051 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 124 " 0.078 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 124 " -0.037 2.00e-02 2.50e+03 pdb=" CH2 TRP C 124 " 0.041 2.00e-02 2.50e+03 ... (remaining 3073 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 36 2.51 - 3.10: 11548 3.10 - 3.70: 26190 3.70 - 4.30: 39628 4.30 - 4.90: 66622 Nonbonded interactions: 144024 Sorted by model distance: nonbonded pdb=" O1G CTP A 602 " pdb="MG MG B 601 " model vdw 1.908 2.170 nonbonded pdb="MG MG A 604 " pdb=" O1G CTP B 603 " model vdw 1.908 2.170 nonbonded pdb=" O1G CTP C 602 " pdb="MG MG D 601 " model vdw 1.908 2.170 nonbonded pdb="MG MG C 604 " pdb=" O1G CTP D 603 " model vdw 1.908 2.170 nonbonded pdb=" O2G CTP D 602 " pdb="MG MG D 604 " model vdw 2.012 2.170 ... (remaining 144019 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 555 or resid 602 or resid 604)) selection = (chain 'B' and (resid 1 through 555 or resid 602 or resid 604)) selection = (chain 'C' and (resid 1 through 555 or resid 602 or resid 604)) selection = (chain 'D' and (resid 1 through 555 or resid 602 or resid 604)) } 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: 1.060 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: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.060 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 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 : 0.014 0.220 17836 Z= 0.833 Angle : 1.905 13.719 24184 Z= 1.228 Chirality : 0.101 0.571 2672 Planarity : 0.014 0.138 3076 Dihedral : 14.556 80.554 6912 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.42 % Allowed : 3.55 % Favored : 96.03 % Cbeta Deviations : 0.40 % 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: -0.74 (0.18), residues: 2140 helix: -0.89 (0.16), residues: 912 sheet: 0.02 (0.26), residues: 356 loop : 0.02 (0.22), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG B 477 TYR 0.091 0.016 TYR A 336 PHE 0.061 0.013 PHE A 163 TRP 0.088 0.016 TRP D 124 HIS 0.013 0.003 HIS C 478 Details of bonding type rmsd/Z covalent geometry : bond 0.01407 / 0.83 (17836) covalent geometry : angle 1.90490 / 1.23 (24184) hydrogen bonds : bond 0.16550 / 11.21 ( 716) hydrogen bonds : angle 6.87626 / 4.72 ( 2064) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 420 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 MET cc_start: 0.8635 (mtt) cc_final: 0.8345 (mtm) REVERT: A 133 VAL cc_start: 0.8253 (t) cc_final: 0.7959 (m) REVERT: A 244 VAL cc_start: 0.8786 (t) cc_final: 0.8572 (t) REVERT: A 283 MET cc_start: 0.7131 (mtp) cc_final: 0.6914 (mtm) REVERT: A 298 THR cc_start: 0.7571 (t) cc_final: 0.7282 (m) REVERT: A 341 ASP cc_start: 0.6147 (m-30) cc_final: 0.5427 (m-30) REVERT: A 361 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.7900 (tp) REVERT: A 481 ARG cc_start: 0.6914 (ptp-110) cc_final: 0.6493 (ptt180) REVERT: A 482 PHE cc_start: 0.8083 (m-80) cc_final: 0.7742 (m-80) REVERT: B 126 MET cc_start: 0.8642 (mtt) cc_final: 0.8351 (mtm) REVERT: B 133 VAL cc_start: 0.8253 (t) cc_final: 0.7960 (m) REVERT: B 244 VAL cc_start: 0.8787 (t) cc_final: 0.8571 (t) REVERT: B 283 MET cc_start: 0.7130 (mtp) cc_final: 0.6912 (mtm) REVERT: B 298 THR cc_start: 0.7572 (t) cc_final: 0.7282 (m) REVERT: B 341 ASP cc_start: 0.6152 (m-30) cc_final: 0.5434 (m-30) REVERT: B 361 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.7898 (tp) REVERT: B 481 ARG cc_start: 0.6921 (ptp-110) cc_final: 0.6501 (ptt180) REVERT: B 482 PHE cc_start: 0.8086 (m-80) cc_final: 0.7743 (m-80) REVERT: C 126 MET cc_start: 0.8635 (mtt) cc_final: 0.8345 (mtm) REVERT: C 133 VAL cc_start: 0.8249 (t) cc_final: 0.7958 (m) REVERT: C 244 VAL cc_start: 0.8786 (t) cc_final: 0.8570 (t) REVERT: C 283 MET cc_start: 0.7133 (mtp) cc_final: 0.6913 (mtm) REVERT: C 298 THR cc_start: 0.7569 (t) cc_final: 0.7276 (m) REVERT: C 341 ASP cc_start: 0.6148 (m-30) cc_final: 0.5429 (m-30) REVERT: C 361 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.7899 (tp) REVERT: C 481 ARG cc_start: 0.6914 (ptp-110) cc_final: 0.6494 (ptt180) REVERT: C 482 PHE cc_start: 0.8087 (m-80) cc_final: 0.7747 (m-80) REVERT: D 126 MET cc_start: 0.8640 (mtt) cc_final: 0.8350 (mtm) REVERT: D 133 VAL cc_start: 0.8250 (t) cc_final: 0.7958 (m) REVERT: D 244 VAL cc_start: 0.8785 (t) cc_final: 0.8568 (t) REVERT: D 283 MET cc_start: 0.7132 (mtp) cc_final: 0.6913 (mtm) REVERT: D 298 THR cc_start: 0.7567 (t) cc_final: 0.7276 (m) REVERT: D 341 ASP cc_start: 0.6153 (m-30) cc_final: 0.5429 (m-30) REVERT: D 361 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7899 (tp) REVERT: D 481 ARG cc_start: 0.6921 (ptp-110) cc_final: 0.6502 (ptt180) REVERT: D 482 PHE cc_start: 0.8087 (m-80) cc_final: 0.7748 (m-80) outliers start: 8 outliers final: 0 residues processed: 428 average time/residue: 0.1547 time to fit residues: 96.0047 Evaluate side-chains 304 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 300 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain D residue 361 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 8.9990 chunk 200 optimal weight: 4.9990 chunk 212 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 ASN A 177 ASN A 412 ASN A 502 GLN B 87 ASN B 177 ASN B 412 ASN B 502 GLN C 87 ASN C 177 ASN C 412 ASN C 502 GLN D 87 ASN D 177 ASN D 412 ASN D 