Starting phenix.real_space_refine on Fri Jul 3 02:46:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9clv_45731/07_2026/9clv_45731.cif Found real_map, /net/cci-nas-00/data/ceres_data/9clv_45731/07_2026/9clv_45731.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9clv_45731/07_2026/9clv_45731.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9clv_45731/07_2026/9clv_45731.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9clv_45731/07_2026/9clv_45731.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9clv_45731/07_2026/9clv_45731.map" } resolution = 3.18 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= 0.003 sd= 0.035 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 K 2 8.98 5 S 44 5.16 5 C 7456 2.51 5 N 1880 2.21 5 O 1953 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 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: 11335 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2833 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 346, 2823 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 18, 'TRANS': 327} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 346, 2823 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 18, 'TRANS': 327} Chain breaks: 2 bond proxies already assigned to first conformer: 2883 Chain: "B" Number of atoms: 2833 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 346, 2823 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 18, 'TRANS': 327} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 346, 2823 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 18, 'TRANS': 327} Chain breaks: 2 bond proxies already assigned to first conformer: 2883 Chain: "C" Number of atoms: 2833 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 346, 2823 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 18, 'TRANS': 327} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 346, 2823 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 18, 'TRANS': 327} Chain breaks: 2 bond proxies already assigned to first conformer: 2883 Chain: "D" Number of atoms: 2833 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 346, 2823 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 18, 'TRANS': 327} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 346, 2823 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 18, 'TRANS': 327} Chain breaks: 2 bond proxies already assigned to first conformer: 2883 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' K': 2} Chain breaks: 2 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AHIS A 451 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS A 451 " occ=0.50 residue: pdb=" N AHIS B 451 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS B 451 " occ=0.50 residue: pdb=" N AHIS C 451 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS C 451 " occ=0.50 residue: pdb=" N AHIS D 451 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS D 451 " occ=0.50 Time building chain proxies: 4.19, per 1000 atoms: 0.37 Number of scatterers: 11335 At special positions: 0 Unit cell: (117.975, 117.975, 113.025, 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) K 2 19.00 S 44 16.00 O 1953 8.00 N 1880 7.00 C 7456 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.03 Conformation dependent library (CDL) restraints added in 887.3 milliseconds 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2600 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 4 sheets defined 70.2% alpha, 0.