Starting phenix.real_space_refine on Mon Jul 6 10:42:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7miv_23866/07_2026/7miv_23866_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7miv_23866/07_2026/7miv_23866.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7miv_23866/07_2026/7miv_23866_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7miv_23866/07_2026/7miv_23866_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7miv_23866/07_2026/7miv_23866.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7miv_23866/07_2026/7miv_23866.map" } resolution = 2.8 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: 7 Type Number sf(0) Gaussians P 12 5.49 5 Mg 4 5.21 5 S 100 5.16 5 C 11108 2.51 5 N 2960 2.21 5 O 3224 1.98 5 H 17412 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 112 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 34820 Number of models: 1 Model: "" Number of chains: 12 Chain: "D" Number of atoms: 8622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 8622 Classifications: {'peptide': 542} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 513} Chain breaks: 2 Chain: "C" Number of atoms: 8622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 8622 Classifications: {'peptide': 542} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 513} Chain breaks: 2 Chain: "H" Number of atoms: 8622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 8622 Classifications: {'peptide': 542} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 513} Chain breaks: 2 Chain: "G" Number of atoms: 8622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 8622 Classifications: {'peptide': 542} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 513} Chain breaks: 2 Chain: "D" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Classifications: {'peptide': 1} Modifications used: {'COO': 1, 'NH3': 1} Chain: "D" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'UTP': 1, 'ZG4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Classifications: {'peptide': 1} Modifications used: {'COO': 1, 'NH3': 1} Chain: "C" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'UTP': 1, 'ZG4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Classifications: {'peptide': 1} Modifications used: {'COO': 1, 'NH3': 1} Chain: "H" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'UTP': 1, 'ZG4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Classifications: {'peptide': 1} Modifications used: {'COO': 1, 'NH3': 1} Chain: "G" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'UTP': 1, 'ZG4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 6.12, per 1000 atoms: 0.18 Number of scatterers: 34820 At special positions: 0 Unit cell: (124.95, 133.35, 89.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 100 16.00 P 12 15.00 Mg 4 11.99 O 3224 8.00 N 2960 7.00 C 11108 6.00 H 17412 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.17 Conformation dependent library (CDL) restraints added in 989.3 milliseconds 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4016 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 16 sheets defined 50.5% alpha, 16.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'D' and resid 15 through 30 Processing helix chain 'D' and resid 46 through 50 removed outlier: 4.224A pdb=" N THR D 49 " --> pdb=" O ASP D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 56 removed outlier: 4.133A pdb=" N HIS D 55 " --> pdb=" O SER D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 78 removed outlier: 4.014A pdb=" N GLY D 72 " --> pdb=" O ASP D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 85 No H-bonds generated for 'chain 'D' and resid 83 through 85' Processing helix chain 'D' and resid 90 through 104 Processing helix chain 'D' and resid 112 through 130 removed outlier: 7.115A pdb=" N THR D 118 " --> pdb=" O VAL D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 155 No H-bonds generated for 'chain 'D' and resid 153 through 155' Processing helix chain 'D' and resid 156 through 167 Processing helix chain 'D' and resid 194 through 207 Processing helix chain 'D' and resid 223 through 235 Processing helix chain 'D' and resid 237 through 239 No H-bonds generated for 'chain 'D' and resid 237 through 239' Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 252 through 261 Processing helix chain 'D' and resid 261 through 271 Processing helix chain 'D' and resid 282 through 295 Processing helix chain 'D' and resid 310 through 313 Processing helix chain 'D' and resid 314 through 328 Processing helix chain 'D' and resid 338 through 342 Processing helix chain 'D' and resid 343 through 350 removed outlier: 3.687A pdb=" N LYS D 347 " --> pdb=" O GLU D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 363 removed outlier: 3.674A pdb=" N PHE D 354 " --> pdb=" O ASP D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 391 Processing helix chain 'D' and resid 399 through 414 Processing helix chain 'D' and resid 462 through 468 removed outlier: 3.761A pdb=" N LYS D 466 " --> pdb=" O SER D 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 492 removed outlier: 3.569A pdb=" N ILE D 489 " --> pdb=" O PRO D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 526 through 531 removed outlier: 3.765A pdb=" N PHE D 529 " --> pdb=" O HIS D 526 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 547 Processing helix chain 'D' and resid 550 through 557 Processing helix chain 'C' and resid 15 through 30 Processing helix chain 'C' and resid 46 through 50 removed outlier: 4.223A pdb=" N THR C 49 " --> pdb=" O ASP C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 56 removed outlier: 4.133A pdb=" N HIS C 55 " --> pdb=" O SER C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 78 removed outlier: 4.015A 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 104 Processing helix chain 'C' and resid 112 through 130 removed outlier: 7.116A pdb=" N THR C 118 " --> pdb=" O VAL C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 155 No H-bonds generated for 'chain 'C' and resid 153 through 155' Processing helix chain 'C' and resid 156 through 167 Processing helix chain 'C' and resid 194 through 207 Processing helix chain 'C' and resid 223 through 235 Processing helix chain 'C' and resid 237 through 239 No H-bonds generated for 'chain 'C' and resid 237 through 239' Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 252 through 261 Processing helix chain 'C' and resid 261 through 271 Processing helix chain 'C' and resid 282 through 295 Processing helix chain 'C' and resid 310 through 313 Processing helix chain 'C' and resid 314 through 328 Processing helix chain 'C' and resid 338 through 342 Processing helix chain 'C' and resid 343 through 350 removed outlier: 3.688A pdb=" N LYS C 347 " --> pdb=" O GLU C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 363 removed outlier: 3.673A pdb=" N PHE C 354 " --> pdb=" O ASP C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 391 Processing helix chain 'C' and resid 399 through 414 Processing helix chain 'C' and resid 462 through 468 removed outlier: 3.761A pdb=" N LYS C 466 " --> pdb=" O SER C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 492 removed outlier: 3.570A pdb=" N ILE C 489 " --> pdb=" O PRO C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 531 removed outlier: 3.764A pdb=" N PHE C 529 " --> pdb=" O HIS C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 547 Processing helix chain 'C' and resid 550 through 557 Processing helix chain 'H' and resid 15 through 30 Processing helix chain 'H' and resid 46 through 50 removed outlier: 4.224A pdb=" N THR H 49 " --> pdb=" O ASP H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 56 removed outlier: 4.134A pdb=" N HIS H 55 " --> pdb=" O SER H 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 78 removed outlier: 4.014A pdb=" N GLY H 72 " --> pdb=" O ASP H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 85 No H-bonds generated for 'chain 'H' and resid 83 through 85' Processing helix chain 'H' and resid 90 through 104 Processing helix chain 'H' and resid 112 through 130 removed outlier: 7.115A pdb=" N THR H 118 " --> pdb=" O VAL H 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 153 through 155 No H-bonds generated for 'chain 'H' and resid 153 through 155' Processing helix chain 'H' and resid 156 through 167 Processing helix chain 'H' and resid 194 through 207 Processing helix chain 'H' and resid 223 through 235 Processing helix chain 'H' and resid 237 through 239 No H-bonds generated for 'chain 'H' and resid 237 through 239' Processing helix chain 'H' and resid 249 through 251 No H-bonds generated for 'chain 'H' and resid 249 through 251' Processing helix chain 'H' and resid 252 through 261 Processing helix chain 'H' and resid 261 through 271 Processing helix chain 'H' and resid 282 through 295 Processing helix chain 'H' and resid 310 through 313 Processing helix chain 'H' and resid 314 through 328 Processing helix chain 'H' and resid 338 through 342 Processing helix chain 'H' and resid 343 through 350 removed outlier: 3.687A pdb=" N LYS H 347 " --> pdb=" O GLU H 343 " (cutoff:3.500A) Processing helix chain 'H' and resid 350 through 363 removed outlier: 3.674A pdb=" N PHE H 354 " --> pdb=" O ASP H 350 " (cutoff:3.500A) Processing helix chain 'H' and resid 377 through 391 Processing helix chain 'H' and resid 399 through 414 Processing helix chain 'H' and resid 462 through 468 removed outlier: 3.761A pdb=" N LYS H 466 " --> pdb=" O SER H 462 " (cutoff:3.500A) Processing helix chain 'H' and resid 486 through 492 removed outlier: 3.569A pdb=" N ILE H 489 " --> pdb=" O PRO H 486 " (cutoff:3.500A) Processing helix chain 'H' and resid 526 through 531 removed outlier: 3.765A