502 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.179154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.137571 restraints weight = 19630.751| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.98 r_work: 0.3086 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17836 Z= 0.141 Angle : 0.597 5.820 24184 Z= 0.316 Chirality : 0.046 0.136 2672 Planarity : 0.005 0.035 3076 Dihedral : 9.846 58.961 2652 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.46 % Allowed : 8.77 % Favored : 89.77 % 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: 0.38 (0.18), residues: 2140 helix: 0.54 (0.17), residues: 940 sheet: 0.15 (0.26), residues: 356 loop : 0.19 (0.23), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 454 TYR 0.011 0.002 TYR C 42 PHE 0.013 0.002 PHE B 424 TRP 0.009 0.002 TRP B 416 HIS 0.004 0.001 HIS B 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (17836) covalent geometry : angle 0.59711 / 0.32 (24184) hydrogen bonds : bond 0.03897 / 2.65 ( 716) hydrogen bonds : angle 4.56296 / 3.09 ( 2064) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 288 time to evaluate : 0.717 Fit side-chains REVERT: A 49 THR cc_start: 0.7913 (m) cc_final: 0.7522 (p) REVERT: A 126 MET cc_start: 0.8479 (mtt) cc_final: 0.8175 (mtp) REVERT: A 220 ASN cc_start: 0.8523 (m110) cc_final: 0.8266 (m110) REVERT: A 294 ARG cc_start: 0.7172 (ptp-170) cc_final: 0.6789 (ptt90) REVERT: A 353 ARG cc_start: 0.5472 (ttp-170) cc_final: 0.5228 (ttp-170) REVERT: A 481 ARG cc_start: 0.7162 (ptp-110) cc_final: 0.6621 (ptt180) REVERT: B 49 THR cc_start: 0.7922 (m) cc_final: 0.7535 (p) REVERT: B 126 MET cc_start: 0.8485 (mtt) cc_final: 0.8177 (mtp) REVERT: B 220 ASN cc_start: 0.8547 (m110) cc_final: 0.8296 (m110) REVERT: B 294 ARG cc_start: 0.7164 (ptp-170) cc_final: 0.6778 (ptt90) REVERT: B 353 ARG cc_start: 0.5445 (ttp-170) cc_final: 0.5191 (ttp-170) REVERT: B 481 ARG cc_start: 0.7147 (ptp-110) cc_final: 0.6613 (ptt180) REVERT: C 49 THR cc_start: 0.7919 (m) cc_final: 0.7522 (p) REVERT: C 126 MET cc_start: 0.8472 (mtt) cc_final: 0.8169 (mtp) REVERT: C 220 ASN cc_start: 0.8530 (m110) cc_final: 0.8271 (m110) REVERT: C 294 ARG cc_start: 0.7176 (ptp-170) cc_final: 0.6790 (ptt90) REVERT: C 353 ARG cc_start: 0.5479 (ttp-170) cc_final: 0.5242 (ttp-170) REVERT: C 481 ARG cc_start: 0.7176 (ptp-110) cc_final: 0.6641 (ptt180) REVERT: D 49 THR cc_start: 0.7924 (m) cc_final: 0.7529 (p) REVERT: D 126 MET cc_start: 0.8482 (mtt) cc_final: 0.8178 (mtp) REVERT: D 220 ASN cc_start: 0.8536 (m110) cc_final: 0.8278 (m110) REVERT: D 294 ARG cc_start: 0.7155 (ptp-170) cc_final: 0.6778 (ptt90) REVERT: D 353 ARG cc_start: 0.5491 (ttp-170) cc_final: 0.5246 (ttp-170) REVERT: D 481 ARG cc_start: 0.7165 (ptp-110) cc_final: 0.6621 (ptt180) outliers start: 28 outliers final: 24 residues processed: 304 average time/residue: 0.1560 time to fit residues: 70.1536 Evaluate side-chains 264 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 240 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 306 LYS Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 293 ASP Chi-restraints excluded: chain B residue 306 LYS Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 293 ASP Chi-restraints excluded: chain C residue 306 LYS Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 523 VAL Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 293 ASP Chi-restraints excluded: chain D residue 306 LYS Chi-restraints excluded: chain D residue 521 VAL Chi-restraints excluded: chain D residue 523 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 12 optimal weight: 5.9990 chunk 84 optimal weight: 0.5980 chunk 187 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 170 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 chunk 32 optimal weight: 0.3980 chunk 46 optimal weight: 10.0000 chunk 154 optimal weight: 10.0000 chunk 147 optimal weight: 10.0000 chunk 192 optimal weight: 0.8980 overall best weight: 1.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.179028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.135574 restraints weight = 19661.678| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.97 r_work: 0.3143 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17836 Z= 0.120 Angle : 0.531 5.912 24184 Z= 0.278 Chirality : 0.044 0.136 2672 Planarity : 0.005 0.036 3076 Dihedral : 9.314 59.909 2644 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.51 % Allowed : 9.60 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.19), residues: 2140 helix: 0.77 (0.17), residues: 976 sheet: 0.01 (0.25), residues: 364 loop : 0.20 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 465 TYR 0.014 0.001 TYR C 42 PHE 0.011 0.001 PHE D 424 TRP 0.011 0.001 TRP B 387 HIS 0.006 0.001 HIS B 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (17836) covalent geometry : angle 0.53095 / 0.28 (24184) hydrogen bonds : bond 0.03613 / 2.45 ( 716) hydrogen bonds : angle 4.07454 / 2.78 ( 2064) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 244 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 THR cc_start: 0.7899 (m) cc_final: 0.7599 (p) REVERT: A 126 MET cc_start: 0.8447 (mtt) cc_final: 0.8111 (mtp) REVERT: A 220 ASN cc_start: 0.8526 (m110) cc_final: 0.8298 (m110) REVERT: A 294 ARG cc_start: 0.7282 (ptp-170) cc_final: 