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 152 through 166 removed outlier: 3.846A pdb=" N PHE A 156 " --> pdb=" O ASN A 152 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASP A 157 " --> pdb=" O ARG A 153 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ALA A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR A 163 " --> pdb=" O ILE A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 187 Processing helix chain 'A' and resid 190 through 202 removed outlier: 4.208A pdb=" N LYS A 196 " --> pdb=" O GLU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 225 removed outlier: 3.553A pdb=" N LEU A 222 " --> pdb=" O ARG A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 254 Processing helix chain 'A' and resid 293 through 316 removed outlier: 3.764A pdb=" N GLU A 299 " --> pdb=" O PHE A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 324 removed outlier: 4.453A pdb=" N SER A 324 " --> pdb=" O LYS A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 335 removed outlier: 3.685A pdb=" N ASP A 332 " --> pdb=" O MET A 328 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ILE A 333 " --> pdb=" O ASN A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 349 removed outlier: 3.670A pdb=" N GLU A 349 " --> pdb=" O THR A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 371 Processing helix chain 'A' and resid 372 through 379 removed outlier: 3.514A pdb=" N LEU A 377 " --> pdb=" O ILE A 374 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG A 379 " --> pdb=" O LYS A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 394 removed outlier: 3.508A pdb=" N GLN A 385 " --> pdb=" O SER A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 421 removed outlier: 3.577A pdb=" N LEU A 398 " --> pdb=" O SER A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 433 No H-bonds generated for 'chain 'A' and resid 431 through 433' Processing helix chain 'A' and resid 434 through 443 Processing helix chain 'A' and resid 454 through 474 removed outlier: 3.558A pdb=" N VAL A 469 " --> pdb=" O ALA A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 488 removed outlier: 3.827A pdb=" N ILE A 479 " --> pdb=" O PRO A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 152 through 166 removed outlier: 3.845A pdb=" N PHE B 156 " --> pdb=" O ASN B 152 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ASP B 157 " --> pdb=" O ARG B 153 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ALA B 158 " --> pdb=" O PRO B 154 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 187 Processing helix chain 'B' and resid 190 through 202 removed outlier: 4.208A pdb=" N LYS B 196 " --> pdb=" O GLU B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 225 removed outlier: 3.554A pdb=" N LEU B 222 " --> pdb=" O ARG B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 254 Processing helix chain 'B' and resid 293 through 316 removed outlier: 3.763A pdb=" N GLU B 299 " --> pdb=" O PHE B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 324 removed outlier: 4.453A pdb=" N SER B 324 " --> pdb=" O LYS B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 335 removed outlier: 3.685A pdb=" N ASP B 332 " --> pdb=" O MET B 328 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ILE B 333 " --> pdb=" O ASN B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 349 removed outlier: 3.671A pdb=" N GLU B 349 " --> pdb=" O THR B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 371 Processing helix chain 'B' and resid 372 through 379 removed outlier: 3.514A pdb=" N LEU B 377 " --> pdb=" O ILE B 374 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG B 379 " --> pdb=" O LYS B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 394 removed outlier: 3.509A pdb=" N GLN B 385 " --> pdb=" O SER B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 421 removed outlier: 3.577A pdb=" N LEU B 398 " --> pdb=" O SER B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 433 No H-bonds generated for 'chain 'B' and resid 431 through 433' Processing helix chain 'B' and resid 434 through 443 Processing helix chain 'B' and resid 454 through 474 removed outlier: 3.558A pdb=" N VAL B 469 " --> pdb=" O ALA B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 488 removed outlier: 3.827A pdb=" N ILE B 479 " --> pdb=" O PRO B 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 124 Processing helix chain 'C' and resid 152 through 166 removed outlier: 3.846A pdb=" N PHE C 156 " --> pdb=" O ASN C 152 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASP C 157 " --> pdb=" O ARG C 153 