pdb=" N PHE H 529 " --> pdb=" O HIS H 526 " (cutoff:3.500A) Processing helix chain 'H' and resid 537 through 547 Processing helix chain 'H' and resid 550 through 557 Processing helix chain 'G' and resid 15 through 30 Processing helix chain 'G' and resid 46 through 50 removed outlier: 4.224A pdb=" N THR G 49 " --> pdb=" O ASP G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 51 through 56 removed outlier: 4.133A pdb=" N HIS G 55 " --> pdb=" O SER G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 78 removed outlier: 4.015A pdb=" N GLY G 72 " --> pdb=" O ASP G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 85 No H-bonds generated for 'chain 'G' and resid 83 through 85' Processing helix chain 'G' and resid 90 through 104 Processing helix chain 'G' and resid 112 through 130 removed outlier: 7.115A pdb=" N THR G 118 " --> pdb=" O VAL G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 153 through 155 No H-bonds generated for 'chain 'G' and resid 153 through 155' Processing helix chain 'G' and resid 156 through 167 Processing helix chain 'G' and resid 194 through 207 Processing helix chain 'G' and resid 223 through 235 Processing helix chain 'G' and resid 237 through 239 No H-bonds generated for 'chain 'G' and resid 237 through 239' Processing helix chain 'G' and resid 249 through 251 No H-bonds generated for 'chain 'G' and resid 249 through 251' Processing helix chain 'G' and resid 252 through 261 Processing helix chain 'G' and resid 261 through 271 Processing helix chain 'G' and resid 282 through 295 Processing helix chain 'G' and resid 310 through 313 Processing helix chain 'G' and resid 314 through 328 Processing helix chain 'G' and resid 338 through 342 Processing helix chain 'G' and resid 343 through 350 removed outlier: 3.688A pdb=" N LYS G 347 " --> pdb=" O GLU G 343 " (cutoff:3.500A) Processing helix chain 'G' and resid 350 through 363 removed outlier: 3.673A pdb=" N PHE G 354 " --> pdb=" O ASP G 350 " (cutoff:3.500A) Processing helix chain 'G' and resid 377 through 391 Processing helix chain 'G' and resid 399 through 414 Processing helix chain 'G' and resid 462 through 468 removed outlier: 3.761A pdb=" N LYS G 466 " --> pdb=" O SER G 462 " (cutoff:3.500A) Processing helix chain 'G' and resid 486 through 492 removed outlier: 3.570A pdb=" N ILE G 489 " --> pdb=" O PRO G 486 " (cutoff:3.500A) Processing helix chain 'G' and resid 526 through 531 removed outlier: 3.764A pdb=" N PHE G 529 " --> pdb=" O HIS G 526 " (cutoff:3.500A) Processing helix chain 'G' and resid 537 through 547 Processing helix chain 'G' and resid 550 through 557 Processing sheet with id=AA1, first strand: chain 'D' and resid 87 through 89 removed outlier: 6.599A pdb=" N LYS D 2 " --> pdb=" O CYS D 143 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ILE D 145 " --> pdb=" O LYS D 2 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ILE D 4 " --> pdb=" O ILE D 145 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N LEU D 147 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL D 6 " --> pdb=" O LEU D 147 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N TYR D 3 " --> pdb=" O TYR D 176 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ILE D 178 " --> pdb=" O TYR D 3 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N LEU D 5 " --> pdb=" O ILE D 178 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N VAL D 180 " --> pdb=" O LEU D 5 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N THR D 7 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N LEU D 182 " --> pdb=" O THR D 7 " (cutoff:3.500A) removed outlier: 8.924A pdb=" N LEU D 213 " --> pdb=" O PHE D 175 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ASN D 177 " --> pdb=" O LEU D 213 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N VAL D 215 " --> pdb=" O ASN D 177 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N HIS D 179 " --> pdb=" O VAL D 215 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N ARG D 217 " --> pdb=" O HIS D 179 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N SER D 181 " --> pdb=" O ARG D 217 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 59 through 60 Processing sheet with id=AA3, first strand: chain 'D' and resid 330 through 337 removed outlier: 6.659A pdb=" N LYS D 297 " --> pdb=" O LYS D 331 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ASN D 333 " --> pdb=" O LYS D 297 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N CYS D 299 " --> pdb=" O ASN D 333 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N MET D 335 " --> pdb=" O CYS D 299 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE D 301 " --> pdb=" O MET D 335 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ILE D 337 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N LEU D 303 " --> pdb=" O ILE D 337 " (cutoff:3.500A) removed outlier: 9.093A pdb=" N GLY D 366 " --> pdb=" O ILE D 298 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N SER D 300 " --> pdb=" O GLY D 366 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N LEU D 368 " --> pdb=" O SER D 300 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ALA D 302 " --> pdb=" O LEU D 368 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N PHE D 520 " --> pdb=" O LEU D 514 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N MET D 509 " --> pdb=" O GLU D 502 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N GLU D 502 " --> pdb=" O MET D 509 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE D 511 " --> pdb=" O VAL D 500 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 420 through 421 removed outlier: 7.372A pdb=" N ASN D 420 " --> pdb=" O LEU D 432 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ILE D 434 " --> pdb=" O ASN D 420 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 87 through 89 removed outlier: 6.600A pdb=" N LYS C 2 " --> pdb=" O CYS C 143 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ILE C 145 " --> pdb=" O LYS C 2 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ILE C 4 " --> pdb=" O ILE C 145 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N LEU C 147 " --> pdb=" O ILE C 4 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL C 6 " --> pdb=" O LEU C 147 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TYR C 3 " --> pdb=" O TYR C 176 " (cutoff:3.500A) removed outlier: 7.764A 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: 7.322A pdb=" N VAL C 180 " --> pdb=" O LEU C 5 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N THR C 7 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N LEU C 182 " --> pdb=" O THR C 7 " (cutoff:3.500A) removed outlier: 8.924A pdb=" N LEU C 213 " --> pdb=" O PHE C 175 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ASN C 177 " --> pdb=" O LEU C 213 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N VAL C 215 " --> pdb=" O ASN C 177 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N HIS C 179 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ARG C 217 " --> pdb=" O HIS C 179 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N SER C 181 " --> pdb=" O ARG C 217 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 59 through 60 Processing sheet with id=AA7, first strand: chain 'C' and resid 330 through 337 removed outlier: 6.659A pdb=" N LYS C 297 " --> pdb=" O LYS C 331 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ASN C 333 " --> pdb=" O LYS C 297 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N CYS C 299 " --> pdb=" O ASN C 333 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N MET C 335 " --> pdb=" O CYS C 299 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE C 301 " --> pdb=" O MET C 335 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ILE C 337 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N LEU C 303 " --> pdb=" O ILE C 337 " (cutoff:3.500A) removed outlier: 9.094A pdb=" N GLY C 366 " --> pdb=" O ILE C 298 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N SER C 300 " --> pdb=" O GLY C 366 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N LEU C 368 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ALA C 302 " --> pdb=" O LEU C 368 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N PHE C 520 " --> pdb=" O LEU C 514 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N MET C 509 " --> pdb=" O GLU C 502 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N GLU C 502 " --> pdb=" O MET C 509 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE C 511 " --> pdb=" O VAL C 500 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 420 through 421 removed outlier: 7.371A pdb=" N ASN C 420 " --> pdb=" O LEU C 432 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ILE C 434 " --> pdb=" O ASN C 420 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 87 through 89 removed outlier: 6.599A pdb=" N LYS H 2 " --> pdb=" O CYS H 143 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ILE H 145 " --> pdb=" O LYS H 2 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ILE H 4 " --> pdb=" O ILE H 145 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N LEU H 147 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL H 6 " --> pdb=" O LEU H 147 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N TYR H 3 " --> pdb=" O TYR H 176 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ILE H 178 " --> pdb=" O TYR H 3 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N LEU H 5 " --> pdb=" O ILE H 178 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N VAL H 180 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N THR H 7 " --> pdb=" O VAL H 180 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N LEU H 182 " --> pdb=" O THR H 7 " (cutoff:3.500A) removed outlier: 8.925A pdb=" N LEU H 213 " --> pdb=" O PHE H 175 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ASN H 177 " --> pdb=" O LEU H 213 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N VAL H 215 " --> pdb=" O ASN H 177 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N HIS H 179 " --> pdb=" O VAL H 215 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N ARG H 217 " --> pdb=" O HIS H 179 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N SER H 181 " --> pdb=" O ARG H 217 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 59 through 60 Processing sheet with id=AB2, first strand: chain 'H' and resid 330 through 337 removed outlier: 6.659A pdb=" N LYS H 297 " --> pdb=" O LYS H 331 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ASN H 333 " --> pdb=" O LYS H 297 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N CYS H 299 " --> pdb=" O ASN H 333 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N MET H 335 " --> pdb=" O CYS H 299 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE H 301 " --> pdb=" O MET H 335 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ILE H 337 " --> pdb=" O ILE H 301 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N LEU H 303 " --> pdb=" O ILE H 337 " (cutoff:3.500A) removed outlier: 9.094A pdb=" N GLY H 366 " --> pdb=" O ILE H 298 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N SER H 300 " --> pdb=" O GLY H 366 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N LEU H 368 " --> pdb=" O SER H 300 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ALA H 302 " --> pdb=" O LEU H 368 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N PHE H 520 " --> pdb=" O LEU H 514 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N MET H 509 " --> pdb=" O GLU H 502 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N GLU H 502 " --> pdb=" O MET H 509 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE H 511 " --> pdb=" O VAL H 500 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 420 through 421 removed outlier: 7.372A pdb=" N ASN H 420 " --> pdb=" O LEU H 432 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ILE H 434 " --> pdb=" O ASN H 420 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 87 through 89 removed outlier: 6.601A pdb=" N LYS G 2 " --> pdb=" O CYS G 143 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ILE G 145 " --> pdb=" O LYS G 2 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ILE G 4 " --> pdb=" O ILE G 145 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N LEU G 147 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL G 6 " --> pdb=" O LEU G 147 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TYR G 3 " --> pdb=" O TYR G 176 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ILE G 178 " --> pdb=" O TYR G 3 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LEU G 5 " --> pdb=" O ILE G 178 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL G 180 " --> pdb=" O LEU G 5 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N THR G 7 " --> pdb=" O VAL G 180 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N LEU G 182 " --> pdb=" O THR G 7 " (cutoff:3.500A) removed outlier: 8.924A pdb=" N LEU G 213 " --> pdb=" O PHE G 175 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ASN G 177 " --> pdb=" O LEU G 213 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N VAL G 215 " --> pdb=" O ASN G 177 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N HIS G 179 " --> pdb=" O VAL G 215 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ARG G 217 " --> pdb=" O HIS G 179 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N SER G 181 " --> pdb=" O ARG G 217 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 59 through 60 Processing sheet with id=AB6, first strand: chain 'G' and resid 330 through 337 removed outlier: 6.659A pdb=" N LYS G 297 " --> pdb=" O LYS G 331 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ASN G 333 " --> pdb=" O LYS G 297 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N CYS G 299 " --> pdb=" O ASN G 333 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N MET G 335 " --> pdb=" O CYS G 299 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE G 301 " --> pdb=" O MET G 335 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ILE G 337 " --> pdb=" O ILE G 301 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N LEU G 303 " --> pdb=" O ILE G 337 " (cutoff:3.500A) removed outlier: 9.093A pdb=" N GLY G 366 " --> pdb=" O ILE G 298 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N SER G 300 " --> pdb=" O GLY G 366 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N LEU G 368 " --> pdb=" O SER G 300 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ALA G 302 " --> pdb=" O LEU G 368 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N PHE G 520 " --> pdb=" O LEU G 514 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N MET G 509 " --> pdb=" O GLU G 502 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N GLU G 502 " --> pdb=" O MET G 509 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE G 511 " --> pdb=" O VAL G 500 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 420 through 421 removed outlier: 7.371A pdb=" N ASN G 420 " --> pdb=" O LEU G 432 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ILE G 434 " --> pdb=" O ASN G 420 " (cutoff:3.500A) 792 hydrogen bonds defined for protein. 2244 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: 8.96 Time building geometry restraints manager: 4.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.14: 17368 1.14 - 1.32: 2876 1.32 - 1.50: 7120 1.50 - 1.67: 7664 1.67 - 1.85: 160 Bond restraints: 35188 Sorted by residual: bond pdb=" CE2 PHE H 499 " pdb=" HE2 PHE H 499 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" CD2 HIS G 245 " pdb=" HD2 HIS G 245 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" NH2 ARG D 291 " pdb="HH22 ARG D 291 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" NH2 ARG C 291 " pdb="HH21 ARG C 291 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N MET G 335 " pdb=" H MET G 335 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 ... (remaining 35183 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.79: 63599 7.79 - 15.59: 189 15.59 - 23.38: 0 23.38 - 31.17: 0 31.17 - 38.97: 4 Bond angle restraints: 63792 Sorted by residual: angle pdb=" CA LEU D 281 " pdb=" N LEU D 281 " pdb=" H LEU D 281 " ideal model delta sigma weight residual 114.00 152.97 -38.97 3.00e+00 1.11e-01 1.69e+02 angle pdb=" CA LEU C 281 " pdb=" N LEU C 281 " pdb=" H LEU C 281 " ideal model delta sigma weight residual 114.00 152.97 -38.97 3.00e+00 1.11e-01 1.69e+02 angle pdb=" CA LEU H 281 " pdb=" N LEU H 281 " pdb=" H LEU H 281 " ideal model delta sigma weight residual 114.00 152.97 -38.97 3.00e+00 1.11e-01 1.69e+02 angle pdb=" CA LEU G 281 " pdb=" N LEU G 281 " pdb=" H LEU G 281 " ideal model delta sigma weight residual 114.00 152.94 -38.94 3.00e+00 1.11e-01 1.68e+02 angle pdb=" N PRO D 538 " pdb=" CA PRO D 538 " pdb=" C PRO D 538 " ideal model delta sigma weight residual 110.70 119.88 -9.18 1.22e+00 6.72e-01 5.66e+01 ... (remaining 63787 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 14680 17.94 - 35.89: 1122 35.89 - 53.83: 453 53.83 - 71.78: 310 71.78 - 89.72: 43 Dihedral angle restraints: 16608 sinusoidal: 9324 harmonic: 7284 Sorted by residual: dihedral pdb=" CA LYS D 169 " pdb=" C LYS D 169 " pdb=" N ALA D 170 " pdb=" CA ALA D 170 " ideal model delta harmonic sigma weight residual 180.00 151.95 28.05 0 5.00e+00 4.00e-02 3.15e+01 dihedral pdb=" CA LYS H 169 " pdb=" C LYS H 169 " pdb=" N ALA H 170 " pdb=" CA ALA H 170 " ideal model delta harmonic sigma weight residual 180.00 151.96 28.04 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA LYS G 169 " pdb=" C LYS G 169 " pdb=" N ALA G 170 " pdb=" CA ALA G 170 " ideal model delta harmonic sigma weight residual 180.00 151.98 28.02 0 5.00e+00 4.00e-02 3.14e+01 ... (remaining 16605 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 1535 0.098 - 0.196: 835 0.196 - 0.294: 250 0.294 - 0.392: 60 0.392 - 0.490: 12 Chirality restraints: 2692 Sorted by residual: chirality pdb=" CB THR D 150 " pdb=" CA THR D 150 " pdb=" OG1 THR D 150 " pdb=" CG2 THR D 150 " both_signs ideal model delta sigma weight residual False 2.55 2.06 0.49 2.00e-01 2.50e+01 6.01e+00 chirality pdb=" CB THR H 150 " pdb=" CA THR H 150 " pdb=" OG1 THR H 150 " pdb=" CG2 THR H 150 " both_signs ideal model delta sigma weight residual False 2.55 2.06 0.49 2.00e-01 2.50e+01 6.01e+00 chirality pdb=" CB THR G 150 " pdb=" CA THR G 150 " pdb=" OG1 THR G 150 " pdb=" CG2 THR G 150 " both_signs ideal model delta sigma weight residual False 2.55 2.06 0.49 2.00e-01 2.50e+01 6.00e+00 ... (remaining 2689 not shown) Planarity restraints: 5116 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 285 " 0.211 2.00e-02 2.50e+03 8.36e-02 2.80e+02 pdb=" CG TRP H 285 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP H 285 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP H 285 " -0.015 2.00e-02 2.50e+03 pdb=" NE1 TRP H 285 " -0.059 2.00e-02 2.50e+03 pdb=" CE2 TRP H 285 " -0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP H 285 " -0.050 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 285 " 0.042 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 285 " -0.043 2.00e-02 2.50e+03 pdb=" CH2 TRP H 285 " 0.048 2.00e-02 2.50e+03 pdb=" HD1 TRP H 285 " -0.028 2.00e-02 2.50e+03 pdb=" HE1 TRP H 285 " -0.118 2.00e-02 2.50e+03 pdb=" HE3 TRP H 285 " -0.082 2.00e-02 2.50e+03 pdb=" HZ2 TRP H 285 " 0.076 2.00e-02 2.50e+03 pdb=" HZ3 TRP H 285 " -0.108 2.00e-02 2.50e+03 pdb=" HH2 TRP H 285 " 0.121 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 285 " 0.210 2.00e-02 2.50e+03 8.36e-02 2.80e+02 