Starting phenix.real_space_refine on Mon Jul 6 09:15:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mig_23850/07_2026/7mig_23850_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mig_23850/07_2026/7mig_23850.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mig_23850/07_2026/7mig_23850.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mig_23850/07_2026/7mig_23850.map" model { file = "/net/cci-nas-00/data/ceres_data/7mig_23850/07_2026/7mig_23850_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mig_23850/07_2026/7mig_23850_trim.cif" } resolution = 2.9 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= 0.263 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: 8 Type Number sf(0) Gaussians P 12 5.49 5 Mg 4 5.21 5 S 96 5.16 5 C 10964 2.51 5 N 2944 2.21 5 O 3220 1.98 5 F 12 1.80 5 H 17020 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 104 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 34272 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 8484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8484 Classifications: {'peptide': 533} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 504} Chain breaks: 4 Chain: "A" Number of atoms: 8484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8484 Classifications: {'peptide': 533} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 504} Chain breaks: 4 Chain: "B" Number of atoms: 8484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8484 Classifications: {'peptide': 533} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 504} Chain breaks: 4 Chain: "E" Number of atoms: 8484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8484 Classifications: {'peptide': 533} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 504} Chain breaks: 4 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 84 Unusual residues: {' MG': 1, 'UTP': 1, 'ZFY': 1} Inner-chain residues flagged as termini: ['pdbres="GLN C 602 "'] Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 3} Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 84 Unusual residues: {' MG': 1, 'UTP': 1, 'ZFY': 1} Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 3} Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 84 Unusual residues: {' MG': 1, 'UTP': 1, 'ZFY': 1} Inner-chain residues flagged as termini: ['pdbres="GLN B 602 "'] Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 3} Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 84 Unusual residues: {' MG': 1, 'UTP': 1, 'ZFY': 1} Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 3} Time building chain proxies: 5.37, per 1000 atoms: 0.16 Number of scatterers: 34272 At special positions: 0 Unit cell: (124.95, 135.45, 85.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 96 16.00 P 12 15.00 Mg 4 11.99 F 12 9.00 O 3220 8.00 N 2944 7.00 C 10964 6.00 H 17020 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 243 " distance=2.05 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 243 " distance=2.05 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 243 " distance=2.05 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 243 " distance=2.05 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: 3.08 Conformation dependent library (CDL) restraints added in 848.8 milliseconds 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3952 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 16 sheets defined 48.5% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'C' and resid 15 through 30 Processing helix chain 'C' and resid 46 through 50 removed outlier: 4.439A pdb=" N THR C 49 " --> pdb=" O ASP C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 78 removed outlier: 4.037A pdb=" N GLY C 72 " --> pdb=" O ASP C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 85 No H-bonds generated for 'chain 'C' and resid 83 through 85' Processing helix chain 'C' and resid 90 through 103 Processing helix chain 'C' and resid 112 through 130 removed outlier: 7.130A pdb=" N THR C 118 " --> pdb=" O VAL C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 170 removed outlier: 4.623A pdb=" N PHE C 168 " --> pdb=" O ARG C 164 " (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 234 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 Processing helix chain 'C' and resid 283 through 294 Processing helix chain 'C' and resid 314 through 329 Processing helix chain 'C' and resid 339 through 343 removed outlier: 3.700A pdb=" N GLU C 343 " --> pdb=" O SER C 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 339 through 343' Processing helix chain 'C' and resid 343 through 350 removed outlier: 3.795A pdb=" N SER C 347 " --> pdb=" O GLU C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 364 Processing helix chain 'C' and resid 377 through 391 Processing helix chain 'C' and resid 399 through 413 Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'C' and resid 487 through 491 Processing helix chain 'C' and resid 526 through 531 removed outlier: 3.754A pdb=" N PHE C 529 " --> pdb=" O HIS C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 548 Processing helix chain 'C' and resid 550 through 555 Processing helix chain 'A' and resid 15 through 30 Processing helix chain 'A' and resid 46 through 50 removed outlier: 4.439A pdb=" N THR A 49 " --> pdb=" O ASP A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 78 removed outlier: 4.036A pdb=" N GLY A 72 " --> pdb=" O ASP A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 85 No H-bonds generated for 'chain 'A' and resid 83 through 85' Processing helix chain 'A' and resid 90 through 103 Processing helix chain 'A' and resid 112 through 130 removed outlier: 7.129A pdb=" N THR A 118 " --> pdb=" O VAL A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 170 removed outlier: 4.624A pdb=" N PHE A 168 " --> pdb=" O ARG A 164 " (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 234 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 Processing helix chain 'A' and resid 283 through 294 Processing helix chain 'A' and resid 314 through 329 Processing helix chain 'A' and resid 339 through 343 removed outlier: 3.700A pdb=" N GLU A 343 " --> pdb=" O SER A 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 339 through 343' Processing helix chain 'A' and resid 343 through 350 removed outlier: 3.795A pdb=" N SER A 347 " --> pdb=" O GLU A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 364 Processing helix chain 'A' and resid 377 through 391 Processing helix chain 'A' and resid 399 through 413 Processing helix chain 'A' and resid 462 through 468 Processing helix chain 'A' and resid 487 through 491 Processing helix chain 'A' and resid 526 through 531 removed outlier: 3.754A pdb=" N PHE A 529 " --> pdb=" O HIS A 526 " (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 30 Processing helix chain 'B' and resid 46 through 50 removed outlier: 4.438A pdb=" N THR B 49 " --> pdb=" O ASP B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 78 removed outlier: 4.036A pdb=" N GLY B 72 " --> pdb=" O ASP B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 85 No H-bonds generated for 'chain 'B' and resid 83 through 85' Processing helix chain 'B' and resid 90 through 103 Processing helix chain 'B' and resid 112 through 130 removed outlier: 7.130A pdb=" N THR B 118 " --> pdb=" O VAL B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 170 removed outlier: 4.622A pdb=" N PHE B 168 " --> pdb=" O ARG B 164 " (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 234 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 Processing helix chain 'B' and resid 283 through 294 Processing helix chain 'B' and resid 314 through 329 Processing helix chain 'B' and resid 339 through 343 removed outlier: 3.699A pdb=" N GLU B 343 " --> pdb=" O SER B 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 339 through 343' Processing helix chain 'B' and resid 343 through 350 removed outlier: 3.795A pdb=" N SER B 347 " --> pdb=" O GLU B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 364 Processing helix chain 'B' and resid 377 through 391 Processing helix chain 'B' and resid 399 through 413 Processing helix chain 'B' and resid 462 through 468 Processing helix chain 'B' and resid 487 through 491 Processing helix chain 'B' and resid 526 through 531 removed outlier: 3.753A pdb=" N PHE B 529 " --> pdb=" O HIS B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 548 Processing helix chain 'B' and resid 550 through 555 Processing helix chain 'E' and resid 15 through 30 Processing helix chain 'E' and resid 46 through 50 removed outlier: 4.440A pdb=" N THR E 49 " --> pdb=" O ASP E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 78 removed outlier: 4.037A pdb=" N GLY E 72 " --> pdb=" O ASP E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 85 No H-bonds generated for 'chain 'E' and resid 83 through 85' Processing helix chain 'E' and resid 90 through 103 Processing helix chain 'E' and resid 112 through 130 removed outlier: 7.129A pdb=" N THR E 118 " --> pdb=" O VAL E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 156 through 170 removed outlier: 4.623A pdb=" N PHE E 168 " --> pdb=" O ARG E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 173 No H-bonds generated for 'chain 'E' and resid 171 through 173' Processing helix chain 'E' and resid 194 through 207 Processing