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ALA C 158 " --> pdb=" O PRO C 154 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR C 163 " --> pdb=" O ILE C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 187 Processing helix chain 'C' and resid 190 through 202 removed outlier: 4.209A pdb=" N LYS C 196 " --> pdb=" O GLU C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 225 removed outlier: 3.553A pdb=" N LEU C 222 " --> pdb=" O ARG C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 254 Processing helix chain 'C' and resid 293 through 316 removed outlier: 3.764A pdb=" N GLU C 299 " --> pdb=" O PHE C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 324 removed outlier: 4.453A pdb=" N SER C 324 " --> pdb=" O LYS C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 335 removed outlier: 3.685A pdb=" N ASP C 332 " --> pdb=" O MET C 328 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ILE C 333 " --> pdb=" O ASN C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 349 removed outlier: 3.671A pdb=" N GLU C 349 " --> pdb=" O THR C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 371 Processing helix chain 'C' and resid 372 through 379 removed outlier: 3.514A pdb=" N LEU C 377 " --> pdb=" O ILE C 374 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG C 379 " --> pdb=" O LYS C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 394 removed outlier: 3.508A pdb=" N GLN C 385 " --> pdb=" O SER C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 421 removed outlier: 3.577A pdb=" N LEU C 398 " --> pdb=" O SER C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 433 No H-bonds generated for 'chain 'C' and resid 431 through 433' Processing helix chain 'C' and resid 434 through 443 Processing helix chain 'C' and resid 454 through 474 removed outlier: 3.558A pdb=" N VAL C 469 " --> pdb=" O ALA C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 488 removed outlier: 3.827A pdb=" N ILE C 479 " --> pdb=" O PRO C 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 124 Processing helix chain 'D' and resid 152 through 166 removed outlier: 3.847A pdb=" N PHE D 156 " --> pdb=" O ASN D 152 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ASP D 157 " --> pdb=" O ARG D 153 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ALA D 158 " --> pdb=" O PRO D 154 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR D 163 " --> pdb=" O ILE D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 187 Processing helix chain 'D' and resid 190 through 202 removed outlier: 4.209A pdb=" N LYS D 196 " --> pdb=" O GLU D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 225 removed outlier: 3.554A pdb=" N LEU D 222 " --> pdb=" O ARG D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 254 Processing helix chain 'D' and resid 293 through 316 removed outlier: 3.764A pdb=" N GLU D 299 " --> pdb=" O PHE D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 324 removed outlier: 4.453A pdb=" N SER D 324 " --> pdb=" O LYS D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 335 removed outlier: 3.685A pdb=" N ASP D 332 " --> pdb=" O MET D 328 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ILE D 333 " --> pdb=" O ASN D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 349 removed outlier: 3.670A pdb=" N GLU D 349 " --> pdb=" O THR D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 371 Processing helix chain 'D' and resid 372 through 379 removed outlier: 3.513A pdb=" N LEU D 377 " --> pdb=" O ILE D 374 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG D 379 " --> pdb=" O LYS D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 394 removed outlier: 3.508A pdb=" N GLN D 385 " --> pdb=" O SER D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 421 removed outlier: 3.578A pdb=" N LEU D 398 " --> pdb=" O SER D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 433 No H-bonds generated for 'chain 'D' and resid 431 through 433' Processing helix chain 'D' and resid 434 through 443 Processing helix chain 'D' and resid 454 through 474 removed outlier: 3.558A pdb=" N VAL D 469 " --> pdb=" O ALA D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 488 removed outlier: 3.827A pdb=" N ILE D 479 " --> pdb=" O PRO D 475 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 105 through 106 Processing sheet with id=AA2, first strand: chain 'B' and resid 105 through 106 Processing sheet with id=AA3, first strand: chain 'C' and resid 105 through 106 Processing sheet with id=AA4, first strand: chain 'D' and resid 105 through 106 632 hydrogen bonds defined for protein. 