pdb=" CG TRP G 285 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP G 285 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP G 285 " -0.017 2.00e-02 2.50e+03 pdb=" NE1 TRP G 285 " -0.059 2.00e-02 2.50e+03 pdb=" CE2 TRP G 285 " -0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP G 285 " -0.049 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 285 " 0.043 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 285 " -0.044 2.00e-02 2.50e+03 pdb=" CH2 TRP G 285 " 0.048 2.00e-02 2.50e+03 pdb=" HD1 TRP G 285 " -0.027 2.00e-02 2.50e+03 pdb=" HE1 TRP G 285 " -0.119 2.00e-02 2.50e+03 pdb=" HE3 TRP G 285 " -0.080 2.00e-02 2.50e+03 pdb=" HZ2 TRP G 285 " 0.076 2.00e-02 2.50e+03 pdb=" HZ3 TRP G 285 " -0.110 2.00e-02 2.50e+03 pdb=" HH2 TRP G 285 " 0.122 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 285 " -0.210 2.00e-02 2.50e+03 8.36e-02 2.80e+02 pdb=" CG TRP C 285 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP C 285 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP C 285 " 0.017 2.00e-02 2.50e+03 pdb=" NE1 TRP C 285 " 0.059 2.00e-02 2.50e+03 pdb=" CE2 TRP C 285 " 0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP C 285 " 0.049 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 285 " -0.043 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 285 " 0.044 2.00e-02 2.50e+03 pdb=" CH2 TRP C 285 " -0.048 2.00e-02 2.50e+03 pdb=" HD1 TRP C 285 " 0.027 2.00e-02 2.50e+03 pdb=" HE1 TRP C 285 " 0.119 2.00e-02 2.50e+03 pdb=" HE3 TRP C 285 " 0.080 2.00e-02 2.50e+03 pdb=" HZ2 TRP C 285 " -0.076 2.00e-02 2.50e+03 pdb=" HZ3 TRP C 285 " 0.110 2.00e-02 2.50e+03 pdb=" HH2 TRP C 285 " -0.122 2.00e-02 2.50e+03 ... (remaining 5113 not shown) Histogram of nonbonded interaction distances: 1.18 - 1.86: 377 1.86 - 2.55: 29455 2.55 - 3.23: 113206 3.23 - 3.92: 153214 3.92 - 4.60: 233442 Nonbonded interactions: 529694 Sorted by model distance: nonbonded pdb=" OD2 ASP C 46 " pdb="HH12 ARG G 102 " model vdw 1.176 2.450 nonbonded pdb="HH12 ARG C 102 " pdb=" OD2 ASP G 46 " model vdw 1.185 2.450 nonbonded pdb="HH11 ARG D 102 " pdb=" OD2 ASP H 46 " model vdw 1.191 2.450 nonbonded pdb=" OD2 ASP D 46 " pdb="HH12 ARG H 102 " model vdw 1.200 2.450 nonbonded pdb="HH22 ARG C 102 " pdb=" OD1 ASP G 46 " model vdw 1.674 2.450 ... (remaining 529689 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 'C' and (resid 1 through 601 or resid 603)) selection = (chain 'D' and (resid 1 through 601 or resid 603)) selection = (chain 'G' and (resid 1 through 601 or resid 603)) selection = (chain 'H' and (resid 1 through 601 or resid 603)) } 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: 1.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.240 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 33.680 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 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 0.127 17776 Z= 0.727 Angle : 2.002 9.916 24092 Z= 1.345 Chirality : 0.129 0.490 2692 Planarity : 0.013 0.106 3072 Dihedral : 14.460 89.721 6860 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.54 % Favored : 96.27 % Rotamer: Outliers : 1.69 % Allowed : 4.76 % Favored : 93.55 % Cbeta Deviations : 0.20 % 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: -1.26 (0.17), residues: 2144 helix: -0.75 (0.15), residues: 916 sheet: -0.32 (0.25), residues: 368 loop : -0.97 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 449 TYR 0.135 0.021 TYR D 176 PHE 0.080 0.018 PHE H 50 TRP 0.125 0.028 TRP D 285 HIS 0.023 0.005 HIS H 480 Details of bonding type rmsd/Z covalent geometry : bond 0.01267 / 0.73 (17776) covalent geometry : angle 2.00249 / 1.35 (24092) hydrogen bonds : bond 0.17187 / 11.50 ( 792) hydrogen bonds : angle 7.68487 / 5.36 ( 2244) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 586 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: 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: D 51 SER cc_start: 0.8470 (t) cc_final: 0.8146 (p) REVERT: D 119 ASP cc_start: 0.7844 (m-30) cc_final: 0.7632 (m-30) REVERT: D 132 SER cc_start: 0.7850 (p) cc_final: 0.7613 (t) REVERT: D 286 LYS cc_start: 0.7673 (ttpt) cc_final: 0.7007 (ttpp) REVERT: D 300 SER cc_start: 0.8448 (m) cc_final: 0.8242 (t) REVERT: D 363 LEU cc_start: 0.8393 (mp) cc_final: 0.8069 (mt) REVERT: D 475 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7742 (mt-10) REVERT: D 502 GLU cc_start: 0.6948 (pt0) cc_final: 0.6686 (pt0) REVERT: C 51 SER cc_start: 0.8472 (t) cc_final: 0.8143 (p) REVERT: C 132 SER cc_start: 0.7863 (p) cc_final: 0.7641 (t) REVERT: C 251 TYR cc_start: 0.8420 (m-80) cc_final: 0.8177 (m-80) REVERT: C 286 LYS cc_start: 0.7687 (ttpt) cc_final: 0.7048 (ttpp) REVERT: C 300 SER cc_start: 0.8435 (m) cc_final: 0.8219 (t) REVERT: C 363 LEU cc_start: 0.8384 (mp) cc_final: 0.8078 (mt) REVERT: C 475 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7738 (mt-10) REVERT: C 502 GLU cc_start: 0.6990 (pt0) cc_final: 0.6728 (pt0) REVERT: H 51 SER cc_start: 0.8394 (t) cc_final: 0.8127 (p) REVERT: H 66 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8203 (mt-10) REVERT: H 119 ASP cc_start: 0.7873 (m-30) cc_final: 0.7668 (m-30) REVERT: H 132 SER cc_start: 0.7852 (p) cc_final: 0.7607 (t) REVERT: H 251 TYR cc_start: 0.8415 (m-80) cc_final: 0.8157 (m-80) REVERT: H 286 LYS cc_start: 0.7647 (ttpt) cc_final: 0.7059 (ttpp) REVERT: H 363 LEU cc_start: 0.8300 (mp) cc_final: 0.8041 (mt) REVERT: H 475 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7760 (mt-10) REVERT: H 502 GLU cc_start: 0.7010 (pt0) cc_final: 0.6716 (pt0) REVERT: G 51 SER cc_start: 0.8441 (t) cc_final: 0.8146 (p) REVERT: G 132 SER cc_start: 0.7862 (p) cc_final: 0.7610 (t) REVERT: G 286 LYS cc_start: 0.7752 (ttpt) cc_final: 0.7450 (ttpp) REVERT: G 363 LEU cc_start: 0.8302 (mp) cc_final: 0.8039 (mt) REVERT: G 466 LYS cc_start: 0.8291 (mttm) cc_final: 0.7946 (mtmp) REVERT: G 475 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7742 (mt-10) outliers start: 32 outliers final: 8 residues processed: 598 average time/residue: 0.9766 time to fit residues: 683.4666 Evaluate side-chains 492 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 484 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain C residue 134 ASP Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain H residue 134 ASP Chi-restraints excluded: chain H residue 308 THR Chi-restraints excluded: chain G residue 134 ASP Chi-restraints excluded: chain G residue 308 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 0.7980 chunk 212 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 122 GLN D 174 ASN D 177 ASN D 185 GLN C 122 GLN C 174 ASN C 177 ASN C 185 GLN H 122 GLN H 174 ASN H 177 ASN H 185 GLN G 122 GLN G 174 ASN G 177 ASN G 185 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.144246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.115666 restraints weight = 58913.862| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.87 r_work: 0.3124 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17776 Z= 0.152 Angle : 0.598 5.163 24092 Z= 0.315 Chirality : 0.047 0.152 2692 Planarity : 0.005 0.058 3072 Dihedral : 6.851 42.371 2624 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.19 % Allowed : 1.54 % Favored : 98.27 % Rotamer: Outliers : 2.59 % Allowed : 12.05 % Favored : 85.36 % 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: -0.32 (0.18), residues: 2144 helix: 0.52 (0.16), residues: 932 sheet: -0.68 (0.25), residues: 372 loop : -0.67 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 269 TYR 0.016 0.002 TYR D 42 PHE 0.021 0.002 PHE C 318 TRP 0.012 0.002 TRP G 387 HIS 0.004 0.001 HIS G 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (17776) covalent geometry : angle 0.59845 / 0.31 (24092) hydrogen bonds : bond 0.03935 / 2.59 ( 792) hydrogen bonds : angle 5.18981 / 3.64 ( 2244) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 501 time to evaluate : 0.962 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: D 51 SER cc_start: 0.8614 (t) cc_final: 0.8410 (p) REVERT: D 54 GLU cc_start: 0.8524 (tp30) cc_final: 0.8216 (mm-30) REVERT: D 70 ASP cc_start: 0.8151 (m-30) cc_final: 0.7913 (m-30) REVERT: D 161 GLU cc_start: 0.8210 (tp30) cc_final: 0.7977 (tp30) REVERT: D 167 GLN cc_start: 0.7972 (tt0) cc_final: 0.7623 (tt0) REVERT: D 176 TYR cc_start: 0.7907 (m-80) cc_final: 0.7576 (m-80) REVERT: D 290 ASP cc_start: 0.7793 (m-30) cc_final: 0.7435 (m-30) REVERT: D 292 TYR cc_start: 0.8317 (t80) cc_final: 0.7975 (t80) REVERT: D 298 ILE cc_start: 0.8718 (mt) cc_final: 0.8469 (mm) REVERT: D 322 GLU cc_start: 0.8647 (mm-30) cc_final: 0.8150 (mm-30) REVERT: D 473 TYR cc_start: 0.8223 (p90) cc_final: 0.8016 (p90) REVERT: D 498 CYS cc_start: 0.7745 (t) cc_final: 0.7142 (t) REVERT: D 502 GLU cc_start: 0.7669 (pt0) cc_final: 0.7079 (pt0) REVERT: C 51 SER cc_start: 0.8625 (t) cc_final: 0.8424 (p) REVERT: C 70 ASP cc_start: 0.8148 (m-30) cc_final: 0.7842 (m-30) REVERT: C 161 GLU cc_start: 0.8216 (tp30) cc_final: 0.7982 (tp30) REVERT: C 167 GLN cc_start: 0.7939 (tt0) cc_final: 0.7595 (tt0) REVERT: C 176 TYR cc_start: 0.7896 (m-80) cc_final: 0.7573 (m-80) REVERT: C 268 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7363 (mt-10) REVERT: C 298 ILE cc_start: 0.8728 (mt) cc_final: 0.8497 (mm) REVERT: C 363 LEU cc_start: 0.8519 (mp) cc_final: 0.8293 (mt) REVERT: C 502 GLU cc_start: 0.7673 (pt0) cc_final: 0.7099 (pt0) REVERT: C 534 MET cc_start: 0.8558 (mmm) cc_final: 0.8315 (mpp) REVERT: H 70 ASP cc_start: 0.8163 (m-30) cc_final: 0.7917 (m-30) REVERT: H 110 THR cc_start: 0.8972 (m) cc_final: 0.8683 (m) REVERT: H 161 GLU cc_start: 0.8221 (tp30) cc_final: 0.7990 (tp30) REVERT: H 176 TYR cc_start: 0.7900 (m-80) cc_final: 0.7586 (m-80) REVERT: H 268 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7351 (mt-10) REVERT: H 298 ILE cc_start: 0.8718 (mt) cc_final: 0.8472 (mm) REVERT: H 322 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8147 (mm-30) REVERT: H 359 GLN cc_start: 0.7926 (tt0) cc_final: 0.7720 (tt0) REVERT: H 363 LEU cc_start: 0.8536 (mp) cc_final: 0.8305 (mt) REVERT: H 502 GLU cc_start: 0.7662 (pt0) cc_final: 0.7226 (pt0) REVERT: H 534 MET cc_start: 0.8590 (mmm) cc_final: 0.8350 (mpp) REVERT: G 70 ASP cc_start: 0.8188 (m-30) cc_final: 0.7894 (m-30) REVERT: G 81 ASN cc_start: 0.8791 (m-40) cc_final: 0.8579 (m-40) REVERT: G 161 GLU cc_start: 0.8137 (tp30) cc_final: 0.7919 (tp30) REVERT: G 167 GLN cc_start: 0.7920 (tt0) cc_final: 0.7594 (tt0) REVERT: G 173 GLU cc_start: 0.7560 (pt0) cc_final: 0.7009 (pm20) REVERT: G 176 TYR cc_start: 0.7894 (m-80) cc_final: 0.7568 (m-80) REVERT: G 298 ILE cc_start: 0.8712 (mt) cc_final: 0.8457 (mm) REVERT: G 359 GLN cc_start: 0.7995 (tt0) cc_final: 0.7775 (tt0) REVERT: G 363 LEU cc_start: 0.8541 (mp) cc_final: 0.8295 (mt) REVERT: G 466 LYS cc_start: 0.8471 (mttm) cc_final: 0.8132 (mtmp) REVERT: G 534 MET cc_start: 0.8562 (mmm) cc_final: 0.8247 (mpp) outliers start: 49 outliers final: 16 residues processed: 522 average time/residue: 1.0690 time to fit residues: 646.8047 Evaluate side-chains 444 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 428 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 311 ARG Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain D residue 537 SER Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 227 LYS Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain H residue 308 THR Chi-restraints excluded: chain H residue 500 VAL Chi-restraints excluded: chain H residue 537 SER Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain G residue 308 THR Chi-restraints excluded: chain G residue 500 VAL Chi-restraints excluded: chain G residue 537 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 139 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 192 optimal weight: 3.9990 chunk 175 optimal weight: 2.9990 chunk 184 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 412 ASN D 556 GLN C 412 ASN C 556 GLN H 167 GLN H 412 ASN G 556 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.138663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.110061 restraints weight = 60235.461| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.88 r_work: 0.3032 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 17776 Z= 0.210 Angle : 0.594 5.128 24092 Z= 0.306 Chirality : 0.048 0.191 2692 Planarity : 0.005 0.081 3072 Dihedral : 7.031 42.815 2616 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.19 % Allowed : 1.73 % Favored : 98.09 % Rotamer: Outliers : 1.59 % Allowed : 16.97 % Favored : 81.45 % 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: 0.12 (0.18), residues: 2144 helix: 1.04 (0.17), residues: 912 sheet: -0.78 (0.25), residues: 368 loop : -0.44 (0.22), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 389 TYR 0.014 0.001 TYR H 42 PHE 0.011 0.002 PHE C 424 TRP 0.012 0.002 TRP G 387 HIS 0.007 0.002 HIS H 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.21 (17776) covalent geometry : angle 0.59405 / 0.31 (24092) hydrogen bonds : bond 0.03621 / 2.38 ( 792) hydrogen bonds : angle 4.78942 / 3.38 ( 2244) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 474 time to evaluate : 0.886 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: D 1 MET cc_start: 0.8393 (ttt) cc_final: 0.8091 (ttt) REVERT: D 70 ASP cc_start: 0.8337 (m-30) cc_final: 0.8034 (m-30) REVERT: D 167 GLN cc_start: 0.8214 (tt0) cc_final: 0.7477 (pt0) REVERT: D 286 LYS cc_start: 0.8006 (ttpt) cc_final: 0.7632 (tttm) REVERT: D 322 GLU cc_start: 0.8782 (mm-30) cc_final: 0.8328 (mm-30) REVERT: D 438 GLU cc_start: 0.5320 (mt-10) cc_final: 0.5078 (mt-10) REVERT: D 473 TYR cc_start: 0.8331 (p90) cc_final: 0.8094 (p90) REVERT: D 498 CYS cc_start: 0.8012 (t) cc_final: 0.7466 (t) REVERT: C 1 MET cc_start: 0.8355 (ttt) cc_final: 0.8038 (ttt) REVERT: C 70 ASP cc_start: 0.8343 (m-30) cc_final: 0.8066 (m-30) REVERT: C 167 GLN cc_start: 0.8205 (tt0) cc_final: 0.7477 (pt0) REVERT: C 268 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7498 (mt-10) REVERT: C 286 LYS cc_start: 0.7997 (ttpt) cc_final: 0.7646 (tttm) REVERT: C 322 GLU cc_start: 0.8758 (mm-30) cc_final: 0.8300 (mm-30) REVERT: C 434 ILE cc_start: 0.7799 (pt) cc_final: 0.7596 (pp) REVERT: C 498 CYS cc_start: 0.8008 (t) cc_final: 0.7472 (t) REVERT: C 534 MET cc_start: 0.8610 (mmm) cc_final: 0.8359 (mpp) REVERT: H 1 MET cc_start: 0.8361 (ttt) cc_final: 0.8059 (ttt) REVERT: H 70 ASP cc_start: 0.8339 (m-30) cc_final: 0.8035 (m-30) REVERT: H 232 MET cc_start: 0.8338 (mmt) cc_final: 0.7998 (mmp) REVERT: H 286 LYS cc_start: 0.7948 (ttpt) cc_final: 0.7553 (tttm) REVERT: H 322 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8283 (mm-30) REVERT: H 434 ILE cc_start: 0.7798 (pt) cc_final: 0.7595 (pp) REVERT: H 476 GLU cc_start: 0.8571 (mm-30) cc_final: 0.8276 (mm-30) REVERT: H 498 CYS cc_start: 0.8010 (t) cc_final: 0.7474 (t) REVERT: H 502 GLU cc_start: 0.7700 (pt0) cc_final: 0.7314 (pt0) REVERT: H 534 MET cc_start: 0.8672 (mmm) cc_final: 0.8422 (mpp) REVERT: G 1 MET cc_start: 0.8374 (ttt) cc_final: 0.8033 (ttt) REVERT: G 70 ASP cc_start: 0.8348 (m-30) cc_final: 0.8103 (m-30) REVERT: G 167 GLN cc_start: 0.8208 (tt0) cc_final: 0.7482 (pt0) REVERT: G 286 LYS cc_start: 0.8041 (ttpt) cc_final: 0.7662 (ttpp) REVERT: G 298 ILE cc_start: 0.8723 (mt) cc_final: 0.8479 (mm) REVERT: G 322 GLU cc_start: 0.8790 (mm-30) cc_final: 0.8303 (mm-30) REVERT: G 438 GLU cc_start: 0.5271 (mt-10) cc_final: 0.5058 (mt-10) REVERT: G 454 ARG cc_start: 0.8262 (ttm110) cc_final: 0.7908 (ttm-80) REVERT: G 534 MET cc_start: 0.8674 (mmm) cc_final: 0.8351 (mpp) outliers start: 30 outliers final: 12 residues processed: 483 average time/residue: 1.0667 time to fit residues: 596.9932 Evaluate side-chains 430 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 418 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain D residue 537 SER Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain H residue 500 VAL Chi-restraints excluded: chain H residue 537 SER Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain G residue 500 VAL Chi-restraints excluded: chain G residue 537 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 45 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 199 optimal weight: 0.9980 chunk 191 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 213 optimal weight: 0.9980 chunk 200 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 556 GLN H 167 GLN H 296 GLN G 412 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.140011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.111737 restraints weight = 59796.868| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.87 r_work: 0.3072 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.4190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17776 Z= 0.149 Angle : 0.526 4.841 24092 Z= 0.266 Chirality : 0.045 0.128 2692 Planarity : 0.005 0.081 3072 Dihedral : 6.378 39.312 2612 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.37 % Allowed : 18.55 % 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: 0.44 (0.18), residues: 2144 helix: 1.42 (0.17), residues: 912 sheet: -0.82 (0.25), residues: 368 loop : -0.30 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 389 TYR 0.014 0.001 TYR H 42 PHE 0.010 0.001 PHE G 318 TRP 0.010 0.002 TRP G 387 HIS 0.005 0.001 HIS C 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (17776) covalent geometry : angle 0.52629 / 0.27 (24092) hydrogen bonds : bond 0.03070 / 2.02 ( 792) hydrogen bonds : angle 4.50140 / 3.18 ( 2244) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 432 time to evaluate : 0.984 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: D 70 ASP cc_start: 0.8435 (m-30) cc_final: 0.8179 (m-30) REVERT: D 167 GLN cc_start: 0.8189 (tt0) cc_final: 0.7496 (pt0) REVERT: D 286 LYS cc_start: 0.7978 (ttpt) cc_final: 0.7649 (tttm) REVERT: D 322 GLU cc_start: 0.8859 (mm-30) cc_final: 0.8390 (mm-30) REVERT: D 363 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8092 (tt) REVERT: D 498 CYS cc_start: 0.7967 (t) cc_final: 0.7284 (t) REVERT: C 70 ASP cc_start: 0.8419 (m-30) cc_final: 0.8136 (m-30) REVERT: C 167 GLN cc_start: 0.8191 (tt0) cc_final: 0.7500 (pt0) REVERT: C 286 LYS cc_start: 0.8003 (ttpt) cc_final: 0.7651 (ttpp) REVERT: C 322 GLU cc_start: 0.8792 (mm-30) cc_final: 0.8351 (mm-30) REVERT: C 476 GLU cc_start: 0.8732 (mm-30) cc_final: 0.8429 (mm-30) REVERT: C 534 MET cc_start: 0.8619 (mmm) cc_final: 0.8351 (mpp) REVERT: H 70 ASP cc_start: 0.8384 (m-30) cc_final: 0.8125 (m-30) REVERT: H 286 LYS cc_start: 0.7935 (ttpt) cc_final: 0.7593 (tttm) REVERT: H 322 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8565 (mm-30) REVERT: H 434 ILE cc_start: 0.7829 (pt) cc_final: 0.7629 (pp) REVERT: H 476 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8189 (mm-30) REVERT: H 502 GLU cc_start: 0.7643 (pt0) cc_final: 0.7287 (pt0) REVERT: H 534 MET cc_start: 0.8671 (mmm) cc_final: 0.8413 (mpp) REVERT: G 1 MET cc_start: 0.8383 (ttt) cc_final: 0.8071 (ttt) REVERT: G 70 ASP cc_start: 0.8403 (m-30) cc_final: 0.8110 (m-30) REVERT: G 136 ASN cc_start: 0.7092 (t0) cc_final: 0.6592 (m110) REVERT: G 167 GLN cc_start: 0.8178 (tt0) cc_final: 0.7480 (pt0) REVERT: G 286 LYS cc_start: 0.8002 (ttpt) cc_final: 0.7647 (tttm) REVERT: G 298 ILE cc_start: 0.8683 (mt) cc_final: 0.8435 (mm) REVERT: G 322 GLU cc_start: 0.8864 (mm-30) cc_final: 0.8547 (mm-30) REVERT: G 534 MET cc_start: 0.8644 (mmm) cc_final: 0.8358 (mpp) outliers start: 26 outliers final: 19 residues processed: 442 average time/residue: 0.9836 time to fit