Starting phenix.real_space_refine on Thu Jul 2 04:09:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o8h_70227/07_2026/9o8h_70227.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o8h_70227/07_2026/9o8h_70227.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9o8h_70227/07_2026/9o8h_70227.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o8h_70227/07_2026/9o8h_70227.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9o8h_70227/07_2026/9o8h_70227.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o8h_70227/07_2026/9o8h_70227.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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: 5 Type Number sf(0) Gaussians S 20 5.16 5 Cl 10 4.86 5 C 3940 2.51 5 N 1200 2.21 5 O 1220 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6390 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 638 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 70, 514 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Conformer: "B" Number of residues, atoms: 70, 514 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} bond proxies already assigned to first conformer: 393 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CL': 1} Chain breaks: 1 Restraints were copied for chains: B, C, D, E, F, G, H, I, J Residues with excluded nonbonded symmetry interactions: 170 residue: pdb=" N AGLY A 326 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY A 326 " occ=0.50 residue: pdb=" N AASN A 327 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN A 327 " occ=0.50 residue: pdb=" N AILE A 328 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE A 328 " occ=0.50 residue: pdb=" N AHIS A 329 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS A 329 " occ=0.50 residue: pdb=" N AHIS A 330 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS A 330 " occ=0.50 residue: pdb=" N ALYS A 331 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS A 331 " occ=0.50 residue: pdb=" N APRO A 332 " occ=0.50 ... (12 atoms not shown) pdb=" CD BPRO A 332 " occ=0.50 residue: pdb=" N AGLY A 333 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY A 333 " occ=0.50 residue: pdb=" N AGLY A 334 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY A 334 " occ=0.50 residue: pdb=" N AGLY A 335 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY A 335 " occ=0.50 residue: pdb=" N AGLN A 336 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN A 336 " occ=0.50 residue: pdb=" N AVAL A 337 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BVAL A 337 " occ=0.50 ... (remaining 158 not shown) Time building chain proxies: 0.74, per 1000 atoms: 0.12 Number of scatterers: 6390 At special positions: 0 Unit cell: (82.39, 123.05, 46.01, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 10 17.00 S 20 16.00 O 1220 8.00 N 1200 7.00 C 3940 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 322 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 322 " distance=2.02 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 322 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 322 " distance=2.03 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 322 " distance=2.03 Simple disulfide: pdb=" SG CYS F 291 " - pdb=" SG CYS F 322 " distance=2.03 Simple disulfide: pdb=" SG CYS G 291 " - pdb=" SG CYS G 322 " distance=2.02 Simple disulfide: pdb=" SG CYS H 291 " - pdb=" SG CYS H 322 " distance=2.03 Simple disulfide: pdb=" SG CYS I 291 " - pdb=" SG CYS I 322 " distance=2.02 Simple disulfide: pdb=" SG CYS J 291 " - pdb=" SG CYS J 322 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.38 Conformation dependent library (CDL) restraints added in 465.2 milliseconds 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1460 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 55.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'H' and resid 274 through 283 removed outlier: 6.561A pdb=" N LYS A 274 " --> pdb=" O VAL E 275 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N ILE E 277 " --> pdb=" O LYS A 274 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N GLN A 276 " --> pdb=" O ILE E 277 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ASN E 279 " --> pdb=" O GLN A 276 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ILE A 278 " --> pdb=" O ASN E 279 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N LYS E 281 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LYS A 280 " --> pdb=" O LYS E 281 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N ASP E 283 " --> pdb=" O LYS A 280 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU A 282 " --> pdb=" O ASP E 283 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LYS E 274 " --> pdb=" O VAL I 275 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N ILE I 277 " --> pdb=" O LYS E 274 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N GLN E 276 " --> pdb=" O ILE I 277 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ASN I 279 " --> pdb=" O GLN E 276 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ILE E 278 " --> pdb=" O ASN I 279 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N LYS I 281 " --> pdb=" O ILE E 278 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LYS E 280 " --> pdb=" O LYS I 281 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N ASP I 283 " --> pdb=" O LYS E 280 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU E 282 " --> pdb=" O ASP I 283 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 294 through 298 removed outlier: 8.899A pdb=" N LYS D 294 " --> pdb=" O ASP H 295 " (cutoff:3.500A) removed outlier: 9.342A pdb=" N ILE H 297 " --> pdb=" O LYS D 294 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N ASN D 296 " --> pdb=" O ILE H 297 " (cutoff:3.500A) removed outlier: 8.905A pdb=" N LYS A 294 " --> pdb=" O ASP D 295 " (cutoff:3.500A) removed outlier: 9.350A pdb=" N ILE D 297 " --> pdb=" O LYS A 294 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N ASN A 296 " --> pdb=" O ILE D 297 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ASP A 295 " --> pdb=" O LYS E 294 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ASN E 296 " --> pdb=" O ASP A 295 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ASP E 295 " --> pdb=" O LYS I 294 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ASN I 296 " --> pdb=" O ASP E 295 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 305 through 310 removed outlier: 6.301A pdb=" N SER D 305 " --> pdb=" O VAL H 306 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N ILE H 308 " --> pdb=" O SER D 305 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N GLN D 307 " --> pdb=" O ILE H 308 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N TYR H 310 " --> pdb=" O GLN D 307 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL D 309 " --> pdb=" O TYR H 310 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N SER A 305 " --> pdb=" O VAL D 306 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ILE D 308 " --> pdb=" O SER A 305 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLN A 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N TYR D 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL A 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 313 through 328 removed outlier: 5.413A pdb=" N ASP A 314 " --> pdb=" O LEU E 315 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LYS E 317 " --> pdb=" O ASP A 314 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N SER A 316 " --> pdb=" O LYS E 317 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N THR E 319 " --> pdb=" O SER A 316 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL A 318 " --> pdb=" O THR E 319 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N LYS E 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N SER A 320 " --> pdb=" O LYS E 321 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N GLY E 323 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N CYS A 322 " --> pdb=" O GLY E 323 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N LEU E 325 " --> pdb=" O CYS A 322 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N SER A 324 " --> pdb=" O LEU E 325 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N AASN E 327 " --> pdb=" O SER A 324 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N AGLY A 326 " --> pdb=" O AASN E 327 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N ASP E 314 " --> pdb=" O LEU I 315 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LYS I 317 " --> pdb=" O ASP E 314 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N SER E 316 " --> pdb=" O LYS I 317 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N THR I 319 " --> pdb=" O SER E 316 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL E 318 " --> pdb=" O THR I 319 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N LYS I 321 " --> pdb=" O VAL E 318 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N SER E 320 " --> pdb=" O LYS I 321 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N GLY I 323 " --> pdb=" O SER E 320 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N CYS E 322 " --> pdb=" O GLY I 323 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N LEU I 325 " --> pdb=" O CYS E 322 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N SER E 324 " --> pdb=" O LEU I 325 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N AASN I 327 " --> pdb=" O SER E 324 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N AGLY E 326 " --> pdb=" O AASN I 327 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 335 through 341 removed outlier: 4.297A pdb=" N BGLN D 336 " --> pdb=" O BGLY H 335 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N BGLN A 336 " --> pdb=" O BGLY D 335 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N AGLY A 335 " --> pdb=" O AGLN E 336 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N AGLU E 338 " --> pdb=" O AGLY A 335 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N AVAL A 337 " --> pdb=" O AGLU E 338 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N ALYS E 340 " --> pdb=" O AVAL A 337 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N AVAL A 339 " --> pdb=" O ALYS E 340 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N AGLY E 335 " --> pdb=" O AGLN I 336 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N AGLU I 338 " --> pdb=" O AGLY E 335 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N AVAL E 337 " --> pdb=" O AGLU I 338 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N ALYS I 340 " --> pdb=" O AVAL E 337 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N AVAL E 339 " --> pdb=" O ALYS I 340 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 274 through 283 removed outlier: 6.561A pdb=" N LYS B 274 " --> pdb=" O VAL C 275 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N ILE C 277 " --> pdb=" O LYS B 274 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N GLN B 276 " --> pdb=" O ILE C 277 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ASN C 279 " --> pdb=" O GLN B 276 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ILE B 278 " --> pdb=" O ASN C 279 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N LYS C 281 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LYS B 280 " --> pdb=" O LYS C 281 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N ASP C 283 " --> pdb=" O LYS B 280 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU B 282 " --> pdb=" O ASP C 283 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LYS C 274 " --> pdb=" O VAL G 275 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N ILE G 277 " --> pdb=" O LYS C 274 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N GLN C 276 " --> pdb=" O ILE G 277 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ASN G 279 " --> pdb=" O GLN C 276 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ILE C 278 " --> pdb=" O ASN G 279 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N LYS G 281 " --> pdb=" O ILE C 278 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LYS C 280 " --> pdb=" O LYS G 281 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N ASP G 283 " --> pdb=" O LYS C 280 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU C 282 " --> pdb=" O ASP G 283 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LYS G 274 " --> pdb=" O VAL J 275 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N ILE J 277 " --> pdb=" O LYS G 274 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N GLN G 276 " --> pdb=" O ILE J 277 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ASN J 279 " --> pdb=" O GLN G 276 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ILE G 278 " --> pdb=" O ASN J 279 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N LYS J 281 " --> pdb=" O ILE G 278 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LYS G 280 " --> pdb=" O LYS J 281 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N ASP J 283 " --> pdb=" O LYS G 280 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU G 282 " --> pdb=" O ASP J 283 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 294 through 298 removed outlier: 8.899A pdb=" N LYS B 294 " --> pdb=" O ASP F 295 " (cutoff:3.500A) removed outlier: 9.342A pdb=" N ILE F 297 " --> pdb=" O LYS B 294 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N ASN B 296 " --> pdb=" O ILE F 297 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ASP B 295 " --> pdb=" O LYS C 294 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ASN C 296 " --> pdb=" O ASP B 295 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ASP C 295 " --> pdb=" O LYS G 294 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ASN G 296 " --> pdb=" O ASP C 295 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ASP G 295 " --> pdb=" O LYS J 294 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ASN J 296 " --> pdb=" O ASP G 295 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 305 through 310 removed outlier: 6.300A pdb=" N SER B 305 " --> pdb=" O VAL F 306 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N ILE F 308 " --> pdb=" O SER B 305 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N GLN B 307 " --> pdb=" O ILE F 308 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N TYR F 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL B 309 " --> pdb=" O TYR F 310 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 313 through 328 removed outlier: 5.420A pdb=" N ASP B 314 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LYS C 317 " --> pdb=" O ASP B 314 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N SER B 316 " --> pdb=" O LYS C 317 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N THR C 319 " --> pdb=" O SER B 316 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL B 318 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N LYS C 321 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N SER B 320 " --> pdb=" O LYS C 321 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N GLY C 323 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N CYS B 322 " --> pdb=" O GLY C 323 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N LEU C 325 " --> pdb=" O CYS B 322 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N SER B 324 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N AASN C 327 " --> pdb=" O SER B 324 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N AGLY B 326 " --> pdb=" O AASN C 327 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N ASP C 314 " --> pdb=" O LEU G 315 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LYS G 317 " --> pdb=" O ASP C 314 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N SER C 316 " --> pdb=" O LYS G 317 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N THR G 319 " --> pdb=" O SER C 316 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL C 318 " --> pdb=" O THR G 319 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N LYS G 321 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N SER C 320 " --> pdb=" O LYS G 321 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N GLY G 323 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N CYS C 322 " --> pdb=" O GLY G 323 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N LEU G 325 " --> pdb=" O CYS C 322 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N SER C 324 " --> pdb=" O LEU G 325 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N AASN G 327 " --> pdb=" O SER C 324 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N AGLY C 326 " --> pdb=" O AASN G 327 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ASP G 314 " --> pdb=" O LEU J 315 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LYS J 317 " --> pdb=" O ASP G 314 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N SER G 316 " --> pdb=" O LYS J 317 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N THR J 319 " --> pdb=" O SER G 316 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL G 318 " --> pdb=" O THR J 319 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N LYS J 321 " --> pdb=" O VAL G 318 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N SER G 320 " --> pdb=" O LYS J 321 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N GLY J 323 " --> pdb=" O SER G 320 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N CYS G 322 " --> pdb=" O GLY J 323 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N LEU J 325 " --> pdb=" O CYS G 322 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N SER G 324 " --> pdb=" O LEU J 325 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N AASN J 327 " --> pdb=" O SER G 324 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N AGLY G 326 " --> pdb=" O AASN J 327 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 335 through 341 removed outlier: 4.298A pdb=" N BGLN B 336 " --> pdb=" O BGLY F 335 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N AGLY B 335 " --> pdb=" O AGLN C 336 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N AGLU C 338 " --> pdb=" O AGLY B 335 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N AVAL B 337 " --> pdb=" O AGLU C 338 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N ALYS C 340 " --> pdb=" O AVAL B 337 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N AVAL B 339 " --> pdb=" O ALYS C 340 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N AGLY C 335 " --> pdb=" O AGLN G 336 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N AGLU G 338 " --> pdb=" O AGLY C 335 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N AVAL C 337 " --> pdb=" O AGLU G 338 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N ALYS G 340 " --> pdb=" O AVAL C 337 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N AVAL C 339 " --> pdb=" O ALYS G 340 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N AGLY G 335 " --> pdb=" O AGLN J 336 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N AGLU J 338 " --> pdb=" O AGLY G 335 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N AVAL G 337 " --> pdb=" O AGLU J 338 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N ALYS J 340 " --> pdb=" O AVAL G 337 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N AVAL G 339 " --> pdb=" O ALYS J 340 " (cutoff:3.500A) 149 hydrogen bonds defined for protein. 447 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: 0.80 Time building geometry restraints manager: 0.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2140 1.34 - 1.45: 824 1.45 - 1.57: 3486 1.57 - 1.68: 0 1.68 - 1.80: 20 Bond restraints: 6470 Sorted by residual: bond pdb=" CA LEU J 315 " pdb=" CB LEU J 315 " ideal model delta sigma weight residual 1.527 1.443 0.083 1.75e-02 3.27e+03 2.27e+01 bond pdb=" CA LEU I 315 " pdb=" CB LEU I 315 " ideal model delta sigma weight residual 1.527 1.443 0.083 1.75e-02 3.27e+03 2.27e+01 bond pdb=" CA LEU G 315 " pdb=" CB LEU G 315 " ideal model delta sigma weight residual 1.527 1.444 0.083 1.75e-02 3.27e+03 2.26e+01 bond pdb=" CA LEU A 315 " pdb=" CB LEU A 315 " ideal model delta sigma weight residual 1.527 1.444 0.083 1.75e-02 3.27e+03 2.25e+01 bond pdb=" CA LEU B 315 " pdb=" CB LEU B 315 " ideal model delta sigma weight residual 1.527 1.444 0.083 1.75e-02 3.27e+03 2.25e+01 ... (remaining 6465 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.08: 6787 1.08 - 2.15: 1400 2.15 - 3.23: 377 3.23 - 4.30: 76 4.30 - 5.38: 10 Bond angle restraints: 8650 Sorted by residual: angle pdb=" CA VAL I 318 " pdb=" C VAL I 318 " pdb=" O VAL I 318 " ideal model delta sigma weight residual 120.53 117.78 2.75 1.07e+00 8.73e-01 6.60e+00 angle pdb=" CA VAL E 318 " pdb=" C VAL E 318 " pdb=" O VAL E 318 " ideal model delta sigma weight residual 120.39 117.72 2.67 1.04e+00 9.25e-01 6.59e+00 angle pdb=" CA VAL F 318 " pdb=" C VAL F 318 " pdb=" O VAL F 318 " ideal model delta sigma weight residual 120.53 117.81 2.72 1.07e+00 8.73e-01 6.49e+00 angle pdb=" CA VAL D 318 " pdb=" C VAL D 318 " pdb=" O VAL D 318 " ideal model delta sigma weight residual 120.39 117.76 2.63 1.04e+00 9.25e-01 6.41e+00 angle pdb=" CA VAL C 318 " pdb=" C VAL C 318 " pdb=" O VAL C 318 " ideal model delta sigma weight residual 120.53 117.83 2.70 1.07e+00 8.73e-01 6.39e+00 ... (remaining 8645 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.52: 3432 14.52 - 29.04: 438 29.04 - 43.56: 70 43.56 - 58.08: 20 58.08 - 72.60: 20 Dihedral angle restraints: 3980 sinusoidal: 1650 harmonic: 2330 Sorted by residual: dihedral pdb=" CA VAL I 313 " pdb=" C VAL I 313 " pdb=" N ASP I 314 " pdb=" CA ASP I 314 " ideal model delta harmonic sigma weight residual -180.00 -158.97 -21.03 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA VAL G 313 " pdb=" C VAL G 313 " pdb=" N ASP G 314 " pdb=" CA ASP G 314 " ideal model delta harmonic sigma weight residual -180.00 -159.00 -21.00 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA VAL B 313 " pdb=" C VAL B 313 " pdb=" N ASP B 314 " pdb=" CA ASP B 314 " ideal model delta harmonic sigma weight residual -180.00 -159.01 -20.99 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 3977 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 502 0.044 - 0.088: 252 0.088 - 0.131: 146 0.131 - 0.175: 11 0.175 - 0.219: 39 Chirality restraints: 950 Sorted by residual: chirality pdb=" CA VAL D 309 " pdb=" N VAL D 309 " pdb=" C VAL D 309 " pdb=" CB VAL D 309 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA VAL C 309 " pdb=" N VAL C 309 " pdb=" C VAL C 309 " pdb=" CB VAL C 309 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA VAL E 309 " pdb=" N VAL E 309 " pdb=" C VAL E 309 " pdb=" CB VAL E 309 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 947 not shown) Planarity restraints: 1130 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 290 " 0.020 2.00e-02 2.50e+03 4.12e-02 1.70e+01 pdb=" C LYS B 290 " -0.071 2.00e-02 2.50e+03 pdb=" O LYS B 290 " 0.027 2.00e-02 2.50e+03 pdb=" N CYS B 291 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS H 290 " -0.020 2.00e-02 2.50e+03 4.12e-02 1.70e+01 pdb=" C LYS H 290 " 0.071 2.00e-02 2.50e+03 pdb=" O LYS H 290 " -0.027 2.00e-02 2.50e+03 pdb=" N CYS H 291 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 290 " -0.020 2.00e-02 2.50e+03 4.10e-02 1.68e+01 pdb=" C LYS A 290 " 0.071 2.00e-02 2.50e+03 pdb=" O LYS A 290 " -0.027 2.00e-02 2.50e+03 pdb=" N CYS A 291 " -0.024 2.00e-02 2.50e+03 ... (remaining 1127 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1485 2.80 - 3.32: 5463 3.32 - 3.85: 10429 3.85 - 4.37: 10666 4.37 - 4.90: 23949 Nonbonded interactions: 51992 Sorted by model distance: nonbonded pdb=" OD1 ASP E 314 " pdb=" OG SER E 316 " model vdw 2.272 3.040 nonbonded pdb=" OD1 ASP J 314 " pdb=" OG SER J 316 " model vdw 2.272 3.040 nonbonded pdb=" OD1 ASP A 314 " pdb=" OG SER A 316 " model vdw 2.273 3.040 nonbonded pdb=" OD1 ASP I 314 " pdb=" OG SER I 316 " model vdw 2.273 3.040 nonbonded pdb=" OD1 ASP D 314 " pdb=" OG SER D 316 " model vdw 2.273 3.040 ... (remaining 51987 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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=0.50 max=1.00 mean=0.81 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: 2.