helix chain 'E' and resid 223 through 234 Processing helix chain 'E' and resid 237 through 239 No H-bonds generated for 'chain 'E' and resid 237 through 239' Processing helix chain 'E' and resid 249 through 251 No H-bonds generated for 'chain 'E' and resid 249 through 251' Processing helix chain 'E' and resid 252 through 260 Processing helix chain 'E' and resid 261 through 270 Processing helix chain 'E' and resid 283 through 294 Processing helix chain 'E' and resid 314 through 329 Processing helix chain 'E' and resid 339 through 343 removed outlier: 3.699A pdb=" N GLU E 343 " --> pdb=" O SER E 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 339 through 343' Processing helix chain 'E' and resid 343 through 350 removed outlier: 3.795A pdb=" N SER E 347 " --> pdb=" O GLU E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 364 Processing helix chain 'E' and resid 377 through 391 Processing helix chain 'E' and resid 399 through 413 Processing helix chain 'E' and resid 462 through 468 Processing helix chain 'E' and resid 487 through 491 Processing helix chain 'E' and resid 526 through 531 removed outlier: 3.755A pdb=" N PHE E 529 " --> pdb=" O HIS E 526 " (cutoff:3.500A) Processing helix chain 'E' and resid 537 through 548 Processing helix chain 'E' and resid 550 through 555 Processing sheet with id=AA1, first strand: chain 'C' and resid 87 through 89 removed outlier: 4.161A pdb=" N GLY C 8 " --> pdb=" O LEU C 147 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N TYR C 3 " --> pdb=" O CYS C 176 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ILE C 178 " --> pdb=" O TYR C 3 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LEU C 5 " --> pdb=" O ILE C 178 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N VAL C 180 " --> pdb=" O LEU C 5 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N THR C 7 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N LEU C 182 " --> pdb=" O THR C 7 " (cutoff:3.500A) removed outlier: 9.243A pdb=" N LEU C 213 " --> pdb=" O PHE C 175 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ASN C 177 " --> pdb=" O LEU C 213 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N VAL C 215 " --> pdb=" O ASN C 177 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N HIS C 179 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ARG C 217 " --> pdb=" O HIS C 179 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N SER C 181 " --> pdb=" O ARG C 217 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 59 through 60 Processing sheet with id=AA3, first strand: chain 'C' and resid 331 through 338 removed outlier: 6.587A pdb=" N CYS C 299 " --> pdb=" O GLU C 333 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N LYS C 335 " --> pdb=" O CYS C 299 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE C 301 " --> pdb=" O LYS C 335 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ILE C 337 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LEU C 303 " --> pdb=" O ILE C 337 " (cutoff:3.500A) removed outlier: 9.280A pdb=" N GLY C 366 " --> pdb=" O THR C 298 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N SER C 300 " --> pdb=" O GLY C 366 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N LEU C 368 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ALA C 302 " --> pdb=" O LEU C 368 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL C 367 " --> pdb=" O LEU C 396 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N VAL C 398 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL C 369 " --> pdb=" O VAL C 398 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N GLY C 501 " --> pdb=" O GLU C 510 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N VAL C 512 " --> pdb=" O PHE C 499 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N PHE C 499 " --> pdb=" O VAL C 512 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 420 through 421 removed outlier: 7.868A pdb=" N ASN C 420 " --> pdb=" O VAL C 432 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL C 434 " --> pdb=" O ASN C 420 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 87 through 89 removed outlier: 4.161A pdb=" N GLY A 8 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N TYR A 3 " --> pdb=" O CYS A 176 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N ILE A 178 " --> pdb=" O TYR A 3 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LEU A 5 " --> pdb=" O ILE A 178 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N VAL A 180 " --> pdb=" O LEU A 5 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N THR A 7 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 8.439A pdb=" N LEU A 182 " --> pdb=" O THR A 7 " (cutoff:3.500A) removed outlier: 9.243A pdb=" N LEU A 213 " --> pdb=" O PHE A 175 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ASN A 177 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N VAL A 215 " --> pdb=" O ASN A 177 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N HIS A 179 " --> pdb=" O VAL A 215 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ARG A 217 " --> pdb=" O HIS A 179 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N SER A 181 " --> pdb=" O ARG A 217 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 59 through 60 Processing sheet with id=AA7, first strand: chain 'A' and resid 331 through 338 removed outlier: 6.587A pdb=" N CYS A 299 " --> pdb=" O GLU A 333 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N LYS A 335 " --> pdb=" O CYS A 299 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE A 301 " --> pdb=" O LYS A 335 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ILE A 337 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LEU A 303 " --> pdb=" O ILE A 337 " (cutoff:3.500A) removed outlier: 9.280A pdb=" N GLY A 366 " --> pdb=" O THR A 298 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N SER A 300 " --> pdb=" O GLY A 366 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N LEU A 368 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ALA A 302 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL A 367 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N VAL A 398 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL A 369 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N GLY A 501 " --> pdb=" O GLU A 510 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N VAL A 512 " --> pdb=" O PHE A 499 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N PHE A 499 " --> pdb=" O VAL A 512 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 420 through 421 removed outlier: 7.868A pdb=" N ASN A 420 " --> pdb=" O VAL A 432 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL A 434 " --> pdb=" O ASN A 420 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 87 through 89 removed outlier: 4.161A pdb=" N GLY B 8 " --> pdb=" O LEU B 147 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N TYR B 3 " --> pdb=" O CYS B 176 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ILE B 178 " --> pdb=" O TYR B 3 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N LEU B 5 " --> pdb=" O ILE B 178 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N VAL B 180 " --> pdb=" O LEU B 5 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N THR B 7 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N LEU B 182 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 9.244A pdb=" N LEU B 213 " --> pdb=" O PHE B 175 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ASN B 177 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N VAL B 215 " --> pdb=" O ASN B 177 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N HIS B 179 " --> pdb=" O VAL B 215 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ARG B 217 " --> pdb=" O HIS B 179 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N SER B 181 " --> pdb=" O ARG B 217 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 59 through 60 Processing sheet with id=AB2, first strand: chain 'B' and resid 331 through 338 removed outlier: 6.587A pdb=" N CYS B 299 " --> pdb=" O GLU B 333 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N LYS B 335 " --> pdb=" O CYS B 299 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE B 301 " --> pdb=" O LYS B 335 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ILE B 337 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LEU B 303 " --> pdb=" O ILE B 337 " (cutoff:3.500A) removed outlier: 9.280A pdb=" N GLY B 366 " --> pdb=" O THR B 298 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N SER B 300 " --> pdb=" O GLY B 366 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N LEU B 368 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ALA B 302 " --> pdb=" O LEU B 368 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL B 367 " --> pdb=" O LEU B 396 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N VAL B 398 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL B 369 " --> pdb=" O VAL B 398 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N GLY B 501 " --> pdb=" O GLU B 510 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N VAL B 512 " --> pdb=" O PHE B 499 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N PHE B 499 " --> pdb=" O VAL B 512 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 420 through 421 removed outlier: 7.868A pdb=" N ASN B 420 " --> pdb=" O