Starting phenix.real_space_refine on Thu Feb 5 13:06:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vmm_65191/02_2026/9vmm_65191.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vmm_65191/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9vmm_65191/02_2026/9vmm_65191.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vmm_65191/02_2026/9vmm_65191.map" model { file = "/net/cci-nas-00/data/ceres_data/9vmm_65191/02_2026/9vmm_65191.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vmm_65191/02_2026/9vmm_65191.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 4.06, per 1000 atoms: 0.23 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: 1.54 Conformation dependent library (CDL) restraints added in 659.5 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: 0.71 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: 3.00 Time building geometry restraints manager: 2.03 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=" C4 CTP D 603 " pdb=" N3 CTP D 603 " ideal model delta sigma weight residual 1.380 1.297 0.083 2.00e-02 2.50e+03 1.74e+01 bond pdb=" C4 CTP B 603 " pdb=" N3 CTP B 603 " ideal model delta sigma weight residual 1.380 1.297 0.083 2.00e-02 2.50e+03 1.74e+01 bond pdb=" C4 CTP C 602 " pdb=" N3 CTP C 602 " ideal model delta sigma weight residual 1.380 1.297 0.083 2.00e-02 2.50e+03 1.74e+01 bond pdb=" C4 CTP A 602 " pdb=" N3 CTP A 602 " ideal model delta sigma weight residual 1.380 1.297 0.083 2.00e-02 2.50e+03 1.74e+01 bond pdb=" C4 CTP A 601 " pdb=" N3 CTP A 601 " ideal model delta sigma weight residual 1.380 1.300 0.080 2.00e-02 2.50e+03 1.59e+01 ... (remaining 17831 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 17808 2.02 - 4.04: 5616 4.04 - 6.05: 668 6.05 - 8.07: 80 8.07 - 10.09: 12 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 - 35.19: 10480 35.19 - 70.38: 196 70.38 - 105.56: 28 105.56 - 140.75: 8 140.75 - 175.94: 8 Dihedral angle restraints: 10720 sinusoidal: 4492 harmonic: 6228 Sorted by residual: dihedral pdb=" O5' CTP B 602 " pdb=" O3A CTP B 602 " pdb=" PA CTP B 602 " pdb=" PB CTP B 602 " ideal model delta sinusoidal sigma weight residual 93.05 -82.89 175.94 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O5' CTP D 602 " pdb=" O3A CTP D 602 " pdb=" PA CTP D 602 " pdb=" PB CTP D 602 " ideal model delta sinusoidal sigma weight residual 93.05 -82.89 175.94 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O5' CTP A 601 " pdb=" O3A CTP A 601 " pdb=" PA CTP A 601 " pdb=" PB CTP A 601 " ideal model delta sinusoidal sigma weight residual 93.05 -82.89 175.94 1 2.00e+01 2.50e-03 4.79e+01 ... (remaining 10717 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 2064 0.114 - 0.229: 532 0.229 - 0.343: 64 0.343 - 0.457: 8 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: 3084 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 3081 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: 0.01 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: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 16.690 Find NCS groups from input model: 0.410 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 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 : 0.013 0.083 17836 Z= 0.791 Angle : 1.851 10.089 24184 Z= 1.219 Chirality : 0.102 0.571 2672 Planarity : 0.014 0.138 3084 Dihedral : 15.933 175.940 6720 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 covalent geometry : bond 0.01306 (17836) covalent geometry : angle 1.85106 (24184) hydrogen bonds : bond 0.16550 ( 716) hydrogen bonds : angle 6.87626 ( 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 : 0.815 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: 0.1579 time to fit residues: 97.3977 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 : 0.660 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3978 r_free = 0.3978 target = 0.179230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.136822 restraints weight = 19645.973| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.14 r_work: 0.3113 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2346 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= 0.142 Angle : 0.644 6.805 24184 Z= 0.326 Chirality : 0.046 0.135 2672 Planarity : 0.005 0.035 3084 Dihedral : 12.150 154.888 2460 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.46 % Allowed : 8.82 % Favored : 89.72 % 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: 0.36 (0.18), residues: 2140 helix: 0.52 (0.17), residues: 940 sheet: 0.13 (0.26), residues: 356 loop : 0.18 (0.23), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 454 TYR 0.013 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 covalent geometry : bond 0.00324 (17836) covalent geometry : angle 0.64387 (24184) hydrogen bonds : bond 0.03921 ( 716) hydrogen bonds : angle 4.57564 ( 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 315 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 287 time to evaluate : 0.603 Fit side-chains REVERT: A 49 THR cc_start: 0.7883 (m) cc_final: 0.7491 (p) REVERT: A 126 MET cc_start: 0.8469 (mtt) cc_final: 0.8164 (mtp) REVERT: A 220 ASN cc_start: 0.8490 (m110) cc_final: 0.8215 (m110) REVERT: A 294 ARG cc_start: 0.7159 (ptp-170) cc_final: 0.6800 (ptt90) REVERT: A 353 ARG cc_start: 0.5432 (ttp-170) cc_final: 0.5179 (ttp-170) REVERT: A 481 ARG cc_start: 0.7153 (ptp-110) cc_final: 0.6637 (ptt180) REVERT: B 49 THR cc_start: 0.7896 (m) cc_final: 0.7507 (p) REVERT: B 126 MET cc_start: 0.8475 (mtt) cc_final: 0.8166 (mtp) REVERT: B 220 ASN cc_start: 0.8513 (m110) cc_final: 0.8246 (m110) REVERT: B 294 ARG cc_start: 0.7140 (ptp-170) cc_final: 0.6785 (ptt90) REVERT: B 353 ARG cc_start: 0.5408 (ttp-170) cc_final: 0.5151 (ttp-170) REVERT: B 481 ARG cc_start: 0.7135 (ptp-110) cc_final: 0.6624 (ptt180) REVERT: C 49 THR cc_start: 0.7895 (m) cc_final: 0.7501 (p) REVERT: C 126 MET cc_start: 0.8462 (mtt) cc_final: 0.8158 (mtp) REVERT: C 220 ASN cc_start: 0.8494 (m110) cc_final: 0.8224 (m110) REVERT: C 294 ARG cc_start: 0.7143 (ptp-170) cc_final: 0.6786 (ptt90) REVERT: C 353 ARG cc_start: 0.5437 (ttp-170) cc_final: 0.5198 (ttp-170) REVERT: C 481 ARG cc_start: 0.7151 (ptp-110) cc_final: 0.6651 (ptt180) REVERT: D 49 THR cc_start: 0.7894 (m) cc_final: 0.7500 (p) REVERT: D 126 MET cc_start: 0.8470 (mtt) cc_final: 0.8163 (mtp) REVERT: D 220 ASN cc_start: 0.8508 (m110) cc_final: 0.8240 (m110) REVERT: D 294 ARG cc_start: 0.7134 (ptp-170) cc_final: 0.6783 (ptt90) REVERT: D 353 ARG cc_start: 0.5453 (ttp-170) cc_final: 0.5204 (ttp-170) REVERT: D 481 ARG cc_start: 0.7155 (ptp-110) cc_final: 0.6635 (ptt180) outliers start: 28 outliers final: 24 residues processed: 303 average time/residue: 0.1443 time to fit residues: 64.4800 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 : 0.647 ------------------------------------------------------------------------------- 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: 10.0000 chunk 187 optimal weight: 0.4980 chunk 30 optimal weight: 6.9990 chunk 170 optimal weight: 2.9990 chunk 52 optimal weight: 9.9990 chunk 32 optimal weight: 0.9990 chunk 46 optimal weight: 10.0000 chunk 154 optimal weight: 9.9990 chunk 147 optimal weight: 0.9980 chunk 192 optimal weight: 5.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.178193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.135178 restraints weight = 19749.108| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.89 r_work: 0.3118 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17836 Z= 0.142 Angle : 0.591 6.618 24184 Z= 0.297 Chirality : 0.046 0.135 2672 Planarity : 0.005 0.039 3084 Dihedral : 9.388 122.824 2452 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.71 % Allowed : 10.44 % Favored : 86.85 % 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: 0.35 (0.18), residues: 2140 helix: 0.66 (0.17), residues: 976 sheet: -0.07 (0.25), residues: 364 loop : 0.05 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 465 TYR 0.015 0.002 TYR C 42 PHE 0.012 0.002 PHE D 424 TRP 0.013 0.002 TRP B 387 HIS 0.006 0.001 HIS C 517 Details of bonding type rmsd covalent geometry : bond 0.00336 (17836) covalent geometry : angle 0.59146 (24184) hydrogen bonds : bond 0.03813 ( 716) hydrogen bonds : angle 4.11325 ( 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 300 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 248 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 THR cc_start: 0.7897 (m) cc_final: 0.7604 (p) REVERT: A 126 MET cc_start: 0.8509 (mtt) cc_final: 0.8160 (mtp) REVERT: A 220 ASN cc_start: 0.8548 (m110) cc_final: 0.8326 (m110) REVERT: A 294 ARG cc_start: 0.7259 (ptp-170) cc_final: 0.6843 (ptt90) REVERT: A 306 LYS cc_start: 0.6869 (OUTLIER) cc_final: 0.6648 (ptpt) REVERT: A 481 ARG cc_start: 0.7065 (ptp-110) cc_final: 0.6507 (ptt180) REVERT: A 513 GLU cc_start: 0.6608 (tt0) cc_final: 0.5915 (pp20) REVERT: B 49 THR cc_start: 0.7902 (m) cc_final: 0.7606 (p) REVERT: B 126 MET cc_start: 0.8520 (mtt) cc_final: 0.8171 (mtp) REVERT: B 220 ASN cc_start: 0.8551 (m110) cc_final: 0.8325 (m110) REVERT: B 294 ARG cc_start: 0.7255 (ptp-170) cc_final: 0.6834 (ptt90) REVERT: B 306 LYS cc_start: 0.6868 (OUTLIER) cc_final: 0.6645 (ptpt) REVERT: B 481 ARG cc_start: 0.7061 (ptp-110) cc_final: 0.6510 (ptt180) REVERT: B 513 GLU cc_start: 0.6613 (tt0) cc_final: 0.5898 (pp20) REVERT: C 49 THR cc_start: 0.7893 (m) cc_final: 0.7598 (p) REVERT: C 126 MET cc_start: 0.8496 (mtt) cc_final: 0.8153 (mtp) REVERT: C 220 ASN cc_start: 0.8554 (m110) cc_final: 0.8332 (m110) REVERT: C 294 ARG cc_start: 0.7235 (ptp-170) cc_final: 0.6822 (ptt90) REVERT: C 306 LYS cc_start: 0.6878 (OUTLIER) cc_final: 0.6653 (ptpt) REVERT: C 481 ARG cc_start: 0.7045 (ptp-110) cc_final: 0.6498 (ptt180) REVERT: C 513 GLU cc_start: 0.6594 (tt0) cc_final: 0.5885 (pp20) REVERT: D 49 THR cc_start: 0.7895 (m) cc_final: 0.7601 (p) REVERT: D 126 MET cc_start: 0.8515 (mtt) cc_final: 0.8167 (mtp) REVERT: D 220 ASN cc_start: 0.8561 (m110) cc_final: 0.8338 (m110) REVERT: D 294 ARG cc_start: 0.7236 (ptp-170) cc_final: 0.6823 (ptt90) REVERT: D 306 LYS cc_start: 0.6876 (OUTLIER) cc_final: 0.6653 (ptpt) REVERT: D 481 ARG cc_start: 0.7051 (ptp-110) cc_final: 0.6495 (ptt180) REVERT: D 513 GLU cc_start: 0.6615 (tt0) cc_final: 0.5920 (pp20) outliers start: 52 outliers final: 40 residues processed: 284 average time/residue: 0.1446 time to fit residues: 61.2899 Evaluate side-chains 276 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 232 time to evaluate : 0.656 ------------------------------------------------------------------------------- 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 288 MET Chi-restraints excluded: chain A residue 306 LYS Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 14 ILE 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 512 VAL Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain C residue 14 ILE 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 512 VAL Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain D residue 14 ILE 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 512 VAL 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: 0.9980 chunk 184 optimal weight: 0.8980 chunk 127 optimal weight: 3.9990 chunk 180 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 202 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 chunk 100 optimal weight: 10.0000 chunk 143 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.178573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.136133 restraints weight = 19649.537| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.98 r_work: 0.3130 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 17836 Z= 0.113 Angle : 0.538 6.505 24184 Z= 0.265 Chirality : 0.044 0.138 2672 Planarity : 0.005 0.037 3084 Dihedral : 8.280 113.095 2452 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.92 % Allowed : 12.37 % Favored : 84.71 % 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: 0.54 (0.18), residues: 2140 helix: 0.96 (0.17), residues: 984 sheet: -0.10 (0.25), residues: 368 loop : 0.01 (0.23), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 465 TYR 0.014 0.001 TYR C 42 PHE 0.008 0.001 PHE C 424 TRP 0.013 0.001 TRP B 387 HIS 0.004 0.001 HIS A 517 Details of bonding type rmsd covalent geometry : bond 0.00261 (17836) covalent geometry : angle 0.53809 (24184) hydrogen bonds : bond 0.03145 ( 716) hydrogen bonds : angle 3.92838 ( 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 285 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 229 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 THR cc_start: 0.7874 (m) cc_final: 0.7617 (p) REVERT: A 126 MET cc_start: 0.8409 (mtt) cc_final: 0.8064 (mtp) REVERT: A 220 ASN cc_start: 0.8519 (m110) cc_final: 0.8292 (m110) REVERT: A 294 ARG cc_start: 0.7225 (ptp-170) cc_final: 0.6842 (ptt90) REVERT: A 361 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.7986 (tp) REVERT: A 481 ARG cc_start: 0.6924 (ptp-110) cc_final: 0.6365 (ptt180) REVERT: A 503 ASP cc_start: 0.6146 (t0) cc_final: 0.5933 (t0) REVERT: B 49 THR cc_start: 0.7876 (m) cc_final: 0.7618 (p) REVERT: B 88 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7865 (tt) REVERT: B 126 MET cc_start: 0.8414 (mtt) cc_final: 0.8068 (mtp) REVERT: B 220 ASN cc_start: 0.8510 (m110) cc_final: 0.8275 (m110) REVERT: B 294 ARG cc_start: 0.7233 (ptp-170) cc_final: 0.6839 (ptt90) REVERT: B 361 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7981 (tp) REVERT: B 481 ARG cc_start: 0.6937 (ptp-110) cc_final: 0.6370 (ptt180) REVERT: B 503 ASP cc_start: 0.6125 (t0) cc_final: 0.5912 (t0) REVERT: C 49 THR cc_start: 0.7870 (m) cc_final: 0.7616 (p) REVERT: C 126 MET cc_start: 0.8406 (mtt) cc_final: 0.8059 (mtp) REVERT: C 220 ASN cc_start: 0.8533 (m110) cc_final: 0.8298 (m110) REVERT: C 294 ARG cc_start: 0.7244 (ptp-170) cc_final: 0.6835 (ptt90) REVERT: C 361 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.7986 (tp) REVERT: C 481 ARG cc_start: 0.6927 (ptp-110) cc_final: 0.6374 (ptt180) REVERT: D 49 THR cc_start: 0.7874 (m) cc_final: 0.7616 (p) REVERT: D 88 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7871 (tt) REVERT: D 126 MET cc_start: 0.8411 (mtt) cc_final: 0.8065 (mtp) REVERT: D 220 ASN cc_start: 0.8538 (m110) cc_final: 0.8306 (m110) REVERT: D 294 ARG cc_start: 0.7230 (ptp-170) cc_final: 0.6837 (ptt90) REVERT: D 361 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7994 (tp) REVERT: D 481 ARG cc_start: 0.6933 (ptp-110) cc_final: 0.6365 (ptt180) REVERT: D 503 ASP cc_start: 0.6123 (t0) cc_final: 0.5915 (t0) outliers start: 56 outliers final: 36 residues processed: 265 average time/residue: 0.1449 time to fit residues: 57.0624 Evaluate side-chains 262 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 220 time to evaluate : 0.692 ------------------------------------------------------------------------------- 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 293 ASP Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 521 VAL 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 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 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 293 ASP Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 521 VAL 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 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 521 VAL 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: 3.9990 chunk 179 optimal weight: 7.9990 chunk 134 optimal weight: 2.9990 chunk 94 optimal weight: 20.0000 chunk 96 optimal weight: 20.0000 chunk 171 optimal weight: 0.9980 chunk 187 optimal weight: 0.0970 chunk 212 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 overall best weight: 1.