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.230 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.083 6480 Z= 0.626 Angle : 0.987 5.380 8670 Z= 0.589 Chirality : 0.070 0.219 950 Planarity : 0.009 0.041 1130 Dihedral : 13.735 72.598 2490 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.29 % Favored : 89.71 % Rotamer: Outliers : 5.48 % Allowed : 19.18 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.66 (0.22), residues: 850 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.78 (0.17), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.004 TYR H 310 HIS 0.002 0.001 HIS E 299 Details of bonding type rmsd/Z covalent geometry : bond 0.01287 / 0.63 ( 6470) covalent geometry : angle 0.98369 / 0.59 ( 8650) SS BOND : bond 0.00575 / 0.39 ( 10) SS BOND : angle 1.85682 / 1.13 ( 20) hydrogen bonds : bond 0.15002 / 9.88 ( 149) hydrogen bonds : angle 10.81816 / 7.20 ( 447) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 155 time to evaluate : 0.121 Fit side-chains REVERT: B 311 LYS cc_start: 0.8846 (mttt) cc_final: 0.8525 (mttm) REVERT: D 280 LYS cc_start: 0.9105 (tttt) cc_final: 0.8815 (tttt) REVERT: F 290 LYS cc_start: 0.8369 (ttpt) cc_final: 0.7219 (ttpt) REVERT: F 311 LYS cc_start: 0.8877 (mttt) cc_final: 0.7539 (pttm) REVERT: H 290 LYS cc_start: 0.8358 (ttpt) cc_final: 0.7231 (ttpt) REVERT: H 311 LYS cc_start: 0.8771 (mttt) cc_final: 0.8508 (mttm) REVERT: I 298 LYS cc_start: 0.8914 (mttt) cc_final: 0.7616 (mmtt) REVERT: I 309 VAL cc_start: 0.9188 (t) cc_final: 0.8922 (p) REVERT: I 311 LYS cc_start: 0.8591 (mttt) cc_final: 0.7700 (mmtt) REVERT: J 298 LYS cc_start: 0.8881 (mttt) cc_final: 0.7486 (mmtt) REVERT: J 311 LYS cc_start: 0.8531 (mttt) cc_final: 0.7534 (mmtt) outliers start: 20 outliers final: 8 residues processed: 165 average time/residue: 0.1134 time to fit residues: 22.7127 Evaluate side-chains 133 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 125 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain H residue 275 VAL Chi-restraints excluded: chain I residue 275 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 9.9990 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 7.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 307 GLN A 327 ASN B ** A 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 ASN ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 ASN B ** B 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 286 ASN C 296 ASN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 ASN B ** C 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 329 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 327 ASN B ** D 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** E 299 HIS E 327 ASN B ** E 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** F 296 ASN ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 327 ASN B ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 296 ASN ** G 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 327 ASN B ** G 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 329 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 327 ASN B I 276 GLN I 299 HIS I 327 ASN B ** I 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 329 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 286 ASN J 296 ASN J 299 HIS J 327 ASN B ** J 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 329 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4871 r_free = 0.4871 target = 0.218410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.174861 restraints weight = 45868.401| |-----------------------------------------------------------------------------| r_work (start): 0.4535 rms_B_bonded: 6.30 r_work: 0.4259 rms_B_bonded: 5.54 restraints_weight: 2.0000 r_work (final): 0.4259 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4251 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4251 r_free = 0.4251 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4250 r_free = 0.4250 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.4250 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6480 Z= 0.181 Angle : 0.637 5.035 8670 Z= 0.341 Chirality : 0.051 0.148 950 Planarity : 0.005 0.030 1130 Dihedral : 6.581 27.856 878 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 3.70 % Allowed : 21.23 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.61 (0.22), residues: 850 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.75 (0.17), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.003 TYR C 310 HIS 0.001 0.001 HIS D 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 ( 6470) covalent geometry : angle 0.63716 / 0.34 ( 8650) SS BOND : bond 0.00063 / 0.04 ( 10) SS BOND : angle 0.54156 / 0.30 ( 20) hydrogen bonds : bond 0.03231 / 2.03 ( 149) hydrogen bonds : angle 7.05734 / 4.72 ( 447) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 143 time to evaluate : 0.190 Fit side-chains REVERT: B 282 LEU cc_start: 0.9025 (mm) cc_final: 0.8822 (mm) REVERT: B 290 LYS cc_start: 0.8796 (ttmt) cc_final: 0.8228 (tttm) REVERT: B 311 LYS cc_start: 0.8887 (mttt) cc_final: 0.8499 (mttm) REVERT: C 290 LYS cc_start: 0.8813 (ttpt) cc_final: 0.8146 (tttp) REVERT: F 290 LYS cc_start: 0.8701 (ttpt) cc_final: 0.7560 (ttpt) REVERT: F 311 LYS cc_start: 0.8593 (mttt) cc_final: 0.7454 (pttm) REVERT: F 320 SER cc_start: 0.9011 (m) cc_final: 0.8757 (p) REVERT: H 311 LYS cc_start: 0.8715 (mttt) cc_final: 0.8384 (mttm) REVERT: J 298 LYS cc_start: 0.8646 (mttt) cc_final: 0.7339 (mmtt) REVERT: J 311 LYS cc_start: 0.8450 (mttt) cc_final: 0.7343 (mmtt) outliers start: 6 outliers final: 5 residues processed: 145 average time/residue: 0.0818 time to fit residues: 15.3747 Evaluate side-chains 139 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 134 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain G residue 275 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 26 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 38 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 68 optimal weight: 0.0370 chunk 20 optimal weight: 20.0000 chunk 40 optimal weight: 6.9990 chunk 27 optimal weight: 30.0000 overall best weight: 2.3464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 307 GLN ** A 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 ASN ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 ASN ** C 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 329 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** F 296 ASN ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 286 ASN G 296 ASN ** G 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 329 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 329 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 296 ASN ** J 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 329 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4832 r_free = 0.4832 target = 0.214733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.169934 restraints weight = 32849.019| |-----------------------------------------------------------------------------| r_work (start): 0.4480 rms_B_bonded: 5.47 r_work: 0.4226 rms_B_bonded: 5.11 restraints_weight: 2.0000 r_work (final): 0.4226 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4167 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4167 r_free = 0.4167 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4167 r_free = 0.4167 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4167 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 6480 Z= 0.199 Angle : 0.615 5.426 8670 Z= 0.325 Chirality : 0.051 0.146 950 Planarity : 0.004 0.026 1130 Dihedral : 6.131 30.102 873 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 4.93 % Allowed : 19.45 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.55 (0.23), residues: 850 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.70 (0.18), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.003 TYR C 310 HIS 0.001 0.001 HIS H 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.20 ( 6470) covalent geometry : angle 0.61470 / 0.33 ( 8650) SS BOND : bond 0.00304 / 0.20 ( 10) SS BOND : angle 0.69125 / 0.39 ( 20) hydrogen bonds : bond 0.02890 / 1.79 ( 149) hydrogen bonds : angle 6.51055 / 4.36 ( 447) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 135 time to evaluate : 0.219 Fit side-chains REVERT: B 282 LEU cc_start: 0.9018 (mm) cc_final: 0.8745 (mm) REVERT: B 290 LYS cc_start: 0.8680 (ttmt) cc_final: 0.8082 (tttm) REVERT: B 311 LYS cc_start: 0.8861 (mttt) cc_final: 0.8470 (mttm) REVERT: F 290 LYS cc_start: 0.8709 (ttpt) cc_final: 0.7548 (ttpt) REVERT: F 311 LYS cc_start: 0.8619 (mttt) cc_final: 0.7453 (pttm) REVERT: F 320 SER cc_start: 0.8937 (m) cc_final: 0.8570 (p) REVERT: H 311 LYS cc_start: 0.8763 (mttt) cc_final: 0.8485 (mttp) REVERT: I 296 ASN cc_start: 0.8287 (m-40) cc_final: 0.7188 (p0) REVERT: J 298 LYS cc_start: 0.8619 (mttt) cc_final: 0.7334 (mmtt) REVERT: J 311 LYS cc_start: 0.8090 (mttt) cc_final: 0.7109 (mmtt) outliers start: 14 outliers final: 11 residues processed: 138 average time/residue: 0.0752 time to fit residues: 13.9681 Evaluate side-chains 141 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 130 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 325 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 36 optimal weight: 0.0010 chunk 58 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 20 optimal weight: 30.0000 chunk 15 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 overall best weight: 2.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 307 GLN ** A 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 ASN ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 ASN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** F 296 ASN ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 286 ASN G 296 ASN ** G 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 329 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 329 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 296 ASN ** J 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 329 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4841 r_free = 0.4841 target = 0.214890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.169614 restraints weight = 37260.052| |-----------------------------------------------------------------------------| r_work (start): 0.4495 rms_B_bonded: 6.98 r_work: 0.4128 rms_B_bonded: 6.27 restraints_weight: 2.0000 r_work (final): 0.4128 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4080 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4080 r_free = 0.4080 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4080 r_free = 0.4080 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4080 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6480 Z= 0.209 Angle : 0.606 5.295 8670 Z= 0.321 Chirality : 0.051 0.147 950 Planarity : 0.004 0.025 1130 Dihedral : 5.983 26.747 873 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 5.21 % Allowed : 20.00 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.50 (0.24), residues: 850 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.66 (0.18), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.015 0.003 TYR C 310 HIS 0.001 0.001 HIS F 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.21 ( 6470) covalent geometry : angle 0.60615 / 0.32 ( 8650) SS BOND : bond 0.00276 / 0.17 ( 10) SS BOND : angle 0.61496 / 0.34 ( 20) hydrogen bonds : bond 0.02602 / 1.58 ( 149) hydrogen bonds : angle 6.19033 / 4.17 ( 447) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 0.201 Fit side-chains REVERT: A 276 GLN cc_start: 0.8897 (tt0) cc_final: 0.8617 (tt0) REVERT: B 282 LEU cc_start: 0.9071 (mm) cc_final: 0.8831 (mm) REVERT: B 290 LYS cc_start: 0.8605 (ttmt) cc_final: 0.8002 (tttm) REVERT: B 311 LYS cc_start: 0.8851 (mttt) cc_final: 0.8474 (mttm) REVERT: F 290 LYS cc_start: 0.8686 (ttpt) cc_final: 0.7471 (ttpt) REVERT: F 311 LYS cc_start: 0.8734 (mttt) cc_final: 0.7343 (pttm) REVERT: F 320 SER cc_start: 0.8946 (m) cc_final: 0.8581 (p) REVERT: H 311 LYS cc_start: 0.8772 (mttt) cc_final: 0.8459 (mttp) REVERT: I 296 ASN cc_start: 0.8429 (m-40) cc_final: 0.7281 (p0) REVERT: J 296 ASN cc_start: 0.8223 (m110) cc_final: 0.7158 (p0) REVERT: J 298 LYS cc_start: 0.8522 (mttt) cc_final: 0.8251 (mtpp) outliers start: 14 outliers final: 12 residues processed: 132 average time/residue: 0.0689 time to fit residues: 12.5551 Evaluate side-chains 140 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 128 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 288 GLN Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 325 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 60 optimal weight: 0.4980 chunk 29 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 37 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 chunk 4 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 ASN A 307 GLN ** A 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 ASN ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 ASN ** D 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 ASN ** E 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** F 299 HIS ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 329 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 296 ASN ** I 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 296 ASN ** I 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 329 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** I 330 HIS A ** J 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 329 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4999 r_free = 0.4999 target = 0.229107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.183312 restraints weight = 36203.928| |-----------------------------------------------------------------------------| r_work (start): 0.4651 rms_B_bonded: 6.52 r_work: 0.4359 rms_B_bonded: 5.89 restraints_weight: 2.0000 r_work (final): 0.4359 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4381 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4381 r_free = 0.4381 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4381 r_free = 0.4381 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4381 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 6480 Z= 0.089 Angle : 0.533 5.721 8670 Z= 0.277 Chirality : 0.049 0.134 950 Planarity : 0.004 0.029 1130 Dihedral : 5.414 24.765 873 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 4.93 % Allowed : 20.41 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.37 (0.24), residues: 850 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.56 (0.19), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR C 310 HIS 0.001 0.000 HIS E 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.09 ( 6470) covalent geometry : angle 0.53360 / 0.28 ( 8650) SS BOND : bond 0.00080 / 0.05 ( 