residues: 508.7956 Evaluate side-chains 431 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 411 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 243 CYS Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 537 SER Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 79 ASP Chi-restraints excluded: chain H residue 220 THR Chi-restraints excluded: chain H residue 243 CYS Chi-restraints excluded: chain H residue 363 LEU Chi-restraints excluded: chain H residue 537 SER Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain G residue 363 LEU Chi-restraints excluded: chain G residue 537 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 26 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 159 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 = 0.3512 r_free = 0.3512 target = 0.137473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.109080 restraints weight = 60221.568| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 1.86 r_work: 0.3021 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.4497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 17776 Z= 0.210 Angle : 0.558 5.475 24092 Z= 0.282 Chirality : 0.046 0.135 2692 Planarity : 0.005 0.083 3072 Dihedral : 6.752 50.608 2612 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.27 % Allowed : 18.97 % Favored : 78.75 % 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: 0.45 (0.18), residues: 2144 helix: 1.41 (0.17), residues: 916 sheet: -0.94 (0.24), residues: 368 loop : -0.21 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 389 TYR 0.014 0.001 TYR H 42 PHE 0.009 0.002 PHE H 77 TRP 0.008 0.002 TRP H 387 HIS 0.007 0.002 HIS C 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.21 (17776) covalent geometry : angle 0.55844 / 0.28 (24092) hydrogen bonds : bond 0.03209 / 2.12 ( 792) hydrogen bonds : angle 4.48735 / 3.18 ( 2244) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 425 time to evaluate : 0.913 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: D 1 MET cc_start: 0.8516 (ttt) cc_final: 0.8107 (ttt) REVERT: D 167 GLN cc_start: 0.8306 (tt0) cc_final: 0.7586 (pt0) REVERT: D 286 LYS cc_start: 0.8066 (ttpt) cc_final: 0.7726 (tttm) REVERT: D 322 GLU cc_start: 0.8794 (mm-30) cc_final: 0.8574 (mm-30) REVERT: D 353 LYS cc_start: 0.7229 (mtmt) cc_final: 0.6903 (mttp) REVERT: D 363 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8189 (tt) REVERT: D 498 CYS cc_start: 0.8060 (t) cc_final: 0.7485 (t) REVERT: C 167 GLN cc_start: 0.8306 (tt0) cc_final: 0.7595 (pt0) REVERT: C 232 MET cc_start: 0.8336 (mmp) cc_final: 0.7536 (tmm) REVERT: C 286 LYS cc_start: 0.8060 (ttpt) cc_final: 0.7698 (tttm) REVERT: C 322 GLU cc_start: 0.8803 (mm-30) cc_final: 0.8594 (mm-30) REVERT: C 363 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8160 (tt) REVERT: C 476 GLU cc_start: 0.8754 (mm-30) cc_final: 0.8527 (mm-30) REVERT: C 498 CYS cc_start: 0.8016 (t) cc_final: 0.7487 (t) REVERT: C 534 MET cc_start: 0.8642 (mmm) cc_final: 0.8337 (mpp) REVERT: H 286 LYS cc_start: 0.8004 (ttpt) cc_final: 0.7658 (tttm) REVERT: H 322 GLU cc_start: 0.8793 (mm-30) cc_final: 0.8574 (mm-30) REVERT: H 363 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8168 (tt) REVERT: H 434 ILE cc_start: 0.7896 (pt) cc_final: 0.7690 (pp) REVERT: H 498 CYS cc_start: 0.8067 (t) cc_final: 0.7473 (t) REVERT: H 534 MET cc_start: 0.8717 (mmm) cc_final: 0.8411 (mpp) REVERT: G 1 MET cc_start: 0.8494 (ttt) cc_final: 0.8158 (ttt) REVERT: G 167 GLN cc_start: 0.8284 (tt0) cc_final: 0.7574 (pt0) REVERT: G 286 LYS cc_start: 0.8053 (ttpt) cc_final: 0.7744 (tttm) REVERT: G 322 GLU cc_start: 0.8806 (mm-30) cc_final: 0.8604 (mm-30) REVERT: G 363 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8167 (tt) REVERT: G 498 CYS cc_start: 0.8020 (t) cc_final: 0.7470 (t) REVERT: G 534 MET cc_start: 0.8653 (mmm) cc_final: 0.8388 (mpp) outliers start: 43 outliers final: 22 residues processed: 447 average time/residue: 0.9054 time to fit residues: 476.6346 Evaluate side-chains 444 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 418 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 243 CYS Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain D residue 537 SER Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 220 THR Chi-restraints excluded: chain H residue 243 CYS Chi-restraints excluded: chain H residue 363 LEU Chi-restraints excluded: chain H residue 500 VAL Chi-restraints excluded: chain H residue 537 SER Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain G residue 243 CYS Chi-restraints excluded: chain G residue 363 LEU Chi-restraints excluded: chain G residue 500 VAL Chi-restraints excluded: chain G residue 537 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 165 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 202 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 77 optimal weight: 0.0870 chunk 145 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 208 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 167 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.139795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.110979 restraints weight = 59240.336| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 1.89 r_work: 0.3044 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.4609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17776 Z= 0.130 Angle : 0.512 6.511 24092 Z= 0.255 Chirality : 0.044 0.130 2692 Planarity : 0.004 0.085 3072 Dihedral : 6.237 46.387 2612 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.74 % Allowed : 19.40 % Favored : 78.86 % 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: 0.75 (0.18), residues: 2144 helix: 1.77 (0.17), residues: 916 sheet: -0.95 (0.24), residues: 368 loop : -0.12 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 389 TYR 0.014 0.001 TYR H 42 PHE 0.015 0.001 PHE D 409 TRP 0.007 0.001 TRP H 387 HIS 0.005 0.001 HIS C 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (17776) covalent geometry : angle 0.51221 / 0.25 (24092) hydrogen bonds : bond 0.02785 / 1.84 ( 792) hydrogen bonds : angle 4.29038 / 3.04 ( 2244) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 432 time to evaluate : 0.929 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: D 167 GLN cc_start: 0.8287 (tt0) cc_final: 0.7628 (pt0) REVERT: D 286 LYS cc_start: 0.8035 (ttpt) cc_final: 0.7724 (tttm) REVERT: D 322 GLU cc_start: 0.8855 (mm-30) cc_final: 0.8573 (mm-30) REVERT: D 363 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8164 (tt) REVERT: D 498 CYS cc_start: 0.7941 (t) cc_final: 0.7300 (t) REVERT: C 167 GLN cc_start: 0.8273 (tt0) cc_final: 0.7615 (pt0) REVERT: C 232 MET cc_start: 0.8324 (mmp) cc_final: 0.7615 (tmm) REVERT: C 268 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7475 (mt-10) REVERT: C 286 LYS cc_start: 0.8044 (ttpt) cc_final: 0.7717 (tttm) REVERT: C 322 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8557 (mm-30) REVERT: C 363 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8160 (tt) REVERT: C 476 GLU cc_start: 0.8726 (mm-30) cc_final: 0.8390 (mm-30) REVERT: C 498 CYS cc_start: 0.7908 (t) cc_final: 0.7230 (t) REVERT: C 534 MET cc_start: 0.8646 (mmm) cc_final: 0.8332 (mpp) REVERT: H 232 MET cc_start: 0.8360 (mmt) cc_final: 0.7521 (tmm) REVERT: H 286 LYS cc_start: 0.7986 (ttpt) cc_final: 0.7567 (tttm) REVERT: H 322 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8568 (mm-30) REVERT: H 363 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8167 (tt) REVERT: H 420 ASN cc_start: 0.8701 (t0) cc_final: 0.8296 (t0) REVERT: H 476 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8362 (mm-30) REVERT: H 498 CYS cc_start: 0.7964 (t) cc_final: 0.7309 (t) REVERT: H 534 MET cc_start: 0.8694 (mmm) cc_final: 0.8383 (mpp) REVERT: G 1 MET cc_start: 0.8512 (ttt) cc_final: 0.8157 (ttt) REVERT: G 167 GLN cc_start: 0.8261 (tt0) cc_final: 0.7597 (pt0) REVERT: G 232 MET cc_start: 0.8384 (mmp) cc_final: 0.7609 (tmm) REVERT: G 286 LYS cc_start: 0.8026 (ttpt) cc_final: 0.7721 (tttm) REVERT: G 322 GLU cc_start: 0.8847 (mm-30) cc_final: 0.8578 (mm-30) REVERT: G 363 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8153 (tt) REVERT: G 498 CYS cc_start: 0.7915 (t) cc_final: 0.7260 (t) REVERT: G 534 MET cc_start: 0.8671 (mmm) cc_final: 0.8352 (mpp) outliers start: 33 outliers final: 16 residues processed: 441 average time/residue: 0.9833 time to fit residues: 506.8410 Evaluate side-chains 435 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 415 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 243 CYS Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 537 SER Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 220 THR Chi-restraints excluded: chain H residue 243 CYS Chi-restraints excluded: chain H residue 363 LEU Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain G residue 243 CYS Chi-restraints excluded: chain G residue 363 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 124 optimal weight: 0.9980 chunk 175 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 167 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 197 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 160 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 = 0.3518 r_free = 0.3518 target = 0.137920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.109116 restraints weight = 59252.449| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.86 r_work: 0.3026 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.4792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17776 Z= 0.178 Angle : 0.535 6.932 24092 Z= 0.267 Chirality : 0.045 0.128 2692 Planarity : 0.005 0.088 3072 Dihedral : 6.547 56.293 2612 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.85 % Allowed : 19.19 % Favored : 78.96 % 