0.6846 (ptt90) REVERT: A 306 LYS cc_start: 0.6892 (OUTLIER) cc_final: 0.6679 (ptpt) REVERT: A 481 ARG cc_start: 0.7013 (ptp-110) cc_final: 0.6431 (ptt180) REVERT: A 498 LYS cc_start: 0.6377 (ttmt) cc_final: 0.5736 (tppt) REVERT: B 49 THR cc_start: 0.7901 (m) cc_final: 0.7603 (p) REVERT: B 126 MET cc_start: 0.8464 (mtt) cc_final: 0.8128 (mtp) REVERT: B 220 ASN cc_start: 0.8532 (m110) cc_final: 0.8301 (m110) REVERT: B 294 ARG cc_start: 0.7270 (ptp-170) cc_final: 0.6840 (ptt90) REVERT: B 306 LYS cc_start: 0.6891 (OUTLIER) cc_final: 0.6676 (ptpt) REVERT: B 481 ARG cc_start: 0.7034 (ptp-110) cc_final: 0.6458 (ptt180) REVERT: C 49 THR cc_start: 0.7894 (m) cc_final: 0.7594 (p) REVERT: C 126 MET cc_start: 0.8439 (mtt) cc_final: 0.8108 (mtp) REVERT: C 220 ASN cc_start: 0.8521 (m110) cc_final: 0.8288 (m110) REVERT: C 294 ARG cc_start: 0.7256 (ptp-170) cc_final: 0.6833 (ptt90) REVERT: C 306 LYS cc_start: 0.6898 (OUTLIER) cc_final: 0.6683 (ptpt) REVERT: C 481 ARG cc_start: 0.7013 (ptp-110) cc_final: 0.6448 (ptt180) REVERT: C 498 LYS cc_start: 0.6379 (ttmt) cc_final: 0.5735 (tppt) REVERT: D 49 THR cc_start: 0.7898 (m) cc_final: 0.7600 (p) REVERT: D 126 MET cc_start: 0.8455 (mtt) cc_final: 0.8119 (mtp) REVERT: D 220 ASN cc_start: 0.8535 (m110) cc_final: 0.8306 (m110) REVERT: D 294 ARG cc_start: 0.7259 (ptp-170) cc_final: 0.6833 (ptt90) REVERT: D 306 LYS cc_start: 0.6906 (OUTLIER) cc_final: 0.6693 (ptpt) REVERT: D 481 ARG cc_start: 0.7015 (ptp-110) cc_final: 0.6441 (ptt180) outliers start: 48 outliers final: 32 residues processed: 272 average time/residue: 0.1529 time to fit residues: 62.0784 Evaluate side-chains 268 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 232 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 306 LYS Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 306 LYS Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 306 LYS Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 288 MET Chi-restraints excluded: chain D residue 306 LYS Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 521 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 191 optimal weight: 20.0000 chunk 193 optimal weight: 0.9990 chunk 184 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 180 optimal weight: 0.0770 chunk 124 optimal weight: 0.9990 chunk 202 optimal weight: 0.8980 chunk 126 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 143 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 overall best weight: 1.1944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.178684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.136515 restraints weight = 19688.836| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.00 r_work: 0.3179 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 17836 Z= 0.100 Angle : 0.488 5.738 24184 Z= 0.251 Chirality : 0.043 0.135 2672 Planarity : 0.004 0.036 3076 Dihedral : 7.181 45.797 2644 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.92 % Allowed : 11.06 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.19), residues: 2140 helix: 1.07 (0.17), residues: 980 sheet: -0.05 (0.25), residues: 368 loop : 0.13 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 465 TYR 0.013 0.001 TYR D 42 PHE 0.008 0.001 PHE B 424 TRP 0.011 0.001 TRP B 387 HIS 0.005 0.001 HIS D 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (17836) covalent geometry : angle 0.48837 / 0.25 (24184) hydrogen bonds : bond 0.03024 / 2.05 ( 716) hydrogen bonds : angle 3.90265 / 2.68 ( 2064) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 236 time to evaluate : 0.708 Fit side-chains REVERT: A 49 THR cc_start: 0.7883 (m) cc_final: 0.7635 (p) REVERT: A 126 MET cc_start: 0.8323 (mtt) cc_final: 0.7963 (mtp) REVERT: A 220 ASN cc_start: 0.8527 (m110) cc_final: 0.8289 (m110) REVERT: A 294 ARG cc_start: 0.7185 (ptp-170) cc_final: 0.6828 (ptt90) REVERT: A 361 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.7955 (tp) REVERT: A 481 ARG cc_start: 0.6905 (ptp-110) cc_final: 0.6378 (ptt180) REVERT: B 49 THR cc_start: 0.7877 (m) cc_final: 0.7630 (p) REVERT: B 88 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7763 (tt) REVERT: B 126 MET cc_start: 0.8343 (mtt) cc_final: 0.7979 (mtp) REVERT: B 220 ASN cc_start: 0.8522 (m110) cc_final: 0.8276 (m110) REVERT: B 294 ARG cc_start: 0.7203 (ptp-170) cc_final: 0.6832 (ptt90) REVERT: B 361 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.7955 (tp) REVERT: B 481 ARG cc_start: 0.6941 (ptp-110) cc_final: 0.6404 (ptt180) REVERT: C 49 THR cc_start: 0.7868 (m) cc_final: 0.7623 (p) REVERT: C 88 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7775 (tt) REVERT: C 126 MET cc_start: 0.8340 (mtt) cc_final: 0.7980 (mtp) REVERT: C 220 ASN cc_start: 0.8536 (m110) cc_final: 0.8298 (m110) REVERT: C 294 ARG cc_start: 0.7215 (ptp-170) cc_final: 0.6829 (ptt90) REVERT: C 361 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.7960 (tp) REVERT: C 481 ARG cc_start: 0.6891 (ptp-110) cc_final: 0.6386 (ptt180) REVERT: D 49 THR cc_start: 0.7865 (m) cc_final: 0.7616 (p) REVERT: D 88 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7770 (tt) REVERT: D 126 MET cc_start: 0.8344 (mtt) cc_final: 0.7980 (mtp) REVERT: D 220 ASN cc_start: 0.8537 (m110) cc_final: 0.8297 (m110) REVERT: D 294 ARG cc_start: 0.7195 (ptp-170) cc_final: 0.6817 (ptt90) REVERT: D 361 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.7957 (tp) REVERT: D 481 ARG cc_start: 0.6914 (ptp-110) cc_final: 0.6382 (ptt180) outliers start: 56 outliers final: 44 residues processed: 264 average time/residue: 0.1507 time to fit residues: 59.6786 Evaluate side-chains 271 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 220 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 513 GLU Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 293 ASP Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 513 GLU Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 232 MET Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 293 ASP Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 513 GLU Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 232 MET Chi-restraints excluded: chain D residue 288 MET Chi-restraints excluded: chain D residue 293 ASP Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 513 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 114 optimal weight: 10.0000 chunk 70 optimal weight: 0.8980 chunk 179 optimal weight: 7.9990 chunk 134 optimal weight: 2.9990 chunk 94 optimal weight: 20.0000 chunk 96 optimal weight: 30.0000 chunk 171 optimal weight: 0.9990 chunk 187 optimal weight: 0.6980 chunk 212 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.176527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.133585 restraints weight = 19466.029| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.82 r_work: 0.3156 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 17836 Z= 0.114 Angle : 0.491 6.057 24184 Z= 0.251 Chirality : 0.043 0.135 2672 Planarity : 0.005 0.036 3076 Dihedral : 6.220 39.044 2644 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.34 % Allowed : 11.64 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.19), residues: 2140 helix: 1.13 (0.17), residues: 980 sheet: -0.07 (0.25), residues: 368 loop : -0.05 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 465 TYR 0.015 0.001 TYR C 42 PHE 0.009 0.001 PHE B 166 TRP 0.010 0.001 TRP B 387 HIS 0.004 0.001 HIS D 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.11 (17836) covalent geometry : angle 0.49097 / 0.25 (24184) hydrogen bonds : bond 0.03231 / 2.18 ( 716) hydrogen bonds : angle 3.82862 / 2.64 ( 2064) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 232 time to evaluate : 0.720 Fit side-chains REVERT: A 88 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7957 (tt) REVERT: A 126 MET cc_start: 0.8537 (mtt) cc_final: 0.8172 (mtp) REVERT: A 294 ARG cc_start: 0.7337 (ptp-170) cc_final: 0.6859 (ptt90) REVERT: A 361 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7838 (tp) REVERT: A 481 ARG cc_start: 0.6977 (ptp-110) cc_final: 0.6365 (ptt180) REVERT: A 513 GLU cc_start: 0.6248 (OUTLIER) cc_final: 0.5370 (pp20) REVERT: A 535 LYS cc_start: 0.7741 (pttm) cc_final: 0.7527 (pttp) REVERT: B 88 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7912 (tt) REVERT: B 126 MET cc_start: 0.8544 (mtt) cc_final: 0.8167 (mtp) REVERT: B 239 GLU cc_start: 0.7817 (mp0) cc_final: 0.7578 (mm-30) REVERT: B 294 ARG cc_start: 0.7362 (ptp-170) cc_final: 0.6865 (ptt90) REVERT: B 361 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7838 (tp) REVERT: B 481 ARG cc_start: 0.7013 (ptp-110) cc_final: 0.6389 (ptt180) REVERT: B 513 GLU cc_start: 0.6256 (OUTLIER) cc_final: 0.5372 (pp20) REVERT: B 535 LYS cc_start: 0.7727 (pttm) cc_final: 0.7524 (pttp) REVERT: C 88 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7916 (tt) REVERT: C 126 MET cc_start: 0.8542 (mtt) cc_final: 0.8168 (mtp) REVERT: C 239 GLU cc_start: 0.7770 (mp0) cc_final: 0.7560 (mm-30) REVERT: C 294 ARG cc_start: 0.7343 (ptp-170) cc_final: 0.6847 (ptt90) REVERT: C 361 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7842 (tp) REVERT: C 481 ARG cc_start: 0.6961 (ptp-110) cc_final: 0.6360 (ptt180) REVERT: C 513 GLU cc_start: 0.6271 (OUTLIER) cc_final: 0.5388 (pp20) REVERT: C 535 LYS cc_start: 0.7721 (pttm) cc_final: 0.7509 (pttp) REVERT: D 88 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7922 (tt) REVERT: D 126 MET cc_start: 0.8540 (mtt) cc_final: 0.8164 (mtp) REVERT: D 294 ARG cc_start: 0.7327 (ptp-170) cc_final: 0.6847 (ptt90) REVERT: D 361 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7839 (tp) REVERT: D 481 ARG cc_start: 0.6996 (ptp-110) cc_final: 0.6381 (ptt180) REVERT: D 513 GLU cc_start: 0.6223 (OUTLIER) cc_final: 0.5354 (pp20) REVERT: D 535 LYS cc_start: 0.7729 (pttm) cc_final: 0.7525 (pttp) outliers start: 64 outliers final: 44 residues processed: 272 average time/residue: 0.1488 time to fit residues: 61.0304 Evaluate side-chains 254 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 198 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 513 GLU Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 293 ASP Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 513 GLU Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 232 MET Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 293 ASP Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 513 GLU Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 232 MET Chi-restraints excluded: chain D residue 288 MET Chi-restraints excluded: chain D residue 293 ASP Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 513 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 150 optimal weight: 30.0000 chunk 174 optimal weight: 0.7980 chunk 183 optimal weight: 7.9990 chunk 9 optimal weight: 0.7980 chunk 132 optimal weight: 5.9990 chunk 44 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 73 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 chunk 162 optimal weight: 9.