VAL B 432 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL B 434 " --> pdb=" O ASN B 420 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 87 through 89 removed outlier: 4.161A pdb=" N GLY E 8 " --> pdb=" O LEU E 147 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N TYR E 3 " --> pdb=" O CYS E 176 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ILE E 178 " --> pdb=" O TYR E 3 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LEU E 5 " --> pdb=" O ILE E 178 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N VAL E 180 " --> pdb=" O LEU E 5 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N THR E 7 " --> pdb=" O VAL E 180 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N LEU E 182 " --> pdb=" O THR E 7 " (cutoff:3.500A) removed outlier: 9.244A pdb=" N LEU E 213 " --> pdb=" O PHE E 175 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ASN E 177 " --> pdb=" O LEU E 213 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N VAL E 215 " --> pdb=" O ASN E 177 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N HIS E 179 " --> pdb=" O VAL E 215 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ARG E 217 " --> pdb=" O HIS E 179 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N SER E 181 " --> pdb=" O ARG E 217 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 59 through 60 Processing sheet with id=AB6, first strand: chain 'E' and resid 331 through 338 removed outlier: 6.587A pdb=" N CYS E 299 " --> pdb=" O GLU E 333 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N LYS E 335 " --> pdb=" O CYS E 299 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE E 301 " --> pdb=" O LYS E 335 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ILE E 337 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LEU E 303 " --> pdb=" O ILE E 337 " (cutoff:3.500A) removed outlier: 9.280A pdb=" N GLY E 366 " --> pdb=" O THR E 298 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N SER E 300 " --> pdb=" O GLY E 366 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N LEU E 368 " --> pdb=" O SER E 300 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ALA E 302 " --> pdb=" O LEU E 368 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL E 367 " --> pdb=" O LEU E 396 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N VAL E 398 " --> pdb=" O VAL E 367 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL E 369 " --> pdb=" O VAL E 398 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N GLY E 501 " --> pdb=" O GLU E 510 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N VAL E 512 " --> pdb=" O PHE E 499 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N PHE E 499 " --> pdb=" O VAL E 512 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 420 through 421 removed outlier: 7.868A pdb=" N ASN E 420 " --> pdb=" O VAL E 432 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL E 434 " --> pdb=" O ASN E 420 " (cutoff:3.500A) 760 hydrogen bonds defined for protein. 2196 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: 8.32 Time building geometry restraints manager: 4.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.15: 16984 1.15 - 1.33: 3773 1.33 - 1.52: 6665 1.52 - 1.70: 7074 1.70 - 1.89: 152 Bond restraints: 34648 Sorted by residual: bond pdb=" N HIS C 179 " pdb=" H HIS C 179 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" CD1 TYR A 106 " pdb=" HD1 TYR A 106 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N HIS E 439 " pdb=" H HIS E 439 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N LEU B 282 " pdb=" H LEU B 282 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N VAL B 432 " pdb=" H VAL B 432 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 ... (remaining 34643 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.15: 58818 4.15 - 8.30: 3858 8.30 - 12.45: 36 12.45 - 16.61: 0 16.61 - 20.76: 4 Bond angle restraints: 62716 Sorted by residual: angle pdb=" N PRO B 538 " pdb=" CA PRO B 538 " pdb=" C PRO B 538 " ideal model delta sigma weight residual 110.70 119.96 -9.26 1.22e+00 6.72e-01 5.77e+01 angle pdb=" N PRO E 538 " pdb=" CA PRO E 538 " pdb=" C PRO E 538 " ideal model delta sigma weight residual 110.70 119.95 -9.25 1.22e+00 6.72e-01 5.74e+01 angle pdb=" N PRO C 538 " pdb=" CA PRO C 538 " pdb=" C PRO C 538 " ideal model delta sigma weight residual 110.70 119.94 -9.24 1.22e+00 6.72e-01 5.74e+01 angle pdb=" N PRO A 538 " pdb=" CA PRO A 538 " pdb=" C PRO A 538 " ideal model delta sigma weight residual 110.70 119.90 -9.20 1.22e+00 6.72e-01 5.69e+01 angle pdb=" CA LEU B 497 " pdb=" N LEU B 497 " pdb=" H LEU B 497 " ideal model delta sigma weight residual 114.00 134.76 -20.76 3.00e+00 1.11e-01 4.79e+01 ... (remaining 62711 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 14235 17.94 - 35.89: 1146 35.89 - 53.83: 550 53.83 - 71.78: 384 71.78 - 89.72: 61 Dihedral angle restraints: 16376 sinusoidal: 9160 harmonic: 7216 Sorted by residual: dihedral pdb=" CB CYS E 218 " pdb=" SG CYS E 218 " pdb=" SG CYS E 243 " pdb=" CB CYS E 243 " ideal model delta sinusoidal sigma weight residual 93.00 -179.28 -87.72 1 1.00e+01 1.00e-02 9.22e+01 dihedral pdb=" CB CYS B 218 " pdb=" SG CYS B 218 " pdb=" SG CYS B 243 " pdb=" CB CYS B 243 " ideal model delta sinusoidal sigma weight residual 93.00 -179.30 -87.70 1 1.00e+01 1.00e-02 9.21e+01 dihedral pdb=" CB CYS C 218 " pdb=" SG CYS C 218 " pdb=" SG CYS C 243 " pdb=" CB CYS C 243 " ideal model delta sinusoidal sigma weight residual 93.00 -179.31 -87.69 1 1.00e+01 1.00e-02 9.21e+01 ... (remaining 16373 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 1464 0.090 - 0.179: 828 0.179 - 0.269: 279 0.269 - 0.359: 49 0.359 - 0.448: 16 Chirality restraints: 2636 Sorted by residual: chirality pdb=" CA PRO B 538 " pdb=" N PRO B 538 " pdb=" C PRO B 538 " pdb=" CB PRO B 538 " both_signs ideal model delta sigma weight residual False 2.72 2.27 0.45 2.00e-01 2.50e+01 5.03e+00 chirality pdb=" CA PRO A 538 " pdb=" N PRO A 538 " pdb=" C PRO A 538 " pdb=" CB PRO A 538 " both_signs ideal model delta sigma weight residual False 2.72 2.27 0.45 2.00e-01 2.50e+01 5.00e+00 chirality pdb=" CA PRO C 538 " pdb=" N PRO C 538 " pdb=" C PRO C 538 " pdb=" CB PRO C 538 " both_signs ideal model delta sigma weight residual False 2.72 2.27 0.45 2.00e-01 2.50e+01 5.00e+00 ... (remaining 2633 not shown) Planarity restraints: 5048 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 387 " -0.128 2.00e-02 2.50e+03 7.45e-02 2.22e+02 pdb=" CG TRP B 387 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP B 387 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TRP B 387 " -0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP B 387 " 0.071 2.00e-02 2.50e+03 pdb=" CE2 TRP B 387 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP B 387 " 0.033 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 387 " -0.051 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 387 " 0.039 2.00e-02 2.50e+03 pdb=" CH2 TRP B 387 " -0.037 2.00e-02 2.50e+03 pdb=" HD1 TRP B 387 " -0.018 2.00e-02 2.50e+03 pdb=" HE1 TRP B 387 " 0.168 2.00e-02 2.50e+03 pdb=" HE3 TRP B 387 " 0.059 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 387 " -0.097 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 387 " 0.102 2.00e-02 2.50e+03 pdb=" HH2 TRP B 387 " -0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 387 " 0.128 2.00e-02 2.50e+03 7.44e-02 2.21e+02 pdb=" CG TRP A 387 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP A 387 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TRP A 387 " 0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP A 387 " -0.071 2.00e-02 2.50e+03 pdb=" CE2 TRP A 387 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A 387 " -0.033 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 387 " 0.051 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 387 " -0.039 2.00e-02 2.50e+03 pdb=" CH2 TRP A 387 " 0.037 2.00e-02 2.50e+03 pdb=" HD1 TRP A 387 " 0.018 2.00e-02 2.50e+03 pdb=" HE1 TRP A 387 " -0.166 2.00e-02 2.50e+03 pdb=" HE3 TRP A 387 " -0.059 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 387 " 0.097 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 387 " -0.102 2.00e-02 2.50e+03 pdb=" HH2 TRP A 387 " 0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 387 " -0.128 2.00e-02 2.50e+03 7.44e-02 2.21e+02 pdb=" CG TRP C 387 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP C 387 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TRP C 387 " -0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP C 387 " 0.071 2.00e-02 2.50e+03 pdb=" CE2 TRP C 387 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP C 387 " 0.033 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 387 " -0.051 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 387 " 0.038 2.00e-02 2.50e+03 pdb=" CH2 TRP C 387 " -0.037 2.00e-02 2.50e+03 pdb=" HD1 TRP C 387 " -0.017 2.00e-02 2.50e+03 pdb=" HE1 TRP C 387 " 0.167 2.00e-02 2.50e+03 pdb=" HE3 TRP C 387 " 0.060 2.00e-02 2.50e+03 pdb=" HZ2 TRP C 387 " -0.097 2.00e-02 2.50e+03 pdb=" HZ3 TRP C 387 " 0.101 2.00e-02 2.50e+03 pdb=" HH2 TRP C 387 " -0.083 2.00e-02 2.50e+03 ... (remaining 5045 not shown) Histogram of nonbonded interaction distances: 1.41 - 2.04: 1404 2.04 - 2.68: 46235 2.68 - 3.32: 110204 3.32 - 3.96: 148103 3.96 - 4.60: 218176 Nonbonded interactions: 524122 Sorted by model distance: nonbonded pdb=" HB ILE A 43 " pdb="HG23 VAL E 111 " model vdw 1.405 2.440 nonbonded pdb=" HB ILE A 43 " pdb="HG22 VAL E 111 " model vdw 1.406 2.440 nonbonded pdb="HG23 VAL A 111 " pdb=" HB ILE E 43 " model vdw 1.408 2.440 nonbonded pdb="HG22 VAL A 111 " pdb=" HB ILE E 43 " model vdw 1.409 2.440 nonbonded pdb=" HB ILE C 43 " pdb="HG23 VAL B 111 " model vdw 1.422 2.440 ... (remaining 524117 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 556) selection = (chain 'B' and resid 1 through 556) selection = (chain 'C' and resid 1 through 556) selection = (chain 'E' and resid 1 through 556) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.140 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 31.590 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:6.