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: 0.73 (0.18), residues: 2144 helix: 1.74 (0.17), residues: 916 sheet: -0.91 (0.24), residues: 368 loop : -0.13 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 389 TYR 0.013 0.001 TYR H 42 PHE 0.020 0.001 PHE D 409 TRP 0.008 0.001 TRP H 387 HIS 0.006 0.001 HIS H 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (17776) covalent geometry : angle 0.53496 / 0.27 (24092) hydrogen bonds : bond 0.02913 / 1.93 ( 792) hydrogen bonds : angle 4.32458 / 3.06 ( 2244) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 418 time to evaluate : 1.003 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: D 1 MET cc_start: 0.8514 (ttt) cc_final: 0.8037 (ttt) REVERT: D 167 GLN cc_start: 0.8321 (tt0) cc_final: 0.7667 (pt0) REVERT: D 286 LYS cc_start: 0.8043 (ttpt) cc_final: 0.7723 (tttm) REVERT: D 363 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8226 (tt) REVERT: D 498 CYS cc_start: 0.8044 (t) cc_final: 0.7469 (t) REVERT: C 1 MET cc_start: 0.8505 (ttt) cc_final: 0.8020 (ttt) REVERT: C 167 GLN cc_start: 0.8284 (tt0) cc_final: 0.7619 (pt0) REVERT: C 232 MET cc_start: 0.8391 (mmp) cc_final: 0.7711 (tmm) REVERT: C 268 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7457 (mt-10) REVERT: C 286 LYS cc_start: 0.8047 (ttpt) cc_final: 0.7723 (tttm) REVERT: C 363 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8219 (tt) REVERT: C 420 ASN cc_start: 0.8891 (t0) cc_final: 0.8614 (t0) REVERT: C 498 CYS cc_start: 0.7992 (t) cc_final: 0.7307 (t) REVERT: C 534 MET cc_start: 0.8646 (mmm) cc_final: 0.8356 (mpp) REVERT: H 1 MET cc_start: 0.8500 (ttt) cc_final: 0.8017 (ttt) REVERT: H 232 MET cc_start: 0.8370 (mmt) cc_final: 0.7532 (tmm) REVERT: H 284 LYS cc_start: 0.8007 (mmtm) cc_final: 0.7587 (mmmm) REVERT: H 286 LYS cc_start: 0.7987 (ttpt) cc_final: 0.7564 (tttm) REVERT: H 363 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8225 (tt) REVERT: H 420 ASN cc_start: 0.8700 (t0) cc_final: 0.8272 (t0) REVERT: H 498 CYS cc_start: 0.8062 (t) cc_final: 0.7422 (t) REVERT: H 534 MET cc_start: 0.8696 (mmm) cc_final: 0.8424 (mpp) REVERT: G 1 MET cc_start: 0.8585 (ttt) cc_final: 0.8175 (ttt) REVERT: G 167 GLN cc_start: 0.8304 (tt0) cc_final: 0.7629 (pt0) REVERT: G 232 MET cc_start: 0.8373 (mmp) cc_final: 0.7617 (tmm) REVERT: G 286 LYS cc_start: 0.8035 (ttpt) cc_final: 0.7714 (tttm) REVERT: G 363 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8217 (tt) REVERT: G 498 CYS cc_start: 0.7992 (t) cc_final: 0.7293 (t) REVERT: G 534 MET cc_start: 0.8676 (mmm) cc_final: 0.8384 (mpp) outliers start: 35 outliers final: 23 residues processed: 433 average time/residue: 0.9880 time to fit residues: 501.1774 Evaluate side-chains 433 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 406 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 243 CYS Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain D residue 537 SER Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 134 ASP Chi-restraints excluded: chain H residue 220 THR Chi-restraints excluded: chain H residue 243 CYS Chi-restraints excluded: chain H residue 363 LEU Chi-restraints excluded: chain H residue 500 VAL Chi-restraints excluded: chain H residue 537 SER Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 134 ASP Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain G residue 243 CYS Chi-restraints excluded: chain G residue 363 LEU Chi-restraints excluded: chain G residue 537 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 44 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 184 optimal weight: 0.0970 chunk 23 optimal weight: 0.8980 chunk 198 optimal weight: 0.5980 chunk 175 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 188 optimal weight: 1.9990 chunk 165 optimal weight: 0.7980 chunk 24 optimal weight: 0.3980 chunk 77 optimal weight: 0.6980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 167 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.140160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.111238 restraints weight = 59123.224| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.88 r_work: 0.3049 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.4875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17776 Z= 0.110 Angle : 0.503 7.286 24092 Z= 0.248 Chirality : 0.044 0.131 2692 Planarity : 0.004 0.092 3072 Dihedral : 6.099 58.164 2612 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.32 % Allowed : 20.14 % Favored : 78.54 % 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: 0.95 (0.18), residues: 2144 helix: 2.03 (0.17), residues: 912 sheet: -0.88 (0.25), residues: 368 loop : -0.11 (0.22), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 389 TYR 0.013 0.001 TYR G 42 PHE 0.022 0.001 PHE D 409 TRP 0.006 0.001 TRP H 387 HIS 0.004 0.001 HIS C 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (17776) covalent geometry : angle 0.50263 / 0.25 (24092) hydrogen bonds : bond 0.02576 / 1.71 ( 792) hydrogen bonds : angle 4.15621 / 2.94 ( 2244) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 435 time to evaluate : 0.898 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: D 1 MET cc_start: 0.8461 (ttt) cc_final: 0.7956 (ttt) REVERT: D 167 GLN cc_start: 0.8239 (tt0) cc_final: 0.7598 (pt0) REVERT: D 232 MET cc_start: 0.8316 (mmp) cc_final: 0.7609 (tmm) REVERT: D 286 LYS cc_start: 0.8037 (ttpt) cc_final: 0.7725 (tttm) REVERT: D 322 GLU cc_start: 0.8647 (mm-30) cc_final: 0.8108 (mm-30) REVERT: D 363 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8176 (tt) REVERT: D 420 ASN cc_start: 0.8935 (t0) cc_final: 0.8683 (t0) REVERT: D 498 CYS cc_start: 0.8014 (t) cc_final: 0.7430 (t) REVERT: C 1 MET cc_start: 0.8422 (ttt) cc_final: 0.7863 (ttt) REVERT: C 167 GLN cc_start: 0.8231 (tt0) cc_final: 0.7594 (pt0) REVERT: C 232 MET cc_start: 0.8379 (mmp) cc_final: 0.7707 (tmm) REVERT: C 286 LYS cc_start: 0.8022 (ttpt) cc_final: 0.7702 (tttm) REVERT: C 363 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8181 (tt) REVERT: C 420 ASN cc_start: 0.8890 (t0) cc_final: 0.8617 (t0) REVERT: C 476 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8429 (mm-30) REVERT: C 498 CYS cc_start: 0.7884 (t) cc_final: 0.7106 (t) REVERT: C 534 MET cc_start: 0.8644 (mmm) cc_final: 0.8308 (mpp) REVERT: H 1 MET cc_start: 0.8415 (ttt) cc_final: 0.7903 (ttt) REVERT: H 232 MET cc_start: 0.8372 (mmt) cc_final: 0.7542 (tmm) REVERT: H 268 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7469 (mt-10) REVERT: H 286 LYS cc_start: 0.7962 (ttpt) cc_final: 0.7551 (tttm) REVERT: H 363 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8171 (tt) REVERT: H 420 ASN cc_start: 0.8703 (t0) cc_final: 0.8284 (t0) REVERT: H 476 GLU cc_start: 0.8652 (mm-30) cc_final: 0.8392 (mm-30) REVERT: H 498 CYS cc_start: 0.7973 (t) cc_final: 0.7248 (t) REVERT: H 534 MET cc_start: 0.8682 (mmm) cc_final: 0.8348 (mpp) REVERT: G 1 MET cc_start: 0.8526 (ttt) cc_final: 0.8132 (ttt) REVERT: G 136 ASN cc_start: 0.7162 (t0) cc_final: 0.6692 (m-40) REVERT: G 167 GLN cc_start: 0.8216 (tt0) cc_final: 0.7560 (pt0) REVERT: G 232 MET cc_start: 0.8345 (mmp) cc_final: 0.7562 (tmm) REVERT: G 286 LYS cc_start: 0.8011 (ttpt) cc_final: 0.7774 (tttm) REVERT: G 363 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8183 (tt) REVERT: G 420 ASN cc_start: 0.8855 (t0) cc_final: 0.8549 (t0) REVERT: G 498 CYS cc_start: 0.7908 (t) cc_final: 0.7167 (t) REVERT: G 534 MET cc_start: 0.8688 (mmm) cc_final: 0.8349 (mpp) outliers start: 25 outliers final: 16 residues processed: 442 average time/residue: 0.9657 time to fit residues: 499.3648 Evaluate side-chains 438 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 418 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 243 CYS Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 537 SER Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 220 THR Chi-restraints excluded: chain H residue 243 CYS Chi-restraints excluded: chain H residue 363 LEU Chi-restraints excluded: chain H residue 537 SER Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain G residue 243 CYS Chi-restraints excluded: chain G residue 363 LEU Chi-restraints excluded: chain G residue 537 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 75 optimal weight: 1.9990 chunk 179 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 214 optimal weight: 0.9990 chunk 180 optimal weight: 0.9980 chunk 141 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 190 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 412 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.139256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.110637 restraints weight = 58967.692| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.84 r_work: 0.3032 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.4961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 17776 Z= 0.200 Angle : 0.542 7.305 24092 Z= 0.273 Chirality : 0.045 0.146 2692 Planarity : 0.005 0.085 3072 Dihedral : 6.511 58.040 2612 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.48 % Allowed : 20.56 % Favored : 77.96 % 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: 0.73 (0.18), residues: 2144 helix: 1.76 (0.17), residues: 916 sheet: -0.90 (0.25), residues: 368 loop : -0.17 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 389 TYR 0.012 0.001 TYR H 42 PHE 0.021 0.002 PHE D 409 TRP 0.008 0.001 TRP H 387 HIS 0.008 0.001 HIS H 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.20 (17776) covalent geometry : angle 0.54243 / 0.27 (24092) hydrogen bonds : bond 0.02956 / 1.96 ( 792) hydrogen bonds : angle 4.29325 / 3.04 ( 2244) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 434 time to evaluate : 0.787 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: D 1 MET cc_start: 