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.177405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.134919 restraints weight = 19575.025| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.02 r_work: 0.3131 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17836 Z= 0.114 Angle : 0.494 6.094 24184 Z= 0.251 Chirality : 0.043 0.137 2672 Planarity : 0.004 0.036 3076 Dihedral : 6.134 37.427 2644 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.71 % Allowed : 12.37 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.19), residues: 2140 helix: 1.19 (0.17), residues: 980 sheet: -0.12 (0.25), residues: 368 loop : -0.13 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 465 TYR 0.015 0.001 TYR C 42 PHE 0.008 0.001 PHE A 166 TRP 0.007 0.001 TRP A 124 HIS 0.004 0.001 HIS D 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.11 (17836) covalent geometry : angle 0.49407 / 0.25 (24184) hydrogen bonds : bond 0.03070 / 2.09 ( 716) hydrogen bonds : angle 3.80954 / 2.63 ( 2064) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 208 time to evaluate : 0.639 Fit side-chains REVERT: A 126 MET cc_start: 0.8438 (mtt) cc_final: 0.8046 (mtp) REVERT: A 294 ARG cc_start: 0.7297 (ptp-170) cc_final: 0.6871 (ptt90) REVERT: A 361 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7850 (tp) REVERT: A 481 ARG cc_start: 0.6877 (ptp-110) cc_final: 0.6304 (ptt180) REVERT: B 88 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7869 (tt) REVERT: B 126 MET cc_start: 0.8431 (mtt) cc_final: 0.8037 (mtp) REVERT: B 294 ARG cc_start: 0.7316 (ptp-170) cc_final: 0.6871 (ptt90) REVERT: B 361 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7852 (tp) REVERT: B 481 ARG cc_start: 0.6894 (ptp-110) cc_final: 0.6299 (ptt180) REVERT: B 499 PHE cc_start: 0.7512 (m-80) cc_final: 0.7157 (m-80) REVERT: C 88 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7883 (tt) REVERT: C 126 MET cc_start: 0.8426 (mtt) cc_final: 0.8037 (mtp) REVERT: C 294 ARG cc_start: 0.7306 (ptp-170) cc_final: 0.6867 (ptt90) REVERT: C 361 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7846 (tp) REVERT: C 481 ARG cc_start: 0.6859 (ptp-110) cc_final: 0.6286 (ptt180) REVERT: D 88 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7880 (tt) REVERT: D 126 MET cc_start: 0.8439 (mtt) cc_final: 0.8045 (mtp) REVERT: D 294 ARG cc_start: 0.7296 (ptp-170) cc_final: 0.6863 (ptt90) REVERT: D 361 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7846 (tp) REVERT: D 481 ARG cc_start: 0.6889 (ptp-110) cc_final: 0.6302 (ptt180) REVERT: D 499 PHE cc_start: 0.7513 (m-80) cc_final: 0.7162 (m-80) outliers start: 71 outliers final: 50 residues processed: 255 average time/residue: 0.1427 time to fit residues: 55.4053 Evaluate side-chains 258 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 201 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 513 GLU Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 293 ASP Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 232 MET Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 293 ASP Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 513 GLU Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 232 MET Chi-restraints excluded: chain D residue 288 MET Chi-restraints excluded: chain D residue 293 ASP Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 512 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 179 optimal weight: 6.9990 chunk 34 optimal weight: 0.5980 chunk 50 optimal weight: 0.3980 chunk 15 optimal weight: 1.9990 chunk 191 optimal weight: 20.0000 chunk 137 optimal weight: 20.0000 chunk 97 optimal weight: 10.0000 chunk 135 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 104 optimal weight: 6.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.175557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.133716 restraints weight = 19757.947| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.07 r_work: 0.3069 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17836 Z= 0.140 Angle : 0.519 5.741 24184 Z= 0.262 Chirality : 0.044 0.138 2672 Planarity : 0.005 0.037 3076 Dihedral : 6.311 41.326 2644 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.03 % Allowed : 13.05 % Favored : 83.92 % 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: 0.52 (0.19), residues: 2140 helix: 1.15 (0.18), residues: 972 sheet: -0.11 (0.25), residues: 364 loop : -0.30 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 454 TYR 0.016 0.001 TYR A 42 PHE 0.010 0.001 PHE D 166 TRP 0.009 0.001 TRP A 124 HIS 0.004 0.001 HIS C 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 (17836) covalent geometry : angle 0.51917 / 0.26 (24184) hydrogen bonds : bond 0.03378 / 2.29 ( 716) hydrogen bonds : angle 3.82644 / 2.65 ( 2064) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 224 time to evaluate : 0.701 Fit side-chains REVERT: A 88 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7836 (tt) REVERT: A 126 MET cc_start: 0.8509 (mtt) cc_final: 0.8134 (mtp) REVERT: A 294 ARG cc_start: 0.7288 (ptp-170) cc_final: 0.6862 (ptt90) REVERT: A 316 SER cc_start: 0.8652 (m) cc_final: 0.8401 (m) REVERT: A 481 ARG cc_start: 0.6973 (ptp-110) cc_final: 0.6400 (ptt180) REVERT: A 513 GLU cc_start: 0.6180 (OUTLIER) cc_final: 0.5406 (pp20) REVERT: B 88 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7899 (tt) REVERT: B 126 MET cc_start: 0.8507 (mtt) cc_final: 0.8130 (mtp) REVERT: B 294 ARG cc_start: 0.7323 (ptp-170) cc_final: 0.6870 (ptt90) REVERT: B 316 SER cc_start: 0.8660 (m) cc_final: 0.8437 (m) REVERT: B 481 ARG cc_start: 0.6960 (ptp-110) cc_final: 0.6384 (ptt180) REVERT: C 88 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7908 (tt) REVERT: C 126 MET cc_start: 0.8486 (mtt) cc_final: 0.8112 (mtp) REVERT: C 294 ARG cc_start: 0.7324 (ptp-170) cc_final: 0.6873 (ptt90) REVERT: C 316 SER cc_start: 0.8662 (m) cc_final: 0.8408 (m) REVERT: C 481 ARG cc_start: 0.6932 (ptp-110) cc_final: 0.6363 (ptt180) REVERT: C 513 GLU cc_start: 0.6227 (OUTLIER) cc_final: 0.5457 (pp20) REVERT: D 88 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7910 (tt) REVERT: D 126 MET cc_start: 0.8511 (mtt) cc_final: 0.8136 (mtp) REVERT: D 294 ARG cc_start: 0.7317 (ptp-170) cc_final: 0.6872 (ptt90) REVERT: D 316 SER cc_start: 0.8667 (m) cc_final: 0.8414 (m) REVERT: D 481 ARG cc_start: 0.6964 (ptp-110) cc_final: 0.6391 (ptt180) outliers start: 58 outliers final: 48 residues processed: 256 average time/residue: 0.1451 time to fit residues: 55.6941 Evaluate side-chains 263 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 209 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 513 GLU Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 513 GLU Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 232 MET Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 293 ASP Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 513 GLU Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 232 MET Chi-restraints excluded: chain D residue 288 MET Chi-restraints excluded: chain D residue 293 ASP Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 513 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 22 optimal weight: 0.9980 chunk 169 optimal weight: 0.8980 chunk 45 optimal weight: 9.9990 chunk 205 optimal weight: 9.9990 chunk 167 optimal weight: 9.9990 chunk 140 optimal weight: 7.9990 chunk 110 optimal weight: 7.9990 chunk 208 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 42 optimal weight: 20.0000 chunk 49 optimal weight: 30.0000 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.174755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.131931 restraints weight = 19634.573| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.00 r_work: 0.3089 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 17836 Z= 0.171 Angle : 0.553 5.924 24184 Z= 0.280 Chirality : 0.045 0.141 2672 Planarity : 0.005 0.039 3076 Dihedral : 6.629 45.580 2644 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.71 % Allowed : 13.20 % Favored : 83.09 % 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: 0.22 (0.18), residues: 2140 helix: 0.93 (0.17), residues: 972 sheet: -0.26 (0.25), residues: 364 loop : -0.49 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 465 TYR 0.017 0.002 TYR D 42 PHE 0.011 0.001 PHE B 166 TRP 0.010 0.001 TRP C 124 HIS 0.004 0.001 HIS B 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.17 (17836) covalent geometry : angle 0.55320 / 0.28 (24184) hydrogen bonds : bond 0.03691 / 2.50 ( 716) hydrogen bonds : angle 3.99689 / 2.78 ( 2064) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 228 time to evaluate : 0.720 Fit side-chains REVERT: A 126 MET cc_start: 0.8538 (mtt) cc_final: 0.8167 (mtm) REVERT: A 294 ARG cc_start: 0.7333 (ptp-170) cc_final: 0.6889 (ptt90) REVERT: A 316 SER cc_start: 0.8626 (m) cc_final: 0.8355 (m) REVERT: A 481 ARG cc_start: 0.6943 (ptp-110) cc_final: 0.6373 (ptt180) REVERT: A 513 GLU cc_start: 0.6345 (OUTLIER) cc_final: 0.5495 (pp20) REVERT: B 88 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7834 (tt) REVERT: B 126 MET cc_start: 0.8545 (mtt) cc_final: 0.8167 (mtm) REVERT: B 294 ARG cc_start: 0.7326 (ptp-170) cc_final: 0.6880 (ptt90) REVERT: B 316 SER cc_start: 0.8619 (m) cc_final: 0.8349 (m) REVERT: B 481 ARG cc_start: 0.6930 (ptp-110) cc_final: 0.6357 (ptt180) REVERT: C 88 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7843 (tt) REVERT: C 126 MET cc_start: 0.8519 (mtt) cc_final: 0.8160 (mtp) REVERT: C 294 ARG cc_start: 0.7303 (ptp-170) cc_final: 0.6861 (ptt90) REVERT: C 316 SER cc_start: 0.8621 (m) cc_final: 0.8352 (m) REVERT: C 481 ARG cc_start: 0.6936 (ptp-110) cc_final: 0.6361 (ptt180) REVERT: C 513 GLU cc_start: 0.6352 (OUTLIER) cc_final: 0.5492 (pp20) REVERT: C 514 LEU cc_start: 0.6219 (OUTLIER) cc_final: 0.5745 (tt) REVERT: D 88 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7847 (tt) REVERT: D 126 MET cc_start: 0.8546 (mtt) cc_final: 0.8171 (mtm) REVERT: D 294 ARG cc_start: 0.7287 (ptp-170) cc_final: 0.6854 (ptt90) REVERT: D 316 SER cc_start: 0.8633 (m) cc_final: 0.8365 (m) REVERT: D 481 ARG cc_start: 0.6951 (ptp-110) cc_final: 0.6380 (ptt180) outliers start: 71 outliers final: 63 residues