10) SS BOND : angle 0.42260 / 0.23 ( 20) hydrogen bonds : bond 0.01812 / 1.13 ( 149) hydrogen bonds : angle 5.54583 / 3.76 ( 447) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 134 time to evaluate : 0.190 Fit side-chains REVERT: B 282 LEU cc_start: 0.8953 (mm) cc_final: 0.8750 (mm) REVERT: D 280 LYS cc_start: 0.9342 (tttt) cc_final: 0.9099 (tttt) REVERT: F 320 SER cc_start: 0.8998 (m) cc_final: 0.8730 (p) REVERT: G 282 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8535 (mm) REVERT: G 290 LYS cc_start: 0.8540 (ttmt) cc_final: 0.8138 (ttmm) REVERT: H 280 LYS cc_start: 0.9075 (tttt) cc_final: 0.8742 (tttm) REVERT: H 290 LYS cc_start: 0.8553 (ttpt) cc_final: 0.7554 (ttpt) REVERT: H 311 LYS cc_start: 0.8461 (mttt) cc_final: 0.8245 (mttm) REVERT: I 296 ASN cc_start: 0.8380 (m110) cc_final: 0.7359 (p0) REVERT: J 296 ASN cc_start: 0.8108 (m110) cc_final: 0.7109 (p0) REVERT: J 298 LYS cc_start: 0.8510 (mttm) cc_final: 0.8187 (mtpp) REVERT: J 311 LYS cc_start: 0.7950 (mttt) cc_final: 0.7128 (mmtt) outliers start: 12 outliers final: 8 residues processed: 140 average time/residue: 0.0759 time to fit residues: 13.9829 Evaluate side-chains 141 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 132 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 282 LEU Chi-restraints excluded: chain G residue 320 SER Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain I residue 325 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 44 optimal weight: 7.9990 chunk 34 optimal weight: 30.0000 chunk 15 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 27 optimal weight: 30.0000 chunk 36 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 276 GLN ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 ASN ** A 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 ASN ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 GLN ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 ASN ** C 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 329 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 ASN ** D 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 ASN ** E 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** F 296 ASN G 296 ASN ** G 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 329 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** H 296 ASN I 276 GLN I 296 ASN ** I 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 329 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** J 296 ASN ** J 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 329 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4784 r_free = 0.4784 target = 0.209702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.163982 restraints weight = 35726.766| |-----------------------------------------------------------------------------| r_work (start): 0.4440 rms_B_bonded: 6.45 r_work: 0.4141 rms_B_bonded: 5.24 restraints_weight: 2.0000 r_work (final): 0.4141 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4131 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4131 r_free = 0.4131 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4130 r_free = 0.4130 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4130 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.050 6480 Z= 0.328 Angle : 0.682 5.762 8670 Z= 0.364 Chirality : 0.053 0.215 950 Planarity : 0.004 0.031 1130 Dihedral : 6.045 32.131 872 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.59 % Allowed : 8.97 % Favored : 90.44 % Rotamer: Outliers : 5.89 % Allowed : 21.37 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.45 (0.24), residues: 850 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.62 (0.19), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.018 0.003 TYR C 310 HIS 0.003 0.001 HIS D 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00753 / 0.33 ( 6470) covalent geometry : angle 0.68065 / 0.36 ( 8650) SS BOND : bond 0.00515 / 0.33 ( 10) SS BOND : angle 1.05233 / 0.61 ( 20) hydrogen bonds : bond 0.02947 / 1.81 ( 149) hydrogen bonds : angle 6.22956 / 4.22 ( 447) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 0.219 Fit side-chains REVERT: B 282 LEU cc_start: 0.9084 (mm) cc_final: 0.8837 (mm) REVERT: B 290 LYS cc_start: 0.8768 (ttmt) cc_final: 0.8253 (ttmm) REVERT: B 311 LYS cc_start: 0.8843 (mttt) cc_final: 0.8460 (mttm) REVERT: F 290 LYS cc_start: 0.8815 (ttpt) cc_final: 0.7621 (ttpt) REVERT: F 311 LYS cc_start: 0.8784 (mttt) cc_final: 0.7555 (pttm) REVERT: F 320 SER cc_start: 0.9093 (m) cc_final: 0.8622 (p) REVERT: I 296 ASN cc_start: 0.8331 (m-40) cc_final: 0.7262 (p0) REVERT: J 296 ASN cc_start: 0.8100 (m-40) cc_final: 0.7054 (p0) outliers start: 19 outliers final: 15 residues processed: 134 average time/residue: 0.0507 time to fit residues: 9.6528 Evaluate side-chains 140 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 GLN Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 288 GLN Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 320 SER Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 325 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 19 optimal weight: 8.9990 chunk 28 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 chunk 7 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 276 GLN ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 ASN A 307 GLN ** A 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 ASN ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 ASN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 ASN ** D 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** E 276 GLN ** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 ASN ** E 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** F 296 ASN ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 296 ASN ** G 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 329 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 296 ASN I 276 GLN ** I 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 296 ASN ** I 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 329 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 296 ASN ** J 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 329 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4973 r_free = 0.4973 target = 0.225433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.179817 restraints weight = 33573.702| |-----------------------------------------------------------------------------| r_work (start): 0.4612 rms_B_bonded: 5.94 r_work: 0.4354 rms_B_bonded: 5.55 restraints_weight: 2.0000 r_work (final): 0.4354 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4364 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4364 r_free = 0.4364 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4365 r_free = 0.4365 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4365 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6480 Z= 0.102 Angle : 0.555 5.912 8670 Z= 0.288 Chirality : 0.050 0.201 950 Planarity : 0.004 0.032 1130 Dihedral : 5.462 29.121 872 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.74 % Allowed : 5.59 % Favored : 93.68 % Rotamer: Outliers : 5.75 % Allowed : 20.96 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.30 (0.25), residues: 850 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.50 (0.19), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR C 310 HIS 0.001 0.000 HIS D 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 ( 6470) covalent geometry : angle 0.55567 / 0.29 ( 8650) SS BOND : bond 0.00083 / 0.06 ( 10) SS BOND : angle 0.43068 / 0.25 ( 20) hydrogen bonds : bond 0.01853 / 1.19 ( 149) hydrogen bonds : angle 5.54040 / 3.79 ( 447) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 141 time to evaluate : 0.171 Fit side-chains REVERT: B 290 LYS cc_start: 0.8560 (ttmt) cc_final: 0.8049 (tttm) REVERT: D 280 LYS cc_start: 0.9327 (tttt) cc_final: 0.9068 (tttt) REVERT: F 320 SER cc_start: 0.9025 (m) cc_final: 0.8662 (p) REVERT: G 290 LYS cc_start: 0.8567 (ttmt) cc_final: 0.8127 (ttmm) REVERT: H 290 LYS cc_start: 0.8515 (ttpt) cc_final: 0.7719 (ttpt) REVERT: I 296 ASN cc_start: 0.8498 (m110) cc_final: 0.7428 (p0) REVERT: J 296 ASN cc_start: 0.8162 (m110) cc_final: 0.7193 (p0) REVERT: J 298 LYS cc_start: 0.8492 (mttm) cc_final: 0.8178 (mtpp) REVERT: J 311 LYS cc_start: 0.8042 (mttt) cc_final: 0.7214 (mmtt) outliers start: 17 outliers final: 11 residues processed: 148 average time/residue: 0.0690 time to fit residues: 13.8019 Evaluate side-chains 153 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 142 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 320 SER Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain I residue 325 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 21 optimal weight: 7.9990 chunk 16 optimal weight: 8.9990 chunk 19 optimal weight: 10.0000 chunk 13 optimal weight: 8.9990 chunk 50 optimal weight: 0.0470 chunk 14 optimal weight: 0.8980 chunk 33 optimal weight: 7.9990 chunk 55 optimal weight: 10.0000 chunk 23 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 overall best weight: 2.3882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 276 GLN ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 ASN ** A 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 ASN ** B 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 GLN ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 ASN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 329 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 ASN ** D 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 ASN ** E 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** F 296 ASN G 296 ASN ** G 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 329 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** H 296 ASN I 276 GLN I 296 ASN ** I 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 329 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** J 296 ASN ** J 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 329 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4879 r_free = 0.4879 target = 0.216717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.169737 restraints weight = 36612.116| |-----------------------------------------------------------------------------| r_work (start): 0.4507 rms_B_bonded: 6.24 r_work: 0.4190 rms_B_bonded: 5.98 restraints_weight: 2.0000 r_work (final): 0.4190 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4186 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4186 r_free = 0.4186 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4185 r_free = 0.4185 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4185 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 6480 Z= 0.195 Angle : 0.613 6.548 8670 Z= 0.321 Chirality : 0.051 0.210 950 Planarity : 0.004 0.035 1130 Dihedral : 5.596 29.117 872 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 1.03 % Allowed : 7.35 % Favored : 91.62 % Rotamer: Outliers : 5.21 % Allowed : 21.78 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.32 (0.25), residues: 850 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.53 (0.19), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.002 TYR C 310 HIS 0.001 0.001 HIS H 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.19 ( 6470) covalent geometry : angle 0.61318 / 0.32 ( 8650) SS BOND : bond 0.00324 / 0.21 ( 10) SS BOND : angle 0.68876 / 0.39 ( 20) hydrogen bonds : bond 0.02382 / 1.48 ( 149) hydrogen bonds : angle 5.72199 / 3.89 ( 447) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 150 time to evaluate : 0.130 Fit side-chains REVERT: B 290 LYS cc_start: 0.8518 (ttmt) cc_final: 0.7951 (tttm) REVERT: B 311 LYS cc_start: 0.8800 (mttt) cc_final: 0.8480 (mttm) REVERT: F 290 LYS cc_start: 0.8596 (ttpt) cc_final: 0.7287 (ttpt) REVERT: F 311 LYS cc_start: 0.8724 (mttt) cc_final: 0.7285 (pttm) REVERT: F 320 SER cc_start: 0.8975 (m) cc_final: 0.8575 (p) REVERT: G 290 LYS cc_start: 0.8442 (ttmt) cc_final: 0.7932 (ttmm) REVERT: H 290 LYS cc_start: 0.8551 (ttpt) cc_final: 0.7751 (ttpt) REVERT: I 296 ASN cc_start: 0.8297 (m-40) cc_final: 0.7256 (p0) REVERT: I 298 LYS cc_start: 0.8595 (mttm) cc_final: 0.7282 (mmtt) REVERT: I 311 LYS cc_start: 0.7970 (mttt) cc_final: 0.7141 (mmtt) REVERT: J 296 ASN cc_start: 0.7751 (m-40) cc_final: 0.6995 (p0) outliers start: 12 outliers final: 11 residues processed: 153 average time/residue: 0.0764 time to fit residues: 15.7280 Evaluate side-chains 151 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 140 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 288 GLN Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 320 SER Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain I residue 325 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 1 optimal weight: 4.9990 chunk 18 optimal weight: 0.4980 chunk 12 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 36 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 276 GLN ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 ASN A 307 GLN ** A 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 ASN ** B 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 GLN ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 ASN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 ASN ** D 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 ASN ** E 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** F 296 ASN ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 296 ASN ** G 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 329 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 296 ASN I 296 ASN ** I 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 329 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** I 330 HIS A J 296 ASN ** J 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 329 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4986 r_free = 0.4986 target = 0.225779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.179321 restraints weight = 34311.087| |-----------------------------------------------------------------------------| r_work (start): 0.4624 rms_B_bonded: 5.85 r_work (final): 0.4624 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4610 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4610 r_free = 0.4610 target_work(ls_wunit_k1) = 0.181 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4611 r_free = 0.4611 target_work(ls_wunit_k1) = 0.181 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4611 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6480 Z= 0.110 Angle : 0.568 6.711 8670 Z= 0.295 Chirality : 0.050 0.195 950 Planarity : 0.004 0.039 1130 Dihedral : 5.304 26.735 872 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.88 % Allowed : 6.62 % Favored : 92.50 % Rotamer: Outliers : 5.07 % Allowed : 22.60 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.25 (0.26), residues: 850 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.47 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR C 310 HIS 0.002 0.000 HIS H 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 ( 6470) covalent geometry : angle 0.56818 / 0.30 ( 8650) SS BOND : bond 0.00135 / 0.08 ( 10) SS BOND : angle 0.45427 / 0.26 ( 20) hydrogen bonds : bond 0.01858 / 1.17 ( 149) hydrogen bonds : angle 5.41647 / 3.71 ( 447) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 149 time to evaluate : 0.231 Fit side-chains REVERT: A 290 LYS cc_start: 0.8130 (ttpt) cc_final: 0.7602 (tttm) REVERT: B 290 LYS cc_start: 0.8186 (ttmt) cc_final: 0.7672 (tttm) REVERT: F 290 LYS cc_start: 0.8200 (ttpt) cc_final: 0.7049 (ttpt) REVERT: F 320 SER cc_start: 0.9001 (m) cc_final: 0.8599 (p) REVERT: G 290 LYS cc_start: 0.8254 (ttmt) cc_final: 0.7821 (ttmm) REVERT: H 290 LYS cc_start: 0.8171 (ttpt) cc_final: 0.7439 (ttpt) REVERT: I 296 ASN cc_start: 0.8051 (m110) cc_final: 0.6984 (p0) REVERT: I 298 LYS cc_start: 0.8467 (mttm) cc_final: 0.6956 (mmtt) REVERT: I 311 LYS cc_start: 0.7466 (mttt) cc_final: 0.6926 (mmtm) REVERT: J 296 ASN cc_start: 0.7675 (m110) cc_final: 0.6701 (p0) REVERT: J 298 LYS cc_start: 0.8251 (mttm) cc_final: 0.6857 (mmtt) REVERT: J 311 LYS cc_start: 0.7836 (mttt) cc_final: 0.6923 (mmtm) REVERT: J 321 LYS cc_start: 0.8847 (mttm) cc_final: 0.7126 (mmmt) outliers start: 11 outliers final: 8 residues processed: 151 average time/residue: 0.0829 time to fit residues: 16.5567 Evaluate side-chains 147 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 139 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 320 SER Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain I residue 325 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 68 optimal weight: 8.9990 chunk 26 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 65 optimal weight: 0.0000 chunk 5 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 50 optimal weight: 0.0570 chunk 15 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.5906 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 276 GLN ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 307 GLN ** A 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 GLN ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** D 276 GLN ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 329 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** H 276 GLN ** H 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 329 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** J 307 GLN ** J 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 329 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** J 330 HIS A Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4983 r_free = 0.4983 target = 0.226821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.178282 restraints weight = 34106.057| |-----------------------------------------------------------------------------| r_work (start): 0.4672 rms_B_bonded: 5.93 r_work: 0.4426 rms_B_bonded: 5.41 restraints_weight: 2.0000 r_work (final): 0.4426 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4626 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4626 r_free = 0.4626 target_work(ls_wunit_k1) = 0.179 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4624 r_free = 0.4624 target_work(ls_wunit_k1) = 0.179 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4624 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.4211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 6480 Z= 0.092 Angle : 0.561 6.741 8670 Z= 0.292 Chirality : 0.050 0.190 950 Planarity : 0.004 0.040 1130 Dihedral : 5.125 26.338 871 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.88 % Allowed : 6.91 % Favored : 92.21 % Rotamer: Outliers : 4.93 % Allowed : 23.01 % Favored : 72.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.12 (0.26), residues: 850 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.37 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.002 TYR C 310 HIS 0.002 0.000 HIS A 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.09 ( 6470) covalent geometry : angle 0.56123 / 0.29 ( 8650) SS BOND : bond 0.00162 / 0.10 ( 10) SS BOND : angle 0.45230 / 0.26 ( 20) hydrogen bonds : bond 0.01928 / 1.16 ( 149) hydrogen bonds : angle 5.27110 / 3.61 ( 447) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 144 time to evaluate : 0.196 Fit side-chains REVERT: A 290 LYS cc_start: 0.8374 (ttpt) cc_final: 0.7830 (tttm) REVERT: D 280 LYS cc_start: 0.9214 (tttt) cc_final: 0.8956 (tttt) REVERT: F 320 SER cc_start: 0.8903 (m) cc_final: 0.8473 (p) REVERT: G 290 LYS cc_start: 0.8273 (ttmt) cc_final: 0.7881 (ttmm) REVERT: G 321 LYS cc_start: 0.8681 (mttm) cc_final: 0.8447 (mttt) REVERT: I 296 ASN cc_start: 0.8173 (m110) cc_final: 0.7063 (p0) REVERT: I 298 LYS cc_start: 0.8170 (mttm) cc_final: 0.6826 (mmtt) REVERT: I 311 LYS cc_start: 0.7617 (mttt) cc_final: 0.6999 (mmtm) REVERT: J 296 ASN cc_start: 0.7196 (m110) cc_final: 0.6630 (p0) REVERT: J 298 LYS cc_start: 0.8174 (mttm) cc_final: 0.6813 (mmtt) REVERT: J 311 LYS cc_start: 0.7740 (mttt) cc_final: 0.6753 (mmtm) REVERT: J 321 LYS cc_start: 0.8833 (mttm) cc_final: 0.7022 (mmmt) outliers start: 10 outliers final: 9 residues processed: 146 average time/residue: 0.0776 time to fit residues: 15.2397 Evaluate side-chains 150 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 141 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 320 SER Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain I residue 325 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 39 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 59 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 38 optimal weight: 0.0070 chunk 11 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 61 optimal weight: 7.9990 chunk 8 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 overall best weight: 1.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 276 GLN ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 ASN ** A 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 ASN ** B 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 GLN ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 ASN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 ASN ** D 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 ASN ** E 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** F 296 ASN ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 296 ASN ** G 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 329 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 296 ASN I 296 ASN ** I 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 329 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** J 296 ASN J 307 GLN ** J 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 329 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** J 330 HIS A Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4940 r_free = 0.4940 target = 0.222246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.173459 restraints weight = 35212.867| |-----------------------------------------------------------------------------| r_work (start): 0.4628 rms_B_bonded: 6.12 r_work: 0.4369 rms_B_bonded: 5.45 restraints_weight: 2.0000 r_work (final): 0.4369 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4549 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4549 r_free = 0.4549 target_work(ls_wunit_k1) = 0.171 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4549 r_free = 0.4549 target_work(ls_wunit_k1) = 0.171 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4549 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6480 Z= 0.120 Angle : 0.572 6.659 8670 Z= 0.297 Chirality : 0.050 0.183 950 Planarity : 0.004 0.037 1130 Dihedral : 5.116 24.627 871 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.88 % Allowed : 6.91 % Favored : 92.21 % Rotamer: Outliers : 5.07 % Allowed : 22.60 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.10 (0.27), residues: 850 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.36 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.002 TYR C 310 HIS 0.001 0.000 HIS H 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 6470) covalent geometry : angle 0.57243 / 0.30 ( 8650) SS BOND : bond 0.00178 / 0.11 ( 10) SS BOND : angle 0.43405 / 0.25 ( 20) hydrogen bonds : bond 0.01994 / 1.22 ( 149) hydrogen bonds : angle 5.28449 / 3.62 ( 447) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1698.77 seconds wall clock time: 30 minutes 30.64 seconds (1830.64 seconds total)