1848 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: 1.56 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2671 1.33 - 1.45: 2489 1.45 - 1.57: 6400 1.57 - 1.69: 0 1.69 - 1.81: 68 Bond restraints: 11628 Sorted by residual: bond pdb=" N PHE D 259 " pdb=" CA PHE D 259 " ideal model delta sigma weight residual 1.463 1.488 -0.025 1.27e-02 6.20e+03 3.88e+00 bond pdb=" N PHE B 259 " pdb=" CA PHE B 259 " ideal model delta sigma weight residual 1.463 1.488 -0.025 1.27e-02 6.20e+03 3.87e+00 bond pdb=" N PHE A 259 " pdb=" CA PHE A 259 " ideal model delta sigma weight residual 1.463 1.488 -0.025 1.27e-02 6.20e+03 3.87e+00 bond pdb=" N PHE C 259 " pdb=" CA PHE C 259 " ideal model delta sigma weight residual 1.463 1.488 -0.025 1.27e-02 6.20e+03 3.82e+00 bond pdb=" C TRP C 436 " pdb=" O TRP C 436 " ideal model delta sigma weight residual 1.236 1.213 0.022 1.17e-02 7.31e+03 3.64e+00 ... (remaining 11623 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.08: 15024 1.08 - 2.16: 564 2.16 - 3.24: 92 3.24 - 4.32: 48 4.32 - 5.40: 28 Bond angle restraints: 15756 Sorted by residual: angle pdb=" C PHE C 259 " pdb=" CA PHE C 259 " pdb=" CB PHE C 259 " ideal model delta sigma weight residual 111.74 106.34 5.40 1.37e+00 5.33e-01 1.56e+01 angle pdb=" C PHE A 259 " pdb=" CA PHE A 259 " pdb=" CB PHE A 259 " ideal model delta sigma weight residual 111.74 106.37 5.37 1.37e+00 5.33e-01 1.54e+01 angle pdb=" C PHE B 259 " pdb=" CA PHE B 259 " pdb=" CB PHE B 259 " ideal model delta sigma weight residual 111.74 106.37 5.37 1.37e+00 5.33e-01 1.54e+01 angle pdb=" C PHE D 259 " pdb=" CA PHE D 259 " pdb=" CB PHE D 259 " ideal model delta sigma weight residual 111.74 106.39 5.35 1.37e+00 5.33e-01 1.52e+01 angle pdb=" CA MET D 442 " pdb=" C MET D 442 " pdb=" O MET D 442 " ideal model delta sigma weight residual 120.42 116.86 3.56 1.06e+00 8.90e-01 1.13e+01 ... (remaining 15751 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.98: 6107 11.98 - 23.97: 529 23.97 - 35.95: 124 35.95 - 47.94: 60 47.94 - 59.92: 36 Dihedral angle restraints: 6856 sinusoidal: 2828 harmonic: 4028 Sorted by residual: dihedral pdb=" N LYS A 382 " pdb=" CA LYS A 382 " pdb=" CB LYS A 382 " pdb=" CG LYS A 382 " ideal model delta sinusoidal sigma weight residual -60.00 -118.05 58.05 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" N LYS B 382 " pdb=" CA LYS B 382 " pdb=" CB LYS B 382 " pdb=" CG LYS B 382 " ideal model delta sinusoidal sigma weight residual -60.00 -118.05 58.05 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" N LYS D 382 " pdb=" CA LYS D 382 " pdb=" CB LYS D 382 " pdb=" CG LYS D 382 " ideal model delta sinusoidal sigma weight residual -60.00 -118.04 58.04 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 6853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1055 0.033 - 0.065: 506 0.065 - 0.098: 131 0.098 - 0.130: 52 0.130 - 0.163: 4 Chirality restraints: 1748 Sorted by residual: chirality pdb=" CA PHE C 259 " pdb=" N PHE C 259 " pdb=" C PHE C 259 " pdb=" CB PHE C 259 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.63e-01 chirality pdb=" CA PHE B 259 " pdb=" N PHE B 259 " pdb=" C PHE B 259 " pdb=" CB PHE B 259 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.50e-01 chirality pdb=" CA PHE A 259 " pdb=" N PHE A 259 " pdb=" C PHE A 259 " pdb=" CB PHE A 259 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.50e-01 ... (remaining 1745 not shown) Planarity restraints: 2004 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 