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.177269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.135541 restraints weight = 19572.298| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.00 r_work: 0.3101 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17836 Z= 0.119 Angle : 0.539 6.536 24184 Z= 0.263 Chirality : 0.044 0.138 2672 Planarity : 0.005 0.037 3084 Dihedral : 7.983 110.227 2452 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.97 % Allowed : 12.32 % Favored : 84.71 % 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: 0.59 (0.18), residues: 2140 helix: 1.12 (0.17), residues: 972 sheet: -0.06 (0.25), residues: 368 loop : -0.14 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 465 TYR 0.015 0.001 TYR D 42 PHE 0.009 0.001 PHE D 166 TRP 0.015 0.001 TRP B 387 HIS 0.002 0.001 HIS D 517 Details of bonding type rmsd covalent geometry : bond 0.00279 (17836) covalent geometry : angle 0.53899 (24184) hydrogen bonds : bond 0.03221 ( 716) hydrogen bonds : angle 3.87801 ( 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 283 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 226 time to evaluate : 0.694 Fit side-chains REVERT: A 126 MET cc_start: 0.8458 (mtt) cc_final: 0.8093 (mtp) REVERT: A 294 ARG cc_start: 0.7272 (ptp-170) cc_final: 0.6864 (ptt90) REVERT: A 361 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.7959 (tp) REVERT: A 481 ARG cc_start: 0.6922 (ptp-110) cc_final: 0.6356 (ptt180) REVERT: B 88 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7835 (tt) REVERT: B 126 MET cc_start: 0.8460 (mtt) cc_final: 0.8075 (mtp) REVERT: B 294 ARG cc_start: 0.7304 (ptp-170) cc_final: 0.6867 (ptt90) REVERT: B 361 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.7956 (tp) REVERT: B 481 ARG cc_start: 0.6946 (ptp-110) cc_final: 0.6373 (ptt180) REVERT: B 513 GLU cc_start: 0.6507 (tt0) cc_final: 0.5779 (pp20) REVERT: C 126 MET cc_start: 0.8454 (mtt) cc_final: 0.8089 (mtp) REVERT: C 294 ARG cc_start: 0.7281 (ptp-170) cc_final: 0.6849 (ptt90) REVERT: C 361 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.7962 (tp) REVERT: C 481 ARG cc_start: 0.6925 (ptp-110) cc_final: 0.6365 (ptt180) REVERT: C 513 GLU cc_start: 0.6505 (tt0) cc_final: 0.5785 (pp20) REVERT: D 88 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7844 (tt) REVERT: D 126 MET cc_start: 0.8453 (mtt) cc_final: 0.8072 (mtp) REVERT: D 294 ARG cc_start: 0.7281 (ptp-170) cc_final: 0.6856 (ptt90) REVERT: D 361 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.7955 (tp) REVERT: D 481 ARG cc_start: 0.6913 (ptp-110) cc_final: 0.6335 (ptt180) REVERT: D 513 GLU cc_start: 0.6486 (tt0) cc_final: 0.5782 (pp20) outliers start: 57 outliers final: 43 residues processed: 255 average time/residue: 0.1445 time to fit residues: 55.5256 Evaluate side-chains 247 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 198 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE 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 523 VAL Chi-restraints excluded: chain B residue 14 ILE 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 523 VAL Chi-restraints excluded: chain C residue 14 ILE 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 523 VAL Chi-restraints excluded: chain D residue 14 ILE 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 523 VAL 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: 1.9990 chunk 183 optimal weight: 8.9990 chunk 9 optimal weight: 0.9990 chunk 132 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 84 optimal weight: 10.0000 chunk 73 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 chunk 162 optimal weight: 10.0000 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.178129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.136453 restraints weight = 19544.956| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 1.88 r_work: 0.3153 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 17836 Z= 0.103 Angle : 0.517 6.500 24184 Z= 0.252 Chirality : 0.043 0.138 2672 Planarity : 0.004 0.036 3084 Dihedral : 7.636 103.330 2452 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.65 % Allowed : 11.90 % Favored : 84.45 % 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: 0.70 (0.19), residues: 2140 helix: 1.26 (0.18), residues: 972 sheet: -0.02 (0.25), residues: 368 loop : -0.15 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 268 TYR 0.014 0.001 TYR C 42 PHE 0.007 0.001 PHE B 166 TRP 0.012 0.001 TRP B 387 HIS 0.003 0.001 HIS D 517 Details of bonding type rmsd covalent geometry : bond 0.00236 (17836) covalent