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 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 0.138 17632 Z= 0.779 Angle : 1.990 11.030 23912 Z= 1.327 Chirality : 0.120 0.448 2636 Planarity : 0.014 0.095 3048 Dihedral : 16.046 89.719 6784 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.63 % Favored : 95.98 % Rotamer: Outliers : 1.48 % Allowed : 6.55 % Favored : 91.97 % Cbeta Deviations : 0.61 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.17), residues: 2092 helix: -1.17 (0.15), residues: 896 sheet: -1.17 (0.26), residues: 344 loop : -0.35 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.002 ARG A 76 TYR 0.075 0.017 TYR A 265 PHE 0.079 0.018 PHE B 50 TRP 0.074 0.020 TRP E 285 HIS 0.022 0.005 HIS A 439 Details of bonding type rmsd/Z covalent geometry : bond 0.01330 / 0.78 (17628) covalent geometry : angle 1.99023 / 1.33 (23904) SS BOND : bond 0.01545 / 0.75 ( 4) SS BOND : angle 2.11472 / 1.05 ( 8) hydrogen bonds : bond 0.16728 / 10.91 ( 760) hydrogen bonds : angle 7.22285 / 5.02 ( 2196) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 500 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 198 GLN cc_start: 0.7345 (mt0) cc_final: 0.7097 (mt0) REVERT: C 265 TYR cc_start: 0.8289 (t80) cc_final: 0.8070 (t80) REVERT: C 335 LYS cc_start: 0.8496 (mttm) cc_final: 0.8253 (mttt) REVERT: C 360 LYS cc_start: 0.7915 (mttt) cc_final: 0.7698 (mtmm) REVERT: C 466 LYS cc_start: 0.8264 (mttt) cc_final: 0.7942 (mtpp) REVERT: A 202 ARG cc_start: 0.7761 (ttp80) cc_final: 0.7500 (ttp-170) REVERT: A 466 LYS cc_start: 0.8213 (mttt) cc_final: 0.7866 (mtmm) REVERT: B 198 GLN cc_start: 0.7259 (mt0) cc_final: 0.6926 (mt0) REVERT: B 322 GLU cc_start: 0.7597 (mm-30) cc_final: 0.7340 (mm-30) REVERT: B 466 LYS cc_start: 0.8191 (mttt) cc_final: 0.7863 (mtpp) REVERT: E 322 GLU cc_start: 0.7585 (mm-30) cc_final: 0.7324 (mm-30) REVERT: E 466 LYS cc_start: 0.8194 (mttt) cc_final: 0.7871 (mtpp) outliers start: 28 outliers final: 5 residues processed: 507 average time/residue: 1.1067 time to fit residues: 641.3144 Evaluate side-chains 352 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 347 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 458 GLN Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain B residue 458 GLN Chi-restraints excluded: chain E residue 458 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.7980 chunk 200 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 177 ASN ** C 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 GLN ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 GLN ** B 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 556 GLN ** E 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 556 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.160581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.133825 restraints weight = 53212.613| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.73 r_work: 0.3239 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17632 Z= 0.175 Angle : 0.668 5.731 23912 Z= 0.351 Chirality : 0.047 0.170 2636 Planarity : 0.006 0.050 3048 Dihedral : 10.930 83.379 2598 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.20 % Favored : 97.61 % Rotamer: Outliers : 2.48 % Allowed : 11.63 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.18), residues: 2092 helix: 0.01 (0.16), residues: 948 sheet: -1.29 (0.26), residues: 344 loop : -0.32 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 127 TYR 0.014 0.002 TYR C 42 PHE 0.016 0.002 PHE B 163 TRP 0.007 0.001 TRP A 387 HIS 0.007 0.002 HIS B 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.18 (17628) covalent geometry : angle 0.66620 / 0.35 (23904) SS BOND : bond 0.00447 / 0.22 ( 4) SS BOND : angle 2.90218 / 1.44 ( 8) hydrogen bonds : bond 0.04855 / 3.29 ( 760) hydrogen bonds : angle 5.14574 / 3.56 ( 2196) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 360 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 157 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.7956 (mmt) REVERT: C 228 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7339 (mm-30) REVERT: C 239 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7487 (mp0) REVERT: C 240 GLN cc_start: 0.8073 (mt0) cc_final: 0.7819 (mt0) REVERT: C 265 TYR cc_start: 0.8560 (t80) cc_final: 0.8289 (t80) REVERT: C 423 GLU cc_start: 0.7237 (tt0) cc_final: 0.6985 (tt0) REVERT: C 466 LYS cc_start: 0.8338 (mttt) cc_final: 0.7984 (mtpp) REVERT: A 101 GLU cc_start: 0.8590 (tm-30) cc_final: 0.7853 (tm-30) REVERT: A 107 LEU cc_start: 0.8309 (mt) cc_final: 0.8049 (mt) REVERT: A 153 ASP cc_start: 0.6995 (m-30) cc_final: 0.6759 (m-30) REVERT: A 239 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7489 (mp0) REVERT: A 240 GLN cc_start: 0.8009 (mt0) cc_final: 0.7660 (mt0) REVERT: A 423 GLU cc_start: 0.7102 (tt0) cc_final: 0.6857 (tt0) REVERT: A 466 LYS cc_start: 0.8320 (mttt) cc_final: 0.7962 (mtpp) REVERT: B 239 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7548 (mp0) REVERT: B 240 GLN cc_start: 0.7985 (mt0) cc_final: 0.7619 (mt0) REVERT: B 466 LYS cc_start: 0.8321 (mttt) cc_final: 0.7942 (mtpp) REVERT: E 239 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7497 (mp0) REVERT: E 240 GLN cc_start: 0.7961 (mt0) cc_final: 0.7601 (mt0) REVERT: E 335 LYS cc_start: 0.8683 (mttm) cc_final: 0.8398 (mttt) REVERT: E 391 GLN cc_start: 0.7800 (mm-40) cc_final: 0.7150 (mp10) REVERT: E 466 LYS cc_start: 0.8337 (mttt) cc_final: 0.7968 (mtpp) outliers start: 47 outliers final: 19 residues processed: 388 average time/residue: 1.1339 time to fit residues: 496.6871 Evaluate side-chains 315 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 294 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 228 GLU Chi-restraints excluded: chain C residue 313 SER Chi-restraints excluded: chain C residue 458 GLN Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 402 MET Chi-restraints excluded: chain B residue 458 GLN Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain E residue 458 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 126 optimal weight: 1.9990 chunk 209 optimal weight: 0.4980 chunk 82 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 204 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 240 GLN C 330 HIS A 87 ASN A 240 GLN A 330 HIS A 391 GLN B 87 ASN B 240 GLN B 330 HIS ** B 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 87 ASN E 240 GLN E 330 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.153691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.125156 restraints weight = 52581.795| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.79 r_work: 0.3145 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17632 Z= 0.189 Angle : 0.604 6.074 23912 Z= 0.315 Chirality : 0.046 0.152 2636 Planarity : 0.006 0.058 3048 Dihedral : 10.152 87.977 2598 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.53 % Favored : 97.28 % Rotamer: Outliers : 2.64 % Allowed : 12.32 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.18), residues: 2092 helix: 0.58 (0.17), residues: 924 sheet: -1.18 (0.27), residues: 336 loop : -0.17 (0.23), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 81 TYR 0.015 0.002 TYR B 42 PHE 0.013 0.002 PHE E 59 TRP 0.007 0.001 TRP A 358 HIS 0.008 0.002 HIS E 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.19 (17628) covalent geometry : angle 0.60097 / 0.31 (23904) SS BOND : bond 0.00374 / 0.18 ( 4) SS BOND : angle 3.19873 / 1.59 ( 8) hydrogen bonds : bond 0.04261 / 2.88 ( 760) hydrogen bonds : angle 4.69996 / 3.27 ( 2196) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 356 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 107 LEU cc_start: 0.8360 (mt) cc_final: 0.8063 (mt) REVERT: C 123 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7842 (mt-10) REVERT: C 157 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.8035 (mmt) REVERT: C 231 SER cc_start: 0.8369 (p) cc_final: 0.8131 (p) REVERT: C 239 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7525 (mp0) REVERT: C 298 THR cc_start: 0.8407 (OUTLIER) cc_final: 0.8128 (p) REVERT: C 324 SER cc_start: 0.9116 (m) cc_final: 0.8909 (m) REVERT: C 391 GLN cc_start: 0.7761 (mm-40) cc_final: 0.7406 (mp10) REVERT: C 423 GLU cc_start: 0.7494 (tt0) cc_final: 0.7175 (tt0) REVERT: C 466 LYS cc_start: 0.8321 (mttt) cc_final: 0.7958 (mtpp) REVERT: C 510 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7591 (mt-10) REVERT: C 554 TYR cc_start: 0.8617 (t80) cc_final: 0.8401 (t80) REVERT: A 107 LEU cc_start: 0.8410 (mt) cc_final: 