0.8584 (ttt) cc_final: 0.8101 (ttt) REVERT: D 33 ARG cc_start: 0.7424 (mtm-85) cc_final: 0.7201 (mtm-85) REVERT: D 167 GLN cc_start: 0.8340 (tt0) cc_final: 0.7648 (pt0) REVERT: D 232 MET cc_start: 0.8390 (mmp) cc_final: 0.7647 (tmm) REVERT: D 286 LYS cc_start: 0.8097 (ttpt) cc_final: 0.7786 (tttm) REVERT: D 294 ARG cc_start: 0.6893 (mtm180) cc_final: 0.6603 (ptp90) REVERT: D 353 LYS cc_start: 0.7209 (mtmt) cc_final: 0.6865 (mttm) REVERT: D 363 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8279 (tt) REVERT: D 463 ILE cc_start: 0.8127 (mt) cc_final: 0.7899 (mp) REVERT: D 498 CYS cc_start: 0.8049 (t) cc_final: 0.7501 (t) REVERT: D 502 GLU cc_start: 0.7482 (pt0) cc_final: 0.6886 (pp20) REVERT: C 1 MET cc_start: 0.8537 (ttt) cc_final: 0.8046 (ttt) REVERT: C 167 GLN cc_start: 0.8334 (tt0) cc_final: 0.7647 (pt0) REVERT: C 232 MET cc_start: 0.8432 (mmp) cc_final: 0.7743 (tmm) REVERT: C 286 LYS cc_start: 0.8094 (ttpt) cc_final: 0.7780 (tttm) REVERT: C 294 ARG cc_start: 0.7056 (mtm180) cc_final: 0.6736 (ptp90) REVERT: C 353 LYS cc_start: 0.7096 (mtmt) cc_final: 0.6744 (mttm) REVERT: C 363 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8276 (tt) REVERT: C 420 ASN cc_start: 0.8970 (t0) cc_final: 0.8719 (t0) REVERT: C 463 ILE cc_start: 0.8121 (mt) cc_final: 0.7901 (mp) REVERT: C 498 CYS cc_start: 0.8063 (t) cc_final: 0.7390 (t) REVERT: C 502 GLU cc_start: 0.7567 (pt0) cc_final: 0.6942 (pp20) REVERT: C 534 MET cc_start: 0.8718 (mmm) cc_final: 0.8378 (mpp) REVERT: H 33 ARG cc_start: 0.7431 (mtm-85) cc_final: 0.7160 (mtm-85) REVERT: H 232 MET cc_start: 0.8402 (mmt) cc_final: 0.7565 (tmm) REVERT: H 268 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7504 (mt-10) REVERT: H 284 LYS cc_start: 0.8048 (mmtm) cc_final: 0.7636 (mmmm) REVERT: H 286 LYS cc_start: 0.8069 (ttpt) cc_final: 0.7666 (tttm) REVERT: H 294 ARG cc_start: 0.7070 (mtm180) cc_final: 0.6753 (ptp-170) REVERT: H 363 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8278 (tt) REVERT: H 420 ASN cc_start: 0.8744 (t0) cc_final: 0.8336 (t0) REVERT: H 463 ILE cc_start: 0.8169 (mt) cc_final: 0.7948 (mp) REVERT: H 498 CYS cc_start: 0.8078 (t) cc_final: 0.7408 (t) REVERT: H 534 MET cc_start: 0.8747 (mmm) cc_final: 0.8449 (mpp) REVERT: G 1 MET cc_start: 0.8604 (ttt) cc_final: 0.8221 (ttt) REVERT: G 167 GLN cc_start: 0.8330 (tt0) cc_final: 0.7635 (pt0) REVERT: G 232 MET cc_start: 0.8470 (mmp) cc_final: 0.7650 (tmm) REVERT: G 286 LYS cc_start: 0.8180 (ttpt) cc_final: 0.7866 (tttm) REVERT: G 311 ARG cc_start: 0.7785 (mmm-85) cc_final: 0.7525 (mmt-90) REVERT: G 363 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8301 (tt) REVERT: G 463 ILE cc_start: 0.8135 (mt) cc_final: 0.7921 (mp) REVERT: G 498 CYS cc_start: 0.8073 (t) cc_final: 0.7418 (t) REVERT: G 534 MET cc_start: 0.8722 (mmm) cc_final: 0.8409 (mpp) outliers start: 28 outliers final: 19 residues processed: 443 average time/residue: 0.9914 time to fit residues: 512.4784 Evaluate side-chains 445 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 422 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 243 CYS Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain D residue 537 SER Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 220 THR Chi-restraints excluded: chain H residue 243 CYS Chi-restraints excluded: chain H residue 363 LEU Chi-restraints excluded: chain H residue 537 SER Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain G residue 243 CYS Chi-restraints excluded: chain G residue 363 LEU Chi-restraints excluded: chain G residue 537 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 123 optimal weight: 0.5980 chunk 141 optimal weight: 0.2980 chunk 90 optimal weight: 0.7980 chunk 213 optimal weight: 0.4980 chunk 41 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 182 optimal weight: 0.9990 chunk 167 optimal weight: 0.7980 chunk 180 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 412 ASN H 167 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.140248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.111614 restraints weight = 59351.965| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.86 r_work: 0.3060 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.5029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17776 Z= 0.113 Angle : 0.509 7.599 24092 Z= 0.252 Chirality : 0.044 0.129 2692 Planarity : 0.004 0.097 3072 Dihedral : 5.853 39.241 2612 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.22 % Allowed : 21.46 % Favored : 77.33 % 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: 0.93 (0.18), residues: 2144 helix: 2.09 (0.17), residues: 908 sheet: -0.92 (0.25), residues: 368 loop : -0.17 (0.22), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG H 389 TYR 0.013 0.001 TYR H 42 PHE 0.021 0.001 PHE H 424 TRP 0.006 0.001 TRP D 358 HIS 0.005 0.001 HIS C 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 (17776) covalent geometry : angle 0.50933 / 0.25 (24092) hydrogen bonds : bond 0.02559 / 1.70 ( 792) hydrogen bonds : angle 4.12723 / 2.92 ( 2244) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 429 time to evaluate : 0.963 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: D 1 MET cc_start: 0.8510 (ttt) cc_final: 0.8036 (ttt) REVERT: D 167 GLN cc_start: 0.8279 (tt0) cc_final: 0.7672 (pt0) REVERT: D 286 LYS cc_start: 0.8007 (ttpt) cc_final: 0.7691 (tttm) REVERT: D 363 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8201 (tt) REVERT: D 420 ASN cc_start: 0.8994 (t0) cc_final: 0.8770 (t0) REVERT: D 463 ILE cc_start: 0.8060 (mt) cc_final: 0.7830 (mp) REVERT: D 498 CYS cc_start: 0.8015 (t) cc_final: 0.7428 (t) REVERT: D 502 GLU cc_start: 0.7481 (pt0) cc_final: 0.6852 (pp20) REVERT: C 1 MET cc_start: 0.8477 (ttt) cc_final: 0.8009 (ttt) REVERT: C 167 GLN cc_start: 0.8289 (tt0) cc_final: 0.7685 (pt0) REVERT: C 232 MET cc_start: 0.8364 (mmp) cc_final: 0.7745 (tmm) REVERT: C 286 LYS cc_start: 0.8048 (ttpt) cc_final: 0.7730 (tttm) REVERT: C 294 ARG cc_start: 0.6981 (mtm180) cc_final: 0.6656 (ptp90) REVERT: C 322 GLU cc_start: 0.8744 (mm-30) cc_final: 0.8167 (mm-30) REVERT: C 333 ASN cc_start: 0.8617 (t0) cc_final: 0.8332 (t0) REVERT: C 363 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8280 (tt) REVERT: C 420 ASN cc_start: 0.8937 (t0) cc_final: 0.8664 (t0) REVERT: C 498 CYS cc_start: 0.7927 (t) cc_final: 0.7143 (t) REVERT: C 502 GLU cc_start: 0.7501 (pt0) cc_final: 0.6852 (pp20) REVERT: C 534 MET cc_start: 0.8635 (mmm) cc_final: 0.8320 (mpp) REVERT: H 1 MET cc_start: 0.8498 (ttt) cc_final: 0.7858 (ttt) REVERT: H 33 ARG cc_start: 0.7371 (mtm-85) cc_final: 0.7132 (mtm-85) REVERT: H 232 MET cc_start: 0.8385 (mmt) cc_final: 0.7507 (tmm) REVERT: H 286 LYS cc_start: 0.7996 (ttpt) cc_final: 0.7598 (tttm) REVERT: H 294 ARG cc_start: 0.6962 (mtm180) cc_final: 0.6637 (ptp-170) REVERT: H 363 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8260 (tt) REVERT: H 420 ASN cc_start: 0.8669 (t0) cc_final: 0.8449 (t0) REVERT: H 498 CYS cc_start: 0.8078 (t) cc_final: 0.7328 (t) REVERT: H 534 MET cc_start: 0.8701 (mmm) cc_final: 0.8406 (mpp) REVERT: G 1 MET cc_start: 0.8557 (ttt) cc_final: 0.8164 (ttt) REVERT: G 167 GLN cc_start: 0.8257 (tt0) cc_final: 0.7646 (pt0) REVERT: G 232 MET cc_start: 0.8372 (mmp) cc_final: 0.7581 (tmm) REVERT: G 286 LYS cc_start: 0.8111 (ttpt) cc_final: 0.7794 (tttm) REVERT: G 363 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8247 (tt) REVERT: G 463 ILE cc_start: 0.8057 (mt) cc_final: 0.7834 (mp) REVERT: G 498 CYS cc_start: 0.7947 (t) cc_final: 0.7180 (t) REVERT: G 534 MET cc_start: 0.8683 (mmm) cc_final: 0.8376 (mpp) outliers start: 23 outliers final: 18 residues processed: 437 average time/residue: 1.0180 time to fit residues: 520.1341 Evaluate side-chains 443 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 421 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 243 CYS Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 537 SER Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 220 THR Chi-restraints excluded: chain H residue 243 CYS Chi-restraints excluded: chain H residue 363 LEU Chi-restraints excluded: chain H residue 537 SER Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain G residue 243 CYS Chi-restraints excluded: chain G residue 363 LEU Chi-restraints excluded: chain G residue 537 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 203 optimal weight: 0.8980 chunk 168 optimal weight: 1.9990 chunk 167 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 210 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 = 0.3542 r_free = 0.3542 target = 0.139535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.110543 restraints weight = 58416.032| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.85 r_work: 0.3025 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.5083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17776 Z= 0.179 Angle : 0.536 7.453 24092 Z= 0.268 Chirality : 0.045 0.128 2692 Planarity : 0.005 0.095 3072 Dihedral : 6.278 43.315 2612 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.48 % Allowed : 21.51 % Favored : 77.01 % 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: 0.80 (0.18), residues: 2144 helix: 1.85 (0.17), residues: 916 sheet: -0.88 (0.25), residues: 368 loop : -0.16 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG H 389 TYR 0.013 0.001 TYR H 42 PHE 0.019 0.001 PHE D 409 TRP 0.007 0.001 TRP H 387 HIS 0.006 0.001 HIS G 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 (17776) covalent geometry : angle 0.53621 / 0.27 (24092) hydrogen bonds : bond 0.02845 / 1.89 ( 792) hydrogen bonds : angle 4.21718 / 2.98 ( 2244) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12298.96 seconds wall clock time: 208 minutes 39.15 seconds (12519.15 seconds total)