260 " -0.254 9.50e-02 1.11e+02 1.14e-01 8.11e+00 pdb=" NE ARG C 260 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG C 260 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG C 260 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 260 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 260 " 0.253 9.50e-02 1.11e+02 1.14e-01 8.03e+00 pdb=" NE ARG A 260 " -0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A 260 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 260 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 260 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 260 " 0.253 9.50e-02 1.11e+02 1.14e-01 8.02e+00 pdb=" NE ARG D 260 " -0.017 2.00e-02 2.50e+03 pdb=" CZ ARG D 260 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG D 260 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG D 260 " 0.007 2.00e-02 2.50e+03 ... (remaining 2001 not shown) Histogram of nonbonded interaction distances: 2.44 - 2.98: 5677 2.98 - 3.52: 13879 3.52 - 4.06: 20184 4.06 - 4.60: 31350 4.60 - 5.14: 41653 Nonbonded interactions: 112743 Sorted by model distance: nonbonded pdb=" NZ LYS C 382 " pdb=" OE1 GLU C 490 " model vdw 2.440 3.120 nonbonded pdb=" NZ LYS A 382 " pdb=" OE1 GLU A 490 " model vdw 2.441 3.120 nonbonded pdb=" NZ LYS B 382 " pdb=" OE1 GLU B 490 " model vdw 2.441 3.120 nonbonded pdb=" NZ LYS D 382 " pdb=" OE1 GLU D 490 " model vdw 2.441 3.120 nonbonded pdb=" O TRP A 436 " pdb=" C TRP A 437 " model vdw 2.494 3.270 ... (remaining 112738 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 103 through 450 or resid 452 through 490)) selection = (chain 'B' and (resid 103 through 450 or resid 452 through 490)) selection = (chain 'C' and (resid 103 through 450 or resid 452 through 490)) selection = (chain 'D' and (resid 103 through 450 or resid 452 through 490)) } 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=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.120 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 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: 17.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 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 : 0.004 0.033 11628 Z= 0.182 Angle : 0.557 5.403 15756 Z= 0.333 Chirality : 0.042 0.163 1748 Planarity : 0.007 0.114 2004 Dihedral : 11.469 59.922 4256 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.60 % Allowed : 7.47 % Favored : 89.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.24), residues: 1372 helix: 0.72 (0.19), residues: 868 sheet: -3.82 (0.77), residues: 40 loop : -0.67 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 260 TYR 0.007 0.001 TYR C 187 PHE 0.011 0.001 PHE B 259 TRP 0.013 0.002 TRP B 436 HIS 0.002 0.001 HIS A 380 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.18 (11628) covalent geometry : angle 0.55704 / 0.33 (15756) hydrogen bonds : bond 0.14653 / 9.59 ( 632) hydrogen bonds : angle 5.14415 / 3.68 ( 1848) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 242 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 LYS cc_start: 0.8343 (mtpt) cc_final: 0.8124 (mtpp) REVERT: A 222 LEU cc_start: 0.8268 (mt) cc_final: 0.7955 (mt) REVERT: A 226 TYR cc_start: 0.8541 (m-80) cc_final: 0.8327 (m-80) REVERT: A 324 SER cc_start: 0.8904 (m) cc_final: 0.8549 (t) REVERT: A 420 GLU cc_start: 0.8335 (mt-10) cc_final: 0.7935 (mt-10) REVERT: A 486 PHE cc_start: 0.9053 (m-80) cc_final: 0.8768 (m-80) REVERT: B 222 LEU cc_start: 0.8272 (mt) cc_final: 0.7958 (mt) REVERT: B 226 TYR cc_start: 0.8546 (m-80) cc_final: 0.8332 (m-80) REVERT: B 246 ILE cc_start: 0.7772 (pt) cc_final: 0.7567 (mt) REVERT: B 324 SER cc_start: 0.8907 (m) cc_final: 0.8561 (t) REVERT: B 420 GLU cc_start: 0.8330 (mt-10) cc_final: 0.7940 (mt-10) REVERT: B 486 PHE cc_start: 0.9054 (m-80) cc_final: 0.8772 (m-80) REVERT: C 196 LYS cc_start: 0.8350 (mtpt) cc_final: 0.8132 (mtpp) REVERT: C 222 LEU cc_start: 0.8268 (mt) cc_final: 0.7953 (mt) REVERT: C 226 TYR cc_start: 0.8549 (m-80) cc_final: 0.8292 (m-80) REVERT: C 324 SER cc_start: 0.8904 (m) cc_final: 0.8540 (t) REVERT: C 420 GLU cc_start: 0.8347 (mt-10) cc_final: 0.7943 (mt-10) REVERT: C 449 ASP cc_start: 0.7721 (m-30) cc_final: 0.7512 (m-30) REVERT: C 486 PHE cc_start: 0.9043 (m-80) cc_final: 0.8749 (m-80) REVERT: C 489 ARG cc_start: 0.7926 (OUTLIER) cc_final: 0.7584 (mtm110) REVERT: D 222 LEU cc_start: 0.8269 (mt) cc_final: 0.7976 (mt) REVERT: D 324 SER cc_start: 0.8918 (m) cc_final: 0.8578 (t) REVERT: D 420 GLU cc_start: 0.8331 (mt-10) cc_final: 0.7934 (mt-10) REVERT: D 486 PHE cc_start: 0.9058 (m-80) cc_final: 0.8773 (m-80) outliers start: 32 outliers final: 8 residues processed: 266 average time/residue: 0.1208 time to fit residues: 43.6349 Evaluate side-chains 160 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 151 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain B residue 364 ARG Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain C residue 364 ARG Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 489 ARG Chi-restraints excluded: chain D residue 364 ARG Chi-restraints excluded: chain D residue 397 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.0050 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.0170 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 0.3980 overall best weight: 0.4032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 217 GLN A 389 GLN A 451 HIS B B 217 GLN B 389 GLN B 451 HIS B C 217 GLN C 389 GLN C 451 HIS B D 217 GLN D 389 GLN D 451 HIS B Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.200238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.173162 restraints weight = 36574.736| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 2.76 r_work: 0.3377 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3292 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3292 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11628 Z= 0.113 Angle : 0.488 5.385 15756 Z= 0.260 Chirality : 0.040 0.127 1748 Planarity : 0.005 0.044 2004 Dihedral : 5.271 45.819 1576 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.14 % Allowed : 11.20 % Favored : 87.66 % 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: 0.76 (0.24), residues: 1372 helix: 1.24 (0.19), residues: 848 sheet: -3.90 (0.78), residues: 40 loop : -0.29 (0.30), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 136 TYR 0.009 0.002 TYR C 339 PHE 0.012 0.001 PHE A 224 TRP 0.004 0.001 TRP A 305 HIS 0.001 0.001 HIS A 380 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (11628) covalent geometry : angle 0.48790 / 0.26 (15756) hydrogen bonds : bond 0.03974 / 2.59 ( 632) hydrogen bonds : angle 3.95798 / 2.77 ( 1848) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 173 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 GLU cc_start: 0.6857 (tp30) cc_final: 0.6524 (mt-10) REVERT: A 486 PHE cc_start: 0.9030 (m-80) cc_final: 0.8813 (m-80) REVERT: A 489 ARG cc_start: 0.8195 (mtp-110) cc_final: 0.7988 (mtm110) REVERT: B 346 GLU cc_start: 0.6866 (tp30) cc_final: 0.6530 (mt-10) REVERT: B 486 PHE cc_start: 0.9023 (m-80) cc_final: 0.8801 (m-80) REVERT: B 489 ARG cc_start: 0.8154 (mtp-110) cc_final: 0.7949 (mtm110) REVERT: C 346 GLU cc_start: 0.6867 (tp30) cc_final: 0.6546 (mt-10) REVERT: D 346 GLU cc_start: 0.6891 (tp30) cc_final: 0.6619 (mt-10) REVERT: D 489 ARG cc_start: 0.8168 (mtp-110) cc_final: 0.7959 (mtm110) outliers start: 14 outliers final: 8 residues processed: 185 average time/residue: 0.1188 time to fit residues: 30.4522 Evaluate side-chains 141 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 133 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain B residue 364 ARG Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain C residue 364 ARG Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain D residue 364 ARG Chi-restraints excluded: chain D residue 397 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 71 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 75 optimal weight: 0.7980 chunk 54 optimal weight: 4.9990 chunk 89 