0.8096 (mt) REVERT: A 231 SER cc_start: 0.8369 (p) cc_final: 0.8130 (p) REVERT: A 239 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7612 (mp0) REVERT: A 298 THR cc_start: 0.8517 (OUTLIER) cc_final: 0.8218 (p) REVERT: A 324 SER cc_start: 0.9097 (m) cc_final: 0.8896 (m) REVERT: A 466 LYS cc_start: 0.8315 (mttt) cc_final: 0.7947 (mtmm) REVERT: A 510 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7557 (mt-10) REVERT: A 554 TYR cc_start: 0.8612 (t80) cc_final: 0.8337 (t80) REVERT: B 62 ASP cc_start: 0.8346 (m-30) cc_final: 0.8134 (m-30) REVERT: B 107 LEU cc_start: 0.8348 (mt) cc_final: 0.8051 (mt) REVERT: B 231 SER cc_start: 0.8407 (p) cc_final: 0.8160 (p) REVERT: B 239 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7583 (mp0) REVERT: B 298 THR cc_start: 0.8406 (OUTLIER) cc_final: 0.8098 (p) REVERT: B 335 LYS cc_start: 0.8785 (mttm) cc_final: 0.8479 (mttt) REVERT: B 341 ASP cc_start: 0.8300 (m-30) cc_final: 0.7913 (m-30) REVERT: B 391 GLN cc_start: 0.7805 (mm-40) cc_final: 0.7355 (mp10) REVERT: B 466 LYS cc_start: 0.8329 (mttt) cc_final: 0.7967 (mtpp) REVERT: B 554 TYR cc_start: 0.8573 (t80) cc_final: 0.8365 (t80) REVERT: E 107 LEU cc_start: 0.8360 (mt) cc_final: 0.8057 (mt) REVERT: E 231 SER cc_start: 0.8397 (p) cc_final: 0.8159 (p) REVERT: E 239 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7523 (mp0) REVERT: E 298 THR cc_start: 0.8404 (OUTLIER) cc_final: 0.8094 (p) REVERT: E 391 GLN cc_start: 0.7801 (mm-40) cc_final: 0.7394 (mp10) REVERT: E 466 LYS cc_start: 0.8341 (mttt) cc_final: 0.7978 (mtpp) REVERT: E 510 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7556 (mt-10) REVERT: E 554 TYR cc_start: 0.8599 (t80) cc_final: 0.8369 (t80) outliers start: 50 outliers final: 9 residues processed: 386 average time/residue: 1.0141 time to fit residues: 449.3419 Evaluate side-chains 346 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 329 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 458 GLN Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 298 THR Chi-restraints excluded: chain E residue 402 MET Chi-restraints excluded: chain E residue 510 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 69 optimal weight: 0.5980 chunk 146 optimal weight: 8.9990 chunk 119 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 131 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 44 optimal weight: 0.3980 chunk 92 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 175 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 502 GLN A 391 GLN A 502 GLN B 502 GLN E 502 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.154121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.126052 restraints weight = 52565.558| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.75 r_work: 0.3149 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.4270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 17632 Z= 0.176 Angle : 0.563 5.559 23912 Z= 0.291 Chirality : 0.044 0.149 2636 Planarity : 0.005 0.066 3048 Dihedral : 9.382 89.102 2590 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.25 % Favored : 97.56 % Rotamer: Outliers : 1.74 % Allowed : 14.75 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.27 (0.19), residues: 2092 helix: 1.02 (0.17), residues: 900 sheet: -1.17 (0.27), residues: 336 loop : 0.02 (0.23), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 376 TYR 0.014 0.001 TYR A 42 PHE 0.011 0.002 PHE A 457 TRP 0.007 0.001 TRP B 358 HIS 0.006 0.001 HIS C 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 (17628) covalent geometry : angle 0.56063 / 0.29 (23904) SS BOND : bond 0.00099 / 0.05 ( 4) SS BOND : angle 3.12486 / 1.54 ( 8) hydrogen bonds : bond 0.03876 / 2.64 ( 760) hydrogen bonds : angle 4.54847 / 3.16 ( 2196) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 346 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 107 LEU cc_start: 0.8422 (mt) cc_final: 0.8119 (mt) REVERT: C 123 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7819 (mt-10) REVERT: C 157 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.8130 (mmm) REVERT: C 231 SER cc_start: 0.8398 (p) cc_final: 0.8148 (p) REVERT: C 240 GLN cc_start: 0.8329 (mt0) cc_final: 0.7801 (mt0) REVERT: C 324 SER cc_start: 0.9071 (m) cc_final: 0.8858 (m) REVERT: C 391 GLN cc_start: 0.7794 (mm-40) cc_final: 0.7460 (mp10) REVERT: C 466 LYS cc_start: 0.8338 (mttt) cc_final: 0.7967 (mtpp) REVERT: C 510 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7522 (mt-10) REVERT: C 554 TYR cc_start: 0.8595 (t80) cc_final: 0.8350 (t80) REVERT: A 107 LEU cc_start: 0.8430 (mt) cc_final: 0.8138 (mt) REVERT: A 231 SER cc_start: 0.8464 (p) cc_final: 0.8201 (p) REVERT: A 240 GLN cc_start: 0.8353 (mt0) cc_final: 0.7821 (mt0) REVERT: A 324 SER cc_start: 0.9084 (m) cc_final: 0.8877 (m) REVERT: A 391 GLN cc_start: 0.7816 (mm-40) cc_final: 0.6963 (mp10) REVERT: A 466 LYS cc_start: 0.8305 (mttt) cc_final: 0.7922 (mtmm) REVERT: A 554 TYR cc_start: 0.8628 (t80) cc_final: 0.8343 (t80) REVERT: B 107 LEU cc_start: 0.8392 (mt) cc_final: 0.8087 (mt) REVERT: B 153 ASP cc_start: 0.7203 (m-30) cc_final: 0.6834 (m-30) REVERT: B 157 MET cc_start: 0.8585 (mmt) cc_final: 0.7924 (mmp) REVERT: B 231 SER cc_start: 0.8409 (p) cc_final: 0.8130 (p) REVERT: B 240 GLN cc_start: 0.8309 (mt0) cc_final: 0.7782 (mt0) REVERT: B 391 GLN cc_start: 0.7844 (mm-40) cc_final: 0.7432 (mp10) REVERT: B 436 MET cc_start: 0.7681 (ttm) cc_final: 0.7379 (ttm) REVERT: B 466 LYS cc_start: 0.8284 (mttt) cc_final: 0.7903 (mtpp) REVERT: B 535 LYS cc_start: 0.7827 (tttt) cc_final: 0.7510 (tttm) REVERT: B 554 TYR cc_start: 0.8610 (t80) cc_final: 0.8364 (t80) REVERT: E 107 LEU cc_start: 0.8420 (mt) cc_final: 0.8110 (mt) REVERT: E 153 ASP cc_start: 0.7356 (m-30) cc_final: 0.7136 (m-30) REVERT: E 231 SER cc_start: 0.8491 (p) cc_final: 0.8229 (p) REVERT: E 391 GLN cc_start: 0.7828 (mm-40) cc_final: 0.7501 (mp10) REVERT: E 466 LYS cc_start: 0.8303 (mttt) cc_final: 0.7932 (mtpp) REVERT: E 554 TYR cc_start: 0.8619 (t80) cc_final: 0.8366 (t80) outliers start: 33 outliers final: 13 residues processed: 361 average time/residue: 1.0610 time to fit residues: 436.7357 Evaluate side-chains 353 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 338 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 458 GLN Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 402 MET Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 402 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 168 optimal weight: 0.9980 chunk 157 optimal weight: 0.2980 chunk 122 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 146 optimal weight: 6.9990 chunk 129 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 177 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 33 HIS A 33 HIS B 33 HIS E 33 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.153287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.125184 restraints weight = 52783.508| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.76 r_work: 0.3151 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.4477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17632 Z= 0.142 Angle : 0.532 5.348 23912 Z= 0.274 Chirality : 0.043 0.141 2636 Planarity : 0.006 0.076 3048 Dihedral : 7.602 89.618 2587 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.80 % Allowed : 15.27 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.19), residues: 2092 helix: 1.29 (0.17), residues: 900 sheet: -1.20 (0.26), residues: 336 loop : 0.07 (0.23), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 376 TYR 0.014 0.001 TYR B 42 PHE 0.010 0.001 PHE A 163 TRP 0.007 0.001 TRP A 358 HIS 0.005 0.001 HIS E 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (17628) covalent geometry : angle 0.52867 / 0.27 (23904) SS BOND : bond 0.00335 / 0.17 ( 4) SS BOND : angle 3.33197 / 1.65 ( 8) hydrogen bonds : bond 0.03539 / 2.41 ( 760) hydrogen bonds : angle 4.38815 / 3.05 ( 2196) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 351 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 107 LEU cc_start: 0.8437 (mt) cc_final: 0.8129 (mt) REVERT: C 141 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.7688 (mt0) REVERT: C 231 SER cc_start: 0.8444 (p) cc_final: 0.8169 (p) REVERT: C 240 GLN cc_start: 0.8277 (mt0) cc_final: 0.7732 (mt0) REVERT: C 324 SER cc_start: 0.9062 (m) cc_final: 0.8852 (m) REVERT: C 335 LYS cc_start: 0.8713 (mttm) cc_final: 0.8426 (mttt) REVERT: C 391 GLN cc_start: 0.7674 (mm-40) cc_final: 0.7349 (mp10) REVERT: C 466 LYS cc_start: 0.8315 (mttt) cc_final: 0.7952 (mtpp) REVERT: C 554 TYR cc_start: 0.8632 (t80) cc_final: 0.8396 (t80) REVERT: A 107 LEU cc_start: 0.8476 (mt) cc_final: 0.8202 (mt) REVERT: A 141 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.7614 (mt0) REVERT: A 153 ASP cc_start: 0.7335 (m-30) cc_final: 0.7118 (m-30) REVERT: A 231 SER cc_start: 0.8478 (p) cc_final: 0.8189 (p) REVERT: A 240 GLN cc_start: 0.8344 (mt0) cc_final: 0.7758 (mt0) REVERT: A 324 SER cc_start: 0.9070 (m) cc_final: 0.8863 (m) REVERT: A 391 GLN cc_start: 0.7975 (mm-40) cc_final: 0.7620 (mp10) REVERT: A 466 LYS cc_start: 0.8270 (mttt) cc_final: 0.7870 (mtmm) REVERT: A 510 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7498 (mt-10) REVERT: A 550 ARG cc_start: 0.7587 (mtt180) cc_final: 0.7383 (mtt180) REVERT: A 554 TYR cc_start: 0.8567 (t80) cc_final: 