processed: 268 average time/residue: 0.1410 time to fit residues: 56.2669 Evaluate side-chains 277 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 208 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 513 GLU Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 513 GLU Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 232 MET Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 513 GLU Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 232 MET Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 288 MET Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 513 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 94 optimal weight: 0.4980 chunk 3 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 161 optimal weight: 8.9990 chunk 133 optimal weight: 0.2980 chunk 78 optimal weight: 4.9990 chunk 152 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 174 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.175364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.133176 restraints weight = 19928.426| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.13 r_work: 0.3100 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 17836 Z= 0.146 Angle : 0.533 6.241 24184 Z= 0.269 Chirality : 0.044 0.139 2672 Planarity : 0.005 0.040 3076 Dihedral : 6.534 47.827 2644 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 4.70 % Allowed : 12.58 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.18), residues: 2140 helix: 0.94 (0.17), residues: 972 sheet: -0.26 (0.26), residues: 364 loop : -0.47 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 376 TYR 0.016 0.002 TYR A 42 PHE 0.010 0.001 PHE A 166 TRP 0.008 0.001 TRP B 387 HIS 0.004 0.001 HIS D 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (17836) covalent geometry : angle 0.53349 / 0.27 (24184) hydrogen bonds : bond 0.03479 / 2.36 ( 716) hydrogen bonds : angle 3.94596 / 2.75 ( 2064) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 216 time to evaluate : 0.613 Fit side-chains REVERT: A 88 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7848 (tt) REVERT: A 126 MET cc_start: 0.8513 (mtt) cc_final: 0.8177 (mtp) REVERT: A 294 ARG cc_start: 0.7360 (ptp-170) cc_final: 0.6925 (ptt90) REVERT: A 316 SER cc_start: 0.8655 (m) cc_final: 0.8400 (m) REVERT: A 361 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7948 (tp) REVERT: A 499 PHE cc_start: 0.7309 (m-80) cc_final: 0.7002 (m-80) REVERT: A 513 GLU cc_start: 0.6297 (OUTLIER) cc_final: 0.5565 (pp20) REVERT: A 514 LEU cc_start: 0.6206 (OUTLIER) cc_final: 0.5772 (tt) REVERT: B 88 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7802 (tt) REVERT: B 126 MET cc_start: 0.8499 (mtt) cc_final: 0.8158 (mtp) REVERT: B 294 ARG cc_start: 0.7363 (ptp-170) cc_final: 0.6929 (ptt90) REVERT: B 316 SER cc_start: 0.8648 (m) cc_final: 0.8398 (m) REVERT: B 361 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7951 (tp) REVERT: C 88 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7808 (tt) REVERT: C 126 MET cc_start: 0.8488 (mtt) cc_final: 0.8153 (mtp) REVERT: C 294 ARG cc_start: 0.7362 (ptp-170) cc_final: 0.6919 (ptt90) REVERT: C 316 SER cc_start: 0.8658 (m) cc_final: 0.8408 (m) REVERT: C 361 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7964 (tp) REVERT: C 499 PHE cc_start: 0.7305 (m-80) cc_final: 0.6994 (m-80) REVERT: C 513 GLU cc_start: 0.6312 (OUTLIER) cc_final: 0.5565 (pp20) REVERT: C 514 LEU cc_start: 0.6222 (OUTLIER) cc_final: 0.5791 (tt) REVERT: D 88 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7811 (tt) REVERT: D 126 MET cc_start: 0.8520 (mtt) cc_final: 0.8180 (mtp) REVERT: D 294 ARG cc_start: 0.7347 (ptp-170) cc_final: 0.6904 (ptt90) REVERT: D 316 SER cc_start: 0.8663 (m) cc_final: 0.8412 (m) REVERT: D 361 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7958 (tp) outliers start: 90 outliers final: 69 residues processed: 266 average time/residue: 0.1336 time to fit residues: 54.8668 Evaluate side-chains 293 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 212 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 513 GLU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 281 MET Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 293 ASP Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 513 GLU Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 232 MET Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 281 MET Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 293 ASP Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 513 GLU Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 232 MET Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 281 MET Chi-restraints excluded: chain D residue 288 MET Chi-restraints excluded: chain D residue 293 ASP Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 513 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 127 optimal weight: 2.9990 chunk 73 optimal weight: 0.1980 chunk 83 optimal weight: 20.0000 chunk 175 optimal weight: 8.9990 chunk 140 optimal weight: 0.0770 chunk 9 optimal weight: 2.9990 chunk 7 optimal weight: 0.4980 chunk 19 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 129 optimal weight: 0.6980 overall best weight: 0.8940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.179306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.137591 