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.197470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.151938 restraints weight = 34909.478| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 4.18 r_work: 0.2939 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2755 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2755 r_free = 0.2755 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2754 r_free = 0.2754 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.2754 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 11628 Z= 0.248 Angle : 0.572 5.416 15756 Z= 0.305 Chirality : 0.045 0.138 1748 Planarity : 0.005 0.049 2004 Dihedral : 5.440 46.520 1572 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.14 % Allowed : 12.26 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.24), residues: 1372 helix: 1.08 (0.18), residues: 868 sheet: -4.45 (0.64), residues: 40 loop : -0.32 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 260 TYR 0.012 0.002 TYR A 447 PHE 0.016 0.002 PHE C 224 TRP 0.006 0.002 TRP B 436 HIS 0.004 0.002 HIS D 380 Details of bonding type rmsd/Z covalent geometry : bond 0.00610 / 0.25 (11628) covalent geometry : angle 0.57224 / 0.31 (15756) hydrogen bonds : bond 0.04464 / 2.96 ( 632) hydrogen bonds : angle 4.05361 / 2.83 ( 1848) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 138 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 GLN cc_start: 0.7947 (mm-40) cc_final: 0.7617 (mm110) REVERT: A 332 ASP cc_start: 0.8023 (m-30) cc_final: 0.7727 (m-30) REVERT: B 188 GLN cc_start: 0.7955 (mm-40) cc_final: 0.7628 (mm110) REVERT: B 332 ASP cc_start: 0.8075 (m-30) cc_final: 0.7785 (m-30) REVERT: C 188 GLN cc_start: 0.7943 (mm-40) cc_final: 0.7614 (mm110) REVERT: C 196 LYS cc_start: 0.8225 (mtpp) cc_final: 0.7900 (mtmm) REVERT: C 332 ASP cc_start: 0.8048 (m-30) cc_final: 0.7759 (m-30) REVERT: D 188 GLN cc_start: 0.7953 (mm-40) cc_final: 0.7620 (mm110) REVERT: D 332 ASP cc_start: 0.8076 (m-30) cc_final: 0.7793 (m-30) REVERT: D 346 GLU cc_start: 0.6943 (tp30) cc_final: 0.6132 (mt-10) outliers start: 14 outliers final: 8 residues processed: 150 average time/residue: 0.1204 time to fit residues: 25.3121 Evaluate side-chains 140 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 132 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain B residue 364 ARG Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain C residue 364 ARG Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain D residue 364 ARG Chi-restraints excluded: chain D residue 397 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 34 optimal weight: 7.9990 chunk 14 optimal weight: 0.5980 chunk 119 optimal weight: 4.9990 chunk 132 optimal weight: 0.7980 chunk 57 optimal weight: 0.5980 chunk 47 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 55 optimal weight: 10.0000 chunk 118 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.202370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.163535 restraints weight = 32950.539| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 3.63 r_work: 0.3076 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2859 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2859 r_free = 0.2859 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2859 r_free = 0.2859 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2859 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11628 Z= 0.116 Angle : 0.476 5.202 15756 Z= 0.252 Chirality : 0.040 0.128 1748 Planarity : 0.005 0.047 2004 Dihedral : 5.054 40.732 1572 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.14 % Allowed : 12.82 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.24), residues: 1372 helix: 1.28 (0.19), residues: 888 sheet: None (None), residues: 0 loop : -0.53 (0.30), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 144 TYR 0.011 0.002 TYR A 161 PHE 0.016 0.001 PHE D 148 TRP 0.007 0.001 TRP C 221 HIS 0.001 0.000 HIS C 380 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (11628) covalent geometry : angle 0.47639 / 0.25 (15756) hydrogen bonds : bond 0.03625 / 