geometry : angle 0.51666 (24184) hydrogen bonds : bond 0.02989 ( 716) hydrogen bonds : angle 3.77445 ( 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 289 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 219 time to evaluate : 0.581 Fit side-chains REVERT: A 88 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7838 (tt) REVERT: A 126 MET cc_start: 0.8413 (mtt) cc_final: 0.8050 (mtp) REVERT: A 294 ARG cc_start: 0.7245 (ptp-170) cc_final: 0.6840 (ptt90) REVERT: A 361 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8061 (tp) REVERT: A 481 ARG cc_start: 0.6912 (ptp-110) cc_final: 0.6352 (ptt180) REVERT: B 88 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7793 (tt) REVERT: B 126 MET cc_start: 0.8408 (mtt) cc_final: 0.8029 (mtp) REVERT: B 294 ARG cc_start: 0.7263 (ptp-170) cc_final: 0.6841 (ptt90) REVERT: B 361 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8057 (tp) REVERT: B 481 ARG cc_start: 0.6908 (ptp-110) cc_final: 0.6334 (ptt180) REVERT: B 513 GLU cc_start: 0.6495 (tt0) cc_final: 0.5841 (pp20) REVERT: C 88 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7826 (tt) REVERT: C 126 MET cc_start: 0.8404 (mtt) cc_final: 0.8038 (mtp) REVERT: C 294 ARG cc_start: 0.7251 (ptp-170) cc_final: 0.6837 (ptt90) REVERT: C 361 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.8052 (tp) REVERT: C 481 ARG cc_start: 0.6877 (ptp-110) cc_final: 0.6312 (ptt180) REVERT: C 513 GLU cc_start: 0.6490 (tt0) cc_final: 0.5835 (pp20) REVERT: D 88 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7800 (tt) REVERT: D 126 MET cc_start: 0.8415 (mtt) cc_final: 0.8039 (mtp) REVERT: D 294 ARG cc_start: 0.7246 (ptp-170) cc_final: 0.6841 (ptt90) REVERT: D 361 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.8058 (tp) REVERT: D 481 ARG cc_start: 0.6907 (ptp-110) cc_final: 0.6333 (ptt180) outliers start: 70 outliers final: 49 residues processed: 256 average time/residue: 0.1367 time to fit residues: 52.7141 Evaluate side-chains 254 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 197 time to evaluate : 0.585 ------------------------------------------------------------------------------- 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 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 361 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 523 VAL 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 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 523 VAL 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 474 LEU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 523 VAL 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 474 LEU Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 523 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 179 optimal weight: 7.9990 chunk 34 optimal weight: 30.0000 chunk 50 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 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: 6.9990 chunk 24 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.174482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.131810 restraints weight = 19780.609| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.84 r_work: 0.3105 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 17836 Z= 0.220 Angle : 0.633 6.694 24184 Z= 0.310 Chirality : 0.048 0.142 2672 Planarity : 0.005 0.041 3084 Dihedral : 8.660 118.530 2452 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.81 % Allowed : 12.68 % Favored : 83.51 % 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: 0.09 (0.18), residues: 2140 helix: 0.82 (0.17), residues: 972 sheet: -0.21 (0.25), residues: 364 loop : -0.62 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 268 TYR 0.020 0.002 TYR D 42 PHE 0.013 0.002 PHE C 166 TRP 0.012 0.002 TRP A 124 HIS 0.005 0.001 HIS D 517 Details of bonding type rmsd covalent geometry : bond 0.00542 (17836) covalent geometry : angle 0.63272 (24184) hydrogen bonds : bond 0.04100 ( 716) hydrogen bonds : angle 4.11729 ( 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 286 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 213 time to evaluate : 0.720 Fit side-chains revert: symmetry clash REVERT: A 88 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7941 (tt) REVERT: A 126 MET cc_start: 0.8680 (mtt) cc_final: 0.8318 (mtm) REVERT: A 294 ARG cc_start: 0.7302 (ptp-170) cc_final: 0.6863 (ptt90) REVERT: A 316 SER cc_start: 0.8769 (m) cc_final: 0.8527 (m) REVERT: A 361 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8029 (tp) REVERT: B 88 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.8020 (tt) REVERT: B 126 MET cc_start: 0.8681 (mtt) cc_final: 0.8318 (mtm) REVERT: B 294 ARG cc_start: 0.7313 (ptp-170) cc_final: 0.6862 (ptt90) REVERT: B 316 SER cc_start: 0.8759 (m) cc_final: 0.8518 (m) REVERT: B 361 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.8027 (tp) REVERT: C 88 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7919 (tt) REVERT: C 126 MET cc_start: 0.8676 (mtt) cc_final: 0.8314 (mtm) REVERT: C 294 ARG cc_start: 0.7317 (ptp-170) cc_final: 0.6842 (ptt90) REVERT: C 316 SER cc_start: 0.8761 (m) cc_final: 0.8514 (m) REVERT: C 361 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8027 (tp) REVERT: D 88 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.8034 (tt) REVERT: D 126 MET cc_start: 0.8688 (mtt) cc_final: 0.8327 (mtm) REVERT: D 294 ARG cc_start: 0.7301 (ptp-170) cc_final: 0.6846 (ptt90) REVERT: D 316 SER cc_start: 0.8771 (m) cc_final: 0.8542 (m) REVERT: D 361 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8025 (tp) REVERT: D 513 GLU cc_start: 0.6164 (tt0) cc_final: 0.5403 (pp20) outliers start: 73 outliers final: 63 residues processed: 253 average time/residue: 0.1338 time to fit residues: 51.7374 Evaluate side-chains 274 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 203 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE 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 263 VAL 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 523 VAL Chi-restraints excluded: chain B residue 14 ILE 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 263 VAL 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 523 VAL Chi-restraints excluded: chain C residue 14 ILE 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 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 523 VAL Chi-restraints excluded: chain D residue 14 ILE 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 247 VAL Chi-restraints excluded: chain D residue 263 VAL 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 523 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 22 optimal weight: 0.8980 chunk 169 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 205 optimal weight: 10.0000 chunk 167 optimal weight: 9.9990 chunk 140 optimal weight: 0.2980 chunk 110 optimal weight: 3.9990 chunk 208 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 42 optimal weight: 30.0000 chunk 49 optimal weight: 30.0000 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.177489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.136040 restraints weight = 19588.513| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 1.92 r_work: 0.3139 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3718 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= 0.103 Angle : 0.532 6.575 24184 Z= 0.260 Chirality : 0.044 0.140 2672 Planarity : 0.004 0.041 3084 Dihedral : 7.834 106.699 2452 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.71 % Allowed : 12.94 % Favored : 83.35 % 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: 0.43 (0.18), residues: 2140 helix: 1.09 (0.17), residues: 972 sheet: -0.12 (0.25), residues: 364 loop : -0.40 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 454 TYR 0.013 0.001 TYR B 42 PHE 0.008 0.001 PHE A 457 TRP 0.012 0.001 TRP B 387 HIS 0.003 0.001 HIS B 517 Details of bonding type rmsd covalent geometry : bond 0.00233 (17836) covalent geometry : angle 0.53221 (24184) hydrogen bonds : bond 0.03093 ( 716) hydrogen bonds : angle 3.83696 ( 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 290 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 219 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7749 (tt) REVERT: A 126 MET cc_start: 0.8460 (mtt) cc_final: 0.8097 (mtp) REVERT: A 294 ARG cc_start: 0.7287 (ptp-170) cc_final: 0.6871 (ptt90) REVERT: A 361 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.8033 (tp) REVERT: A 499 PHE cc_start: 0.7303 (m-80) cc_final: 0.7073 (m-80) REVERT: A 513 GLU cc_start: 0.6280 (tt0) cc_final: 0.5516 (pp20) REVERT: B 88 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7749 (tt) REVERT: B 126 MET cc_start: 0.8465 (mtt) cc_final: 0.8098 (mtp) REVERT: B 294 ARG cc_start: 0.7335 (ptp-170) cc_final: 0.6896 (ptt90) REVERT: B 361 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.8041 (tp) REVERT: B 499 PHE cc_start: 0.7377 (m-80) cc_final: 0.7118 (m-80) REVERT: B 513 GLU cc_start: 0.6549 (tt0) cc_final: 0.5793 (pp20) REVERT: C 88 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7733 (tt) REVERT: C 126 MET cc_start: 0.8448 (mtt) cc_final: 0.8085 (mtp) REVERT: C 294 ARG cc_start: 0.7299 (ptp-170) cc_final: 0.6897 (ptt90) REVERT: C 361 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.8030 (tp) REVERT: C 513 GLU cc_start: 0.6534 (tt0) cc_final: 0.5795 (pp20) REVERT: D 88 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7759 (tt) REVERT: D 126 MET cc_start: 0.8479 (mtt) cc_final: 0.8115 (mtp) REVERT: D 294 ARG cc_start: 0.7314 (ptp-170) cc_final: 0.6899 (ptt90) REVERT: D 361 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.8031 (tp) REVERT: D 499 PHE cc_start: 0.7394 (m-80) cc_final: 0.6977 (m-80) REVERT: D 513 GLU cc_start: 0.5845 (tt0) cc_final: 0.5321 (pp20) outliers start: 71 outliers final: 55 residues processed: 262 average time/residue: 0.1263 time to fit residues: 50.6903 Evaluate side-chains 268 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 205 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE 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 224 THR Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 