restraints weight = 19367.094| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.02 r_work: 0.3137 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 17836 Z= 0.094 Angle : 0.485 6.041 24184 Z= 0.246 Chirality : 0.042 0.138 2672 Planarity : 0.004 0.040 3076 Dihedral : 6.111 49.386 2644 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.71 % Allowed : 13.36 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.19), residues: 2140 helix: 1.15 (0.17), residues: 972 sheet: -0.33 (0.26), residues: 380 loop : -0.26 (0.23), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 353 TYR 0.012 0.001 TYR A 42 PHE 0.006 0.001 PHE A 166 TRP 0.011 0.001 TRP D 387 HIS 0.004 0.001 HIS B 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.09 (17836) covalent geometry : angle 0.48470 / 0.25 (24184) hydrogen bonds : bond 0.02912 / 1.97 ( 716) hydrogen bonds : angle 3.82671 / 2.66 ( 2064) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 219 time to evaluate : 0.623 Fit side-chains REVERT: A 71 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7710 (mp) REVERT: A 88 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7776 (tt) REVERT: A 126 MET cc_start: 0.8488 (mtt) cc_final: 0.8154 (mtp) REVERT: A 294 ARG cc_start: 0.7313 (ptp-170) cc_final: 0.6869 (ptt90) REVERT: A 361 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7970 (tp) REVERT: A 481 ARG cc_start: 0.6983 (ptp-110) cc_final: 0.6405 (ptt180) REVERT: A 499 PHE cc_start: 0.7198 (m-80) cc_final: 0.6901 (m-80) REVERT: A 513 GLU cc_start: 0.6130 (OUTLIER) cc_final: 0.5380 (pp20) REVERT: A 514 LEU cc_start: 0.6171 (OUTLIER) cc_final: 0.5723 (tt) REVERT: B 71 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7721 (mp) REVERT: B 88 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7778 (tt) REVERT: B 126 MET cc_start: 0.8488 (mtt) cc_final: 0.8152 (mtp) REVERT: B 294 ARG cc_start: 0.7336 (ptp-170) cc_final: 0.6887 (ptt90) REVERT: B 361 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7977 (tp) REVERT: B 481 ARG cc_start: 0.6995 (ptp-110) cc_final: 0.6403 (ptt180) REVERT: C 71 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7720 (mp) REVERT: C 88 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7780 (tt) REVERT: C 126 MET cc_start: 0.8469 (mtt) cc_final: 0.8133 (mtp) REVERT: C 294 ARG cc_start: 0.7342 (ptp-170) cc_final: 0.6895 (ptt90) REVERT: C 361 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7975 (tp) REVERT: C 481 ARG cc_start: 0.6987 (ptp-110) cc_final: 0.6405 (ptt180) REVERT: C 499 PHE cc_start: 0.7207 (m-80) cc_final: 0.6909 (m-80) REVERT: C 513 GLU cc_start: 0.6134 (OUTLIER) cc_final: 0.5388 (pp20) REVERT: C 514 LEU cc_start: 0.6193 (OUTLIER) cc_final: 0.5760 (tt) REVERT: D 71 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7709 (mp) REVERT: D 88 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7780 (tt) REVERT: D 126 MET cc_start: 0.8496 (mtt) cc_final: 0.8162 (mtp) REVERT: D 294 ARG cc_start: 0.7322 (ptp-170) cc_final: 0.6868 (ptt90) REVERT: D 361 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7969 (tp) REVERT: D 481 ARG cc_start: 0.6999 (ptp-110) cc_final: 0.6424 (ptt180) outliers start: 71 outliers final: 42 residues processed: 261 average time/residue: 0.1417 time to fit residues: 55.6416 Evaluate side-chains 267 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 209 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 513 GLU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 232 MET Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 513 GLU Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 232 MET Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 288 MET Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 512 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 118 optimal weight: 9.9990 chunk 83 optimal weight: 20.0000 chunk 52 optimal weight: 5.9990 chunk 43 optimal weight: 0.2980 chunk 86 optimal weight: 6.9990 chunk 101 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 chunk 212 optimal weight: 6.9990 chunk 205 optimal weight: 3.9990 chunk 66 optimal weight: 9.9990 chunk 84 optimal weight: 3.9990 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.176212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.134151 restraints weight = 19551.114| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.31 r_work: 0.3042 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 17836 Z= 0.193 Angle : 0.585 6.274 24184 Z= 0.294 Chirality : 0.046 0.140 2672 Planarity : 0.005 0.043 3076 Dihedral : 6.937 54.066 2644 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.44 % Allowed : 13.78 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.18), residues: 2140 helix: 0.81 (0.17), residues: 972 sheet: -0.36 (0.26), residues: 376 loop : -0.60 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 508 TYR 0.019 0.002 TYR D 42 PHE 0.028 0.002 PHE D 499 TRP 0.011 0.002 TRP C 124 HIS 0.005 0.001 HIS D 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.19 (17836) covalent geometry : angle 0.58463 / 0.29 (24184) hydrogen bonds : bond 0.03914 / 2.64 ( 716) hydrogen bonds : angle 4.10745 / 2.87 ( 2064) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3827.96 seconds wall clock time: 66 minutes 44.20 seconds (4004.20 seconds total)