0.8302 (t80) REVERT: B 107 LEU cc_start: 0.8425 (mt) cc_final: 0.8120 (mt) REVERT: B 155 GLU cc_start: 0.8149 (mp0) cc_final: 0.7944 (mp0) REVERT: B 157 MET cc_start: 0.8637 (mmt) cc_final: 0.8361 (mmm) REVERT: B 231 SER cc_start: 0.8424 (p) cc_final: 0.8149 (p) REVERT: B 240 GLN cc_start: 0.8298 (mt0) cc_final: 0.7738 (mt0) REVERT: B 391 GLN cc_start: 0.7880 (mm-40) cc_final: 0.7529 (mp10) REVERT: B 466 LYS cc_start: 0.8296 (mttt) cc_final: 0.7909 (mtpp) REVERT: B 554 TYR cc_start: 0.8616 (t80) cc_final: 0.8362 (t80) REVERT: E 107 LEU cc_start: 0.8466 (mt) cc_final: 0.8150 (mt) REVERT: E 203 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7301 (tp30) REVERT: E 231 SER cc_start: 0.8522 (p) cc_final: 0.8233 (p) REVERT: E 335 LYS cc_start: 0.8754 (mttm) cc_final: 0.8449 (mttt) REVERT: E 391 GLN cc_start: 0.7823 (mm-40) cc_final: 0.7528 (mp10) REVERT: E 466 LYS cc_start: 0.8281 (mttt) cc_final: 0.7879 (mtmm) REVERT: E 554 TYR cc_start: 0.8570 (t80) cc_final: 0.8313 (t80) outliers start: 34 outliers final: 11 residues processed: 372 average time/residue: 1.0776 time to fit residues: 457.2469 Evaluate side-chains 360 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 345 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 141 GLN Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain A residue 141 GLN Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 402 MET Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 402 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 38 optimal weight: 0.9980 chunk 171 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 143 optimal weight: 0.8980 chunk 167 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 66 optimal weight: 0.0270 overall best weight: 0.9840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 87 ASN B 329 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.151507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.124240 restraints weight = 53061.917| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.69 r_work: 0.3134 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.4664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 17632 Z= 0.160 Angle : 0.540 5.336 23912 Z= 0.277 Chirality : 0.043 0.155 2636 Planarity : 0.005 0.066 3048 Dihedral : 6.743 39.217 2584 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.85 % Allowed : 16.38 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.19), residues: 2092 helix: 1.33 (0.17), residues: 900 sheet: -1.15 (0.26), residues: 336 loop : 0.08 (0.23), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 81 TYR 0.014 0.001 TYR C 42 PHE 0.009 0.001 PHE B 59 TRP 0.006 0.001 TRP A 358 HIS 0.006 0.001 HIS C 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (17628) covalent geometry : angle 0.53610 / 0.28 (23904) SS BOND : bond 0.00728 / 0.36 ( 4) SS BOND : angle 3.62562 / 1.79 ( 8) hydrogen bonds : bond 0.03539 / 2.41 ( 760) hydrogen bonds : angle 4.35908 / 3.03 ( 2196) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 346 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 107 LEU cc_start: 0.8472 (mt) cc_final: 0.8168 (mt) REVERT: C 141 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.7640 (mt0) REVERT: C 153 ASP cc_start: 0.7222 (m-30) cc_final: 0.6951 (m-30) REVERT: C 157 MET cc_start: 0.8665 (mmm) cc_final: 0.8075 (mmp) REVERT: C 231 SER cc_start: 0.8408 (p) cc_final: 0.8136 (p) REVERT: C 240 GLN cc_start: 0.8489 (mt0) cc_final: 0.7862 (mt0) REVERT: C 324 SER cc_start: 0.9068 (m) cc_final: 0.8850 (m) REVERT: C 391 GLN cc_start: 0.7739 (mm-40) cc_final: 0.7436 (mp10) REVERT: C 466 LYS cc_start: 0.8311 (mttt) cc_final: 0.7927 (mtpp) REVERT: C 481 ARG cc_start: 0.7647 (OUTLIER) cc_final: 0.6821 (ttm-80) REVERT: C 554 TYR cc_start: 0.8620 (t80) cc_final: 0.8337 (t80) REVERT: A 107 LEU cc_start: 0.8492 (mt) cc_final: 0.8232 (mt) REVERT: A 141 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.7624 (mt0) REVERT: A 231 SER cc_start: 0.8468 (p) cc_final: 0.8191 (p) REVERT: A 240 GLN cc_start: 0.8495 (mt0) cc_final: 0.7868 (mt0) REVERT: A 324 SER cc_start: 0.9066 (m) cc_final: 0.8852 (m) REVERT: A 391 GLN cc_start: 0.7774 (mm-40) cc_final: 0.7436 (mp10) REVERT: A 466 LYS cc_start: 0.8287 (mttt) cc_final: 0.7886 (mtmm) REVERT: A 550 ARG cc_start: 0.7523 (mtt180) cc_final: 0.7258 (mtt180) REVERT: A 554 TYR cc_start: 0.8564 (t80) cc_final: 0.8310 (t80) REVERT: B 107 LEU cc_start: 0.8453 (mt) cc_final: 0.8150 (mt) REVERT: B 157 MET cc_start: 0.8659 (mmt) cc_final: 0.8358 (mmm) REVERT: B 231 SER cc_start: 0.8406 (p) cc_final: 0.8133 (p) REVERT: B 240 GLN cc_start: 0.8458 (mt0) cc_final: 0.7878 (mt0) REVERT: B 391 GLN cc_start: 0.7731 (mm-40) cc_final: 0.7375 (mp10) REVERT: B 466 LYS cc_start: 0.8302 (mttt) cc_final: 0.7911 (mtpp) REVERT: B 481 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.7199 (ttm170) REVERT: B 510 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7353 (mt-10) REVERT: B 550 ARG cc_start: 0.7515 (mtt180) cc_final: 0.7258 (mtt180) REVERT: B 554 TYR cc_start: 0.8591 (t80) cc_final: 0.8347 (t80) REVERT: E 107 LEU cc_start: 0.8503 (mt) cc_final: 0.8191 (mt) REVERT: E 231 SER cc_start: 0.8528 (p) cc_final: 0.8247 (p) REVERT: E 391 GLN cc_start: 0.7710 (mm-40) cc_final: 0.7407 (mp10) REVERT: E 466 LYS cc_start: 0.8295 (mttt) cc_final: 0.7908 (mtpp) REVERT: E 481 ARG cc_start: 0.7614 (OUTLIER) cc_final: 0.7078 (ttm170) REVERT: E 550 ARG cc_start: 0.7534 (mtt180) cc_final: 0.7299 (mtt180) REVERT: E 554 TYR cc_start: 0.8566 (t80) cc_final: 0.8324 (t80) outliers start: 35 outliers final: 14 residues processed: 367 average time/residue: 1.0797 time to fit residues: 451.4918 Evaluate side-chains 365 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 345 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 141 GLN Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 481 ARG Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 141 GLN Chi-restraints excluded: chain A residue 157 MET Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 402 MET Chi-restraints excluded: chain B residue 481 ARG Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 402 MET Chi-restraints excluded: chain E residue 481 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 37 optimal weight: 0.9980 chunk 44 optimal weight: 0.3980 chunk 160 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 154 optimal weight: 4.9990 chunk 18 optimal weight: 0.4980 chunk 97 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.152731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.125677 restraints weight = 53021.968| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.68 r_work: 0.3213 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.4799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17632 Z= 0.133 Angle : 0.521 5.235 23912 Z= 0.267 Chirality : 0.042 0.140 2636 Planarity : 0.005 0.070 3048 Dihedral : 6.448 39.516 2584 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.64 % Allowed : 17.49 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.68 (0.19), residues: 2092 helix: 1.47 (0.18), residues: 908 sheet: -1.19 (0.26), residues: 336 loop : 0.19 (0.23), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 376 TYR 0.014 0.001 TYR C 42 PHE 0.009 0.001 PHE A 163 TRP 0.007 0.001 TRP B 358 HIS 0.005 0.001 HIS C 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (17628) covalent geometry : angle 0.51600 / 0.26 (23904) SS BOND : bond 0.00483 / 0.23 ( 4) SS BOND : angle 3.80956 / 1.89 ( 8) hydrogen bonds : bond 0.03319 / 2.26 ( 760) hydrogen bonds : angle 4.26674 / 2.96 ( 2196) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 352 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 107 LEU cc_start: 0.8496 (mt) cc_final: 0.8208 (mt) REVERT: C 141 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.7625 (mt0) REVERT: C 231 SER cc_start: 0.8436 (p) cc_final: 0.8161 (p) REVERT: C 240 GLN cc_start: 0.8372 (mt0) cc_final: 0.7738 (mt0) REVERT: C 324 SER cc_start: 0.9055 (m) cc_final: 0.8835 (m) REVERT: C 391 GLN cc_start: 0.7729 (mm-40) cc_final: 0.7463 (mp10) REVERT: C 466 LYS cc_start: 0.8304 (mttt) cc_final: 0.7936 (mtpp) REVERT: C 481 ARG cc_start: 0.7680 (OUTLIER) cc_final: 0.7413 (ttm-80) REVERT: C 550 ARG cc_start: 0.7541 (mtt180) cc_final: 0.7292 (mtt180) REVERT: C 554 TYR cc_start: 0.8633 (t80) cc_final: 0.8343 (t80) REVERT: A 107 LEU cc_start: 0.8529 (mt) cc_final: 0.8255 (mt) REVERT: A 141 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.7598 (mt0) REVERT: A 231 SER cc_start: 0.8446 (p) cc_final: 0.8173 (p) REVERT: A 240 GLN cc_start: 0.8413 (mt0) cc_final: 0.7788 (mt0) REVERT: A 324 SER cc_start: 0.9045 (m) cc_final: 0.8830 (m) REVERT: A 391 GLN cc_start: 0.7793 (mm-40) cc_final: 0.7498 (mp10) REVERT: A 466 LYS cc_start: 0.8286 (mttt) cc_final: 0.7895 (mtmm) REVERT: A 481 ARG cc_start: 0.7689 (OUTLIER) cc_final: 0.7322 (ttm-80) REVERT: A 550 ARG cc_start: 0.7551 (mtt180) cc_final: 0.7222 (mtt180) REVERT: A 554 TYR cc_start: 0.8591 (t80) cc_final: 0.8281 (t80) REVERT: B 107 LEU cc_start: 0.8503 (mt) cc_final: 0.8212 (mt) REVERT: B 157 MET cc_start: 0.8681 (mmt) cc_final: 0.8370 (mmm) REVERT: B 231 SER cc_start: 0.8413 (p) cc_final: 0.8126 (p) REVERT: B 240 GLN cc_start: 0.8348 (mt0) cc_final: 0.7783 (mt0) REVERT: B 391 GLN cc_start: 0.7742 (mm-40) cc_final: 0.7434 (mp10) REVERT: B 466 LYS cc_start: 0.8290 (mttt) cc_final: 0.7893 (mtpp) REVERT: B 481 ARG cc_start: 0.7618 (OUTLIER) cc_final: 0.7293 (ttm-80) REVERT: B 554 TYR cc_start: 0.8587 (t80) cc_final: 0.8293 (t80) REVERT: E 107 LEU cc_start: 0.8522 (mt) cc_final: 0.8259 (mt) REVERT: E 203 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7311 (tp30) REVERT: E 231 SER cc_start: 0.8528 (p) cc_final: 0.8277 (p) REVERT: E 335 LYS cc_start: 0.8764 (mttm) cc_final: 0.8524 (mttt) REVERT: E 391 GLN cc_start: 0.7731 (mm-40) cc_final: 0.7446 (mp10) REVERT: E 466 LYS cc_start: 0.8302 (mttt) cc_final: 0.7918 (mtpp) REVERT: E 510 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7349 (mt-10) REVERT: E 550 ARG cc_start: 0.7509 (mtt180) cc_final: 0.7172 (mtt180) REVERT: E 554 TYR cc_start: 0.8604 (t80) cc_final: 0.8310 (t80) outliers start: 31 outliers final: 12 residues processed: 370 average time/residue: 1.1048 time to fit residues: 462.9574 Evaluate side-chains 360 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 341 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 141 GLN Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 481 ARG Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 141 GLN Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain A residue 481 ARG Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 402 MET Chi-restraints excluded: chain B residue 481 ARG Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 402 MET Chi-restraints excluded: chain E residue 510 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 126 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 197 optimal weight: 0.5980 chunk 159 optimal weight: 1.9990 chunk 125 optimal weight: 0.5980 chunk 180 optimal weight: 0.0270 chunk 20 optimal weight: 0.9990 chunk 174 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 overall best weight: 0.6240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 329 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.152477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.125004 restraints weight = 52591.080| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.70 r_work: 0.3141 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.4925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 17632 Z= 0.127 Angle : 0.578 22.100 23912 Z= 0.295 Chirality : 0.043 0.247 2636 Planarity : 0.005 0.069 3048 Dihedral : 6.341 37.081 2584 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.74 % Allowed : 18.02 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.19), residues: 2092 helix: 1.56 (0.18), residues: 908 sheet: -1.25 (0.26), residues: 336 loop : 0.31 (0.23), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 81 TYR 0.014 0.001 TYR C 42 PHE 0.008 0.001 PHE B 163 TRP 0.007 0.001 TRP C 358 HIS 0.004 0.001 HIS C 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (17628) covalent geometry : angle 0.52339 / 0.27 (23904) SS BOND : bond 0.00147 / 0.07 ( 4) SS BOND : angle 13.40630 / 6.60 ( 8) hydrogen bonds : bond 0.03233 / 2.20 ( 760) hydrogen bonds : angle 4.26419 / 2.96 ( 2196) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 348 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 107 LEU cc_start: 0.8484 (mt) cc_final: 0.8204 (mt) REVERT: C 141 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.7630 (mt0) REVERT: C 142 VAL cc_start: 0.8839 (p) cc_final: 0.8561 (t) REVERT: C 220 ASN cc_start: 0.8583 (m110) cc_final: 0.8347 (m-40) REVERT: C 231 SER cc_start: 0.8425 (p) cc_final: 0.8146 (p) REVERT: C 240 GLN cc_start: 0.8377 (mt0) cc_final: 0.7752 (mt0) REVERT: C 324 SER cc_start: 0.9047 (m) cc_final: 0.8830 (m) REVERT: C 391 GLN cc_start: 0.7731 (mm-40) cc_final: 0.7450 (mp10) REVERT: C 466 LYS cc_start: 0.8287 (mttt) cc_final: 0.7908 (mtpp) REVERT: C 481 ARG cc_start: 0.7670 (OUTLIER) cc_final: 0.7295 (ttm-80) REVERT: C 509 MET cc_start: 0.8271 (mmp) cc_final: 0.8046 (mmm) REVERT: C 550 ARG cc_start: 0.7550 (mtt180) cc_final: 0.7190 (mtt180) REVERT: C 554 TYR cc_start: 0.8591 (t80) cc_final: 0.8313 (t80) REVERT: A 107 LEU cc_start: 0.8496 (mt) cc_final: 0.8225 (mt) REVERT: A 141 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.7621 (mt0) REVERT: A 220 ASN cc_start: 0.8576 (m110) cc_final: 0.8338 (m-40) REVERT: A 231 SER cc_start: 0.8436 (p) cc_final: 0.8165 (p) REVERT: A 240 GLN cc_start: 0.8397 (mt0) cc_final: 0.7753 (mt0) REVERT: A 324 SER cc_start: 0.9045 (m) cc_final: 0.8830 (m) REVERT: A 391 GLN cc_start: 0.7754 (mm-40) cc_final: 0.7467 (mp10) REVERT: A 466 LYS cc_start: 0.8279 (mttt) cc_final: 0.7957 (mtmm) REVERT: A 481 ARG cc_start: 0.7663 (OUTLIER) cc_final: 0.7319 (ttm-80) REVERT: A 550 ARG cc_start: 0.7531 (mtt180) cc_final: 0.7201 (mtt180) REVERT: A 554 TYR cc_start: 0.8568 (t80) cc_final: 0.8256 (t80) REVERT: B 107 LEU cc_start: 0.8481 (mt) cc_final: 0.8201 (mt) REVERT: B 142 VAL cc_start: 0.8831 (p) cc_final: 0.8563 (t) REVERT: B 157 MET cc_start: 0.8695 (mmt) cc_final: 0.8388 (mmm) REVERT: B 231 SER cc_start: 0.8429 (p) cc_final: 0.8141 (p) REVERT: B 240 GLN cc_start: 0.8306 (mt0) cc_final: 0.7702 (mt0) REVERT: B 391 GLN cc_start: 0.7725 (mm-40) cc_final: 0.7416 (mp10) REVERT: B 466 LYS cc_start: 0.8279 (mttt) cc_final: 0.7887 (mtpp) REVERT: B 481 ARG cc_start: 0.7656 (OUTLIER) cc_final: 0.7342 (ttm-80) REVERT: B 554 TYR cc_start: 0.8565 (t80) cc_final: 0.8277 (t80) REVERT: E 107 LEU cc_start: 0.8503 (mt) cc_final: 0.8221 (mt) REVERT: E 142 VAL cc_start: 0.8845 (p) cc_final: 0.8596 (t) REVERT: E 203 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7298 (tp30) REVERT: E 231 SER cc_start: 0.8521 (p) cc_final: 0.8251 (p) REVERT: E 240 GLN cc_start: 0.8271 (mt0) cc_final: 0.7708 (mt0) REVERT: E 265 TYR cc_start: 0.8775 (t80) cc_final: 0.8351 (t80) REVERT: E 335 LYS cc_start: 0.8750 (mttm) cc_final: 0.8502 (mttt) REVERT: E 391 GLN cc_start: 0.7747 (mm-40) cc_final: 0.7476 (mp10) REVERT: E 466 LYS cc_start: 0.8297 (mttt) cc_final: 0.7916 (mtpp) REVERT: E 481 ARG cc_start: 0.7680 (OUTLIER) cc_final: 0.6714 (ttm-80) REVERT: E 510 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7399 (mt-10) REVERT: E 550 ARG cc_start: 0.7559 (mtt180) cc_final: 0.7313 (mtt180) REVERT: E 554 TYR cc_start: 0.8581 (t80) cc_final: 0.8297 (t80) outliers start: 33 outliers final: 12 residues processed: 367 average time/residue: 1.0785 time to fit residues: 450.9196 Evaluate side-chains 363 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 343 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 141 GLN Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 481 ARG Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 141 GLN Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain A residue 481 ARG Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 402 MET Chi-restraints excluded: chain B residue 481 ARG Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 402 MET Chi-restraints excluded: chain E residue 481 ARG Chi-restraints excluded: chain E residue 510 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 191 optimal weight: 1.9990 chunk 68 optimal weight: 0.0570 chunk 170 optimal weight: 0.5980 chunk 119 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 187 optimal weight: 2.9990 chunk 70 optimal weight: 0.0170 chunk 132 optimal weight: 0.7980 chunk 76 optimal weight: 0.0970 chunk 205 optimal weight: 3.9990 chunk 141 optimal weight: 0.9980 overall best weight: 0.3134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.154226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.126740 restraints weight = 52307.339| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.70 r_work: 0.3165 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.5027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 17632 Z= 0.099 Angle : 0.533 16.643 23912 Z= 0.272 Chirality : 0.042 0.201 2636 Planarity : 0.005 0.074 3048 Dihedral : 5.964 36.395 2584 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.95 % Allowed : 18.66 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.19), residues: 2092 helix: 1.73 (0.18), residues: 920 sheet: -1.16 (0.26), residues: 328 loop : 0.52 (0.24), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 81 TYR 0.014 0.001 TYR C 42 PHE 0.007 0.001 PHE E 50 TRP 0.009 0.001 TRP C 358 HIS 0.002 0.001 HIS C 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (17628) covalent geometry : angle 0.50114 / 0.26 (23904) SS BOND : bond 0.00746 / 0.36 ( 4) SS BOND : angle 9.95028 / 4.74 ( 8) hydrogen bonds : bond 0.03008 / 2.04 ( 760) hydrogen bonds : angle 4.15236 / 2.88 ( 2196) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 353 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 107 LEU cc_start: 0.8391 (mt) cc_final: 0.8135 (mt) REVERT: C 141 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.7639 (mt0) REVERT: C 142 VAL cc_start: 0.8832 (p) cc_final: 0.8577 (t) REVERT: C 220 ASN cc_start: 0.8477 (m110) cc_final: 0.8246 (m-40) REVERT: C 231 SER cc_start: 0.8405 (p) cc_final: 0.8130 (p) REVERT: C 240 GLN cc_start: 0.8225 (mt0) cc_final: 0.7627 (mt0) REVERT: C 324 SER cc_start: 0.9012 (m) cc_final: 0.8807 (m) REVERT: C 391 GLN cc_start: 0.7728 (mm-40) cc_final: 0.7468 (mp10) REVERT: C 466 LYS cc_start: 0.8234 (mttt) cc_final: 0.7906 (mtmm) REVERT: C 481 ARG cc_start: 0.7659 (OUTLIER) cc_final: 0.6797 (ttm-80) REVERT: C 550 ARG cc_start: 0.7538 (mtt180) cc_final: 0.7185 (mtt180) REVERT: C 554 TYR cc_start: 0.8587 (t80) cc_final: 0.8329 (t80) REVERT: A 107 LEU cc_start: 0.8417 (mt) cc_final: 0.8160 (mt) REVERT: A 142 VAL cc_start: 0.8845 (p) cc_final: 0.8592 (t) REVERT: A 220 ASN cc_start: 0.8453 (m110) cc_final: 0.8200 (m-40) REVERT: A 231 SER cc_start: 0.8432 (p) cc_final: 0.8156 (p) REVERT: A 240 GLN cc_start: 0.8291 (mt0) cc_final: 0.7732 (mt0) REVERT: A 391 GLN cc_start: 0.7739 (mm-40) cc_final: 0.7479 (mp10) REVERT: A 466 LYS cc_start: 0.8240 (mttt) cc_final: 0.7921 (mtmm) REVERT: A 481 ARG cc_start: 0.7674 (OUTLIER) cc_final: 0.7310 (ttm-80) REVERT: A 550 ARG cc_start: 0.7545 (mtt180) cc_final: 0.7216 (mtt180) REVERT: A 554 TYR cc_start: 0.8571 (t80) cc_final: 0.8274 (t80) REVERT: B 142 VAL cc_start: 0.8807 (p) cc_final: 0.8579 (t) REVERT: B 157 MET cc_start: 0.8667 (mmt) cc_final: 0.8365 (mmm) REVERT: B 231 SER cc_start: 0.8426 (p) cc_final: 0.8137 (p) REVERT: B 240 GLN cc_start: 0.8269 (mt0) cc_final: 0.7703 (mt0) REVERT: B 391 GLN cc_start: 0.7710 (mm-40) cc_final: 0.7412 (mp10) REVERT: B 466 LYS cc_start: 0.8250 (mttt) cc_final: 0.7872 (mtpp) REVERT: B 481 ARG cc_start: 0.7638 (OUTLIER) cc_final: 0.6589 (ttm-80) REVERT: B 554 TYR cc_start: 0.8567 (t80) cc_final: 0.8298 (t80) REVERT: E 107 LEU cc_start: 0.8416 (mt) cc_final: 0.8157 (mt) REVERT: E 142 VAL cc_start: 0.8804 (p) cc_final: 0.8588 (t) REVERT: E 203 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7266 (tp30) REVERT: E 231 SER cc_start: 0.8479 (p) cc_final: 0.8196 (p) REVERT: E 240 GLN cc_start: 0.8247 (mt0) cc_final: 0.7686 (mt0) REVERT: E 335 LYS cc_start: 0.8692 (mttm) cc_final: 0.8447 (mttt) REVERT: E 391 GLN cc_start: 0.7683 (mm-40) cc_final: 0.7440 (mp10) REVERT: E 466 LYS cc_start: 0.8266 (mttt) cc_final: 0.7949 (mtmm) REVERT: E 481 ARG cc_start: 0.7645 (OUTLIER) cc_final: 0.6872 (ttm-80) REVERT: E 509 MET cc_start: 0.8217 (mmp) cc_final: 0.7993 (mmm) REVERT: E 550 ARG cc_start: 0.7545 (mtt180) cc_final: 0.7301 (mtt180) REVERT: E 554 TYR cc_start: 0.8583 (t80) cc_final: 0.8310 (t80) outliers start: 18 outliers final: 6 residues processed: 362 average time/residue: 1.0909 time to fit residues: 451.9127 Evaluate side-chains 355 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 343 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 141 GLN Chi-restraints excluded: chain C residue 481 ARG Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 481 ARG Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 481 ARG Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 481 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 3 optimal weight: 0.9990 chunk 119 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 194 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 131 optimal weight: 0.5980 chunk 149 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 GLN B 165 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.151733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.123985 restraints weight = 52816.681| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.72 r_work: 0.3148 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.5064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17632 Z= 0.144 Angle : 0.533 9.027 23912 Z= 0.272 Chirality : 0.043 0.191 2636 Planarity : 0.005 0.074 3048 Dihedral : 6.425 36.840 2584 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.90 % Allowed : 18.55 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.90 (0.19), residues: 2092 helix: 1.63 (0.18), residues: 916 sheet: -1.22 (0.26), residues: 336 loop : 0.42 (0.24), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 81 TYR 0.013 0.001 TYR C 42 PHE 0.010 0.001 PHE C 163 TRP 0.007 0.001 TRP A 488 HIS 0.006 0.001 HIS C 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 (17628) covalent geometry : angle 0.52202 / 0.27 (23904) SS BOND : bond 0.00781 / 0.37 ( 4) SS BOND : angle 5.91274 / 3.03 ( 8) hydrogen bonds : bond 0.03251 / 2.20 ( 760) hydrogen bonds : angle 4.23700 / 2.94 ( 2196) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 342 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 107 LEU cc_start: 0.8505 (mt) cc_final: 0.8258 (mt) REVERT: C 141 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.7664 (mt0) REVERT: C 142 VAL cc_start: 0.8859 (p) cc_final: 0.8593 (t) REVERT: C 220 ASN cc_start: 0.8564 (m110) cc_final: 0.8362 (m-40) REVERT: C 231 SER cc_start: 0.8445 (p) cc_final: 0.8172 (p) REVERT: C 240 GLN cc_start: 0.8299 (mt0) cc_final: 0.7748 (mt0) REVERT: C 324 SER cc_start: 0.9027 (m) cc_final: 0.8814 (m) REVERT: C 391 GLN cc_start: 0.7722 (mm-40) cc_final: 0.7503 (mp10) REVERT: C 466 LYS cc_start: 0.8266 (mttt) cc_final: 0.7928 (mtmm) REVERT: C 481 ARG cc_start: 0.7715 (OUTLIER) cc_final: 0.7302 (ttm-80) REVERT: C 550 ARG cc_start: 0.7596 (mtt180) cc_final: 0.7327 (mtt180) REVERT: C 554 TYR cc_start: 0.8577 (t80) cc_final: 0.8262 (t80) REVERT: A 107 LEU cc_start: 0.8529 (mt) cc_final: 0.8267 (mt) REVERT: A 142 VAL cc_start: 0.8863 (p) cc_final: 0.8601 (t) REVERT: A 220 ASN cc_start: 0.8386 (m110) cc_final: 0.8170 (m-40) REVERT: A 231 SER cc_start: 0.8478 (p) cc_final: 0.8199 (p) REVERT: A 240 GLN cc_start: 0.8311 (mt0) cc_final: 0.7639 (mt0) REVERT: A 391 GLN cc_start: 0.7742 (mm-40) cc_final: 0.7515 (mp10) REVERT: A 466 LYS cc_start: 0.8256 (mttt) cc_final: 0.7929 (mtmm) REVERT: A 481 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.7332 (ttm-80) REVERT: A 550 ARG cc_start: 0.7590 (mtt180) cc_final: 0.7275 (mtt180) REVERT: A 554 TYR cc_start: 0.8595 (t80) cc_final: 0.8326 (t80) REVERT: B 107 LEU cc_start: 0.8502 (mt) cc_final: 0.8259 (mt) REVERT: B 142 VAL cc_start: 0.8814 (p) cc_final: 0.8575 (t) REVERT: B 157 MET cc_start: 0.8710 (mmt) cc_final: 0.8402 (mmm) REVERT: B 220 ASN cc_start: 0.8535 (m110) cc_final: 0.8316 (m-40) REVERT: B 231 SER cc_start: 0.8470 (p) cc_final: 0.8182 (p) REVERT: B 240 GLN cc_start: 0.8315 (mt0) cc_final: 0.7752 (mt0) REVERT: B 391 GLN cc_start: 0.7739 (mm-40) cc_final: 0.7457 (mp10) REVERT: B 466 LYS cc_start: 0.8261 (mttt) cc_final: 0.7877 (mtpp) REVERT: B 481 ARG cc_start: 0.7684 (OUTLIER) cc_final: 0.6727 (ttm-80) REVERT: B 554 TYR cc_start: 0.8575 (t80) cc_final: 0.8302 (t80) REVERT: E 107 LEU cc_start: 0.8522 (mt) cc_final: 0.8272 (mt) REVERT: E 142 VAL cc_start: 0.8821 (p) cc_final: 0.8592 (t) REVERT: E 203 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7292 (tp30) REVERT: E 220 ASN cc_start: 0.8574 (m110) cc_final: 0.8361 (m-40) REVERT: E 231 SER cc_start: 0.8478 (p) cc_final: 0.8186 (p) REVERT: E 240 GLN cc_start: 0.8386 (mt0) cc_final: 0.7789 (mt0) REVERT: E 265 TYR cc_start: 0.8785 (t80) cc_final: 0.8302 (t80) REVERT: E 335 LYS cc_start: 0.8775 (mttm) cc_final: 0.8514 (mttt) REVERT: E 391 GLN cc_start: 0.7720 (mm-40) cc_final: 0.7498 (mp10) REVERT: E 466 LYS cc_start: 0.8285 (mttt) cc_final: 0.7962 (mtmm) REVERT: E 481 ARG cc_start: 0.7738 (OUTLIER) cc_final: 0.6920 (ttm-80) REVERT: E 509 MET cc_start: 0.8286 (mmp) cc_final: 0.8052 (mmm) REVERT: E 550 ARG cc_start: 0.7591 (mtt180) cc_final: 0.7347 (mtt180) REVERT: E 554 TYR cc_start: 0.8611 (t80) cc_final: 0.8321 (t80) outliers start: 17 outliers final: 9 residues processed: 349 average time/residue: 1.1013 time to fit residues: 437.2952 Evaluate side-chains 353 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 338 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 141 GLN Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain C residue 481 ARG Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain A residue 481 ARG Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 481 ARG Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 481 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 193 optimal weight: 1.9990 chunk 154 optimal weight: 0.7980 chunk 104 optimal weight: 0.5980 chunk 192 optimal weight: 0.7980 chunk 140 optimal weight: 1.9990 chunk 138 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 186 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 359 GLN E 359 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.150779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.123208 restraints weight = 52919.295| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.71 r_work: 0.3115 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.5133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 17632 Z= 0.160 Angle : 0.539 7.260 23912 Z= 0.276 Chirality : 0.043 0.196 2636 Planarity : 0.006 0.076 3048 Dihedral : 6.477 37.684 2584 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.16 % Allowed : 18.76 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.83 (0.19), residues: 2092 helix: 1.57 (0.17), residues: 912 sheet: -1.23 (0.26), residues: 336 loop : 0.37 (0.23), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 81 TYR 0.014 0.001 TYR C 525 PHE 0.009 0.001 PHE E 163 TRP 0.008 0.001 TRP E 488 HIS 0.006 0.001 HIS C 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (17628) covalent geometry : angle 0.53209 / 0.27 (23904) SS BOND : bond 0.00632 / 0.30 ( 4) SS BOND : angle 4.88456 / 2.53 ( 8) hydrogen bonds : bond 0.03340 / 2.26 ( 760) hydrogen bonds : angle 4.25635 / 2.95 ( 2196) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11377.74 seconds wall clock time: 192 minutes 50.35 seconds (11570.35 seconds total)