263 VAL 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 474 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain B residue 14 ILE 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 224 THR Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 263 VAL 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 523 VAL Chi-restraints excluded: chain C residue 14 ILE 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 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 293 ASP 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 523 VAL Chi-restraints excluded: chain D residue 14 ILE 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 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 293 ASP 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 523 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 94 optimal weight: 20.0000 chunk 3 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 161 optimal weight: 5.9990 chunk 133 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 152 optimal weight: 6.9990 chunk 86 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 chunk 174 optimal weight: 0.0030 chunk 80 optimal weight: 0.6980 overall best weight: 1.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.176382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.134283 restraints weight = 19790.293| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 1.93 r_work: 0.3113 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 17836 Z= 0.123 Angle : 0.545 6.567 24184 Z= 0.265 Chirality : 0.044 0.139 2672 Planarity : 0.004 0.041 3084 Dihedral : 7.698 102.211 2452 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 4.12 % Allowed : 12.84 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.19), residues: 2140 helix: 1.10 (0.17), residues: 972 sheet: -0.21 (0.25), residues: 376 loop : -0.43 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 465 TYR 0.015 0.001 TYR D 42 PHE 0.009 0.001 PHE A 166 TRP 0.012 0.001 TRP C 387 HIS 0.003 0.001 HIS D 517 Details of bonding type rmsd covalent geometry : bond 0.00293 (17836) covalent geometry : angle 0.54467 (24184) hydrogen bonds : bond 0.03286 ( 716) hydrogen bonds : angle 3.85833 ( 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 305 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 226 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7782 (tt) REVERT: A 126 MET cc_start: 0.8486 (mtt) cc_final: 0.8116 (mtp) REVERT: A 294 ARG cc_start: 0.7342 (ptp-170) cc_final: 0.6889 (ptt90) REVERT: A 316 SER cc_start: 0.8654 (m) cc_final: 0.8398 (m) REVERT: A 361 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.8026 (tp) REVERT: A 481 ARG cc_start: 0.6946 (ptp-110) cc_final: 0.6361 (ptt180) REVERT: A 513 GLU cc_start: 0.6316 (OUTLIER) cc_final: 0.5602 (pp20) REVERT: B 88 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7772 (tt) REVERT: B 126 MET cc_start: 0.8488 (mtt) cc_final: 0.8116 (mtp) REVERT: B 294 ARG cc_start: 0.7344 (ptp-170) cc_final: 0.6883 (ptt90) REVERT: B 316 SER cc_start: 0.8692 (m) cc_final: 0.8431 (m) REVERT: B 361 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.8034 (tp) REVERT: C 88 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7763 (tt) REVERT: C 126 MET cc_start: 0.8475 (mtt) cc_final: 0.8104 (mtp) REVERT: C 294 ARG cc_start: 0.7306 (ptp-170) cc_final: 0.6873 (ptt90) REVERT: C 361 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.8026 (tp) REVERT: C 499 PHE cc_start: 0.7434 (m-80) cc_final: 0.7082 (m-80) REVERT: D 88 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7780 (tt) REVERT: D 126 MET cc_start: 0.8493 (mtt) cc_final: 0.8121 (mtp) REVERT: D 294 ARG cc_start: 0.7306 (ptp-170) cc_final: 0.6882 (ptt90) REVERT: D 361 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.8025 (tp) REVERT: D 513 GLU cc_start: 0.5947 (tt0) cc_final: 0.5368 (pp20) outliers start: 79 outliers final: 62 residues processed: 272 average time/residue: 0.1387 time to fit residues: 57.8612 Evaluate side-chains 288 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 217 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE 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 224 THR Chi-restraints excluded: chain A residue 232 MET 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 523 VAL Chi-restraints excluded: chain B residue 14 ILE 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 224 THR Chi-restraints excluded: chain B residue 232 MET 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 523 VAL Chi-restraints excluded: chain C residue 14 ILE 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 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 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 523 VAL Chi-restraints excluded: chain D residue 14 ILE 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 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 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 523 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 127 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 83 optimal weight: 20.0000 chunk 175 optimal weight: 1.9990 chunk 140 optimal weight: 0.0980 chunk 9 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 129 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.180878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.137398 restraints weight = 19400.512| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 1.93 r_work: 0.3161 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.3919 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= 0.091 Angle : 0.517 6.501 24184 Z= 0.251 Chirality : 0.043 0.136 2672 Planarity : 0.004 0.040 3084 Dihedral : 7.113 87.199 2452 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.08 % Allowed : 13.36 % Favored : 83.56 % 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: 0.61 (0.19), residues: 2140 helix: 1.29 (0.18), residues: 972 sheet: -0.18 (0.25), residues: 380 loop : -0.28 (0.23), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 465 TYR 0.012 0.001 TYR B 42 PHE 0.006 0.001 PHE D 159 TRP 0.013 0.001 TRP C 387 HIS 0.003 0.001 HIS A 517 Details of bonding type rmsd covalent geometry : bond 0.00201 (17836) covalent geometry : angle 0.51655 (24184) hydrogen bonds : bond 0.02841 ( 716) hydrogen bonds : angle 3.76710 ( 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 277 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 218 time to evaluate : 0.762 Fit side-chains REVERT: A 88 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7645 (tt) REVERT: A 126 MET cc_start: 0.8479 (mtt) cc_final: 0.8149 (mtp) REVERT: A 294 ARG cc_start: 0.7376 (ptp-170) cc_final: 0.6900 (ptt90) REVERT: A 361 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.8010 (tp) REVERT: A 498 LYS cc_start: 0.6222 (ttmt) cc_final: 0.6005 (ptmt) REVERT: A 499 PHE cc_start: 0.7415 (m-80) cc_final: 0.7205 (m-80) REVERT: B 88 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7638 (tt) REVERT: B 126 MET cc_start: 0.8482 (mtt) cc_final: 0.8149 (mtp) REVERT: B 294 ARG cc_start: 0.7383 (ptp-170) cc_final: 0.6899 (ptt90) REVERT: C 88 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7629 (tt) REVERT: C 126 MET cc_start: 0.8466 (mtt) cc_final: 0.8132 (mtp) REVERT: C 294 ARG cc_start: 0.7339 (ptp-170) cc_final: 0.6883 (ptt90) REVERT: C 499 PHE cc_start: 0.7332 (m-80) cc_final: 0.7051 (m-80) REVERT: D 88 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7669 (tt) REVERT: D 126 MET cc_start: 0.8478 (mtt) cc_final: 0.8146 (mtp) REVERT: D 294 ARG cc_start: 0.7333 (ptp-170) cc_final: 0.6872 (ptt90) REVERT: D 513 GLU cc_start: 0.5820 (tt0) cc_final: 0.5215 (pp20) outliers start: 59 outliers final: 46 residues processed: 253 average time/residue: 0.1459 time to fit residues: 56.1943 Evaluate side-chains 255 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 204 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE 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 293 ASP Chi-restraints excluded: chain A residue 303 LEU 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 523 VAL Chi-restraints excluded: chain B residue 14 ILE 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 293 ASP 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 523 VAL Chi-restraints excluded: chain C residue 14 ILE 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 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 523 VAL Chi-restraints excluded: chain D residue 14 ILE 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 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 523 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 118 optimal weight: 2.9990 chunk 83 optimal weight: 20.0000 chunk 52 optimal weight: 3.9990 chunk 43 optimal weight: 8.9990 chunk 86 optimal weight: 10.0000 chunk 101 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 212 optimal weight: 3.9990 chunk 205 optimal weight: 9.9990 chunk 66 optimal weight: 6.9990 chunk 84 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.175016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.132743 restraints weight = 19580.558| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.17 r_work: 0.3023 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 17836 Z= 0.238 Angle : 0.663 6.721 24184 Z= 0.325 Chirality : 0.049 0.143 2672 Planarity : 0.005 0.045 3084 Dihedral : 8.339 104.105 2452 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.65 % Allowed : 13.26 % 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: -0.12 (0.18), residues: 2140 helix: 0.66 (0.17), residues: 972 sheet: -0.24 (0.26), residues: 364 loop : -0.80 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 479 TYR 0.022 0.002 TYR B 42 PHE 0.014 0.002 PHE C 310 TRP 0.013 0.002 TRP A 124 HIS 0.005 0.001 HIS C 517 Details of bonding type rmsd covalent geometry : bond 0.00591 (17836) covalent geometry : angle 0.66333 (24184) hydrogen bonds : bond 0.04288 ( 716) hydrogen bonds : angle 4.23040 ( 2064) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3672.69 seconds wall clock time: 63 minutes 55.89 seconds (3835.89 seconds total)