2.40 ( 632) hydrogen bonds : angle 3.75051 / 2.62 ( 1848) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 143 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 GLN cc_start: 0.7920 (mm-40) cc_final: 0.7593 (mm110) REVERT: A 332 ASP cc_start: 0.8016 (m-30) cc_final: 0.7699 (m-30) REVERT: A 486 PHE cc_start: 0.8974 (m-80) cc_final: 0.8693 (m-80) REVERT: B 150 ASP cc_start: 0.8872 (OUTLIER) cc_final: 0.8589 (t70) REVERT: B 188 GLN cc_start: 0.7870 (mm-40) cc_final: 0.7536 (mm110) REVERT: B 332 ASP cc_start: 0.8005 (m-30) cc_final: 0.7685 (m-30) REVERT: B 486 PHE cc_start: 0.8974 (m-80) cc_final: 0.8695 (m-80) REVERT: C 150 ASP cc_start: 0.8918 (OUTLIER) cc_final: 0.8626 (t0) REVERT: C 188 GLN cc_start: 0.7880 (mm-40) cc_final: 0.7551 (mm110) REVERT: C 332 ASP cc_start: 0.7973 (m-30) cc_final: 0.7661 (m-30) REVERT: C 486 PHE cc_start: 0.8989 (m-80) cc_final: 0.8710 (m-80) REVERT: D 150 ASP cc_start: 0.8913 (OUTLIER) cc_final: 0.8612 (t0) REVERT: D 188 GLN cc_start: 0.7875 (mm-40) cc_final: 0.7555 (mm110) REVERT: D 332 ASP cc_start: 0.8045 (m-30) cc_final: 0.7754 (m-30) REVERT: D 486 PHE cc_start: 0.8989 (m-80) cc_final: 0.8708 (m-80) outliers start: 14 outliers final: 4 residues processed: 154 average time/residue: 0.1176 time to fit residues: 25.9836 Evaluate side-chains 137 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 130 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 364 ARG Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 364 ARG Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 364 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 95 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 2 optimal weight: 9.9990 chunk 65 optimal weight: 0.6980 chunk 98 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 30 optimal weight: 0.0370 chunk 90 optimal weight: 0.8980 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.201325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.156716 restraints weight = 38334.855| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 4.29 r_work: 0.3020 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2804 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2804 r_free = 0.2804 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2804 r_free = 0.2804 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2804 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 11628 Z= 0.124 Angle : 0.490 6.257 15756 Z= 0.263 Chirality : 0.041 0.120 1748 Planarity : 0.005 0.047 2004 Dihedral : 4.620 40.831 1560 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.81 % Allowed : 14.20 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.24), residues: 1372 helix: 1.40 (0.19), residues: 872 sheet: -4.48 (0.60), residues: 40 loop : -0.48 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 144 TYR 0.015 0.002 TYR A 161 PHE 0.025 0.001 PHE A 314 TRP 0.005 0.001 TRP C 221 HIS 0.001 0.001 HIS C 380 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.12 (11628) covalent geometry : angle 0.49041 / 0.26 (15756) hydrogen bonds : bond 0.03642 / 2.41 ( 632) hydrogen bonds : angle 3.70408 / 2.59 ( 1848) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 135 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 ASP cc_start: 0.8871 (OUTLIER) cc_final: 0.8582 (t70) REVERT: A 188 GLN cc_start: 0.7975 (mm-40) cc_final: 0.7677 (mm110) REVERT: A 332 ASP cc_start: 0.8020 (m-30) cc_final: 0.7688 (m-30) REVERT: A 486 PHE cc_start: 0.9004 (m-80) cc_final: 0.8745 (m-80) REVERT: B 188 GLN cc_start: 0.7946 (mm-40) cc_final: 0.7641 (mm110) REVERT: B 196 LYS cc_start: 0.7974 (OUTLIER) cc_final: 0.7736 (ptmt) REVERT: B 332 ASP cc_start: 0.8015 (m-30) cc_final: 0.7679 (m-30) REVERT: B 486 PHE cc_start: 0.9005 (m-80) cc_final: 0.8748 (m-80) REVERT: C 150 ASP cc_start: 0.8899 (OUTLIER) cc_final: 0.8616 (t70) REVERT: C 188 GLN cc_start: 0.7928 (mm-40) cc_final: 0.7614 (mm110) REVERT: C 332 ASP cc_start: 0.8003 (m-30) cc_final: 0.7691 (m-30) REVERT: C 486 PHE cc_start: 0.9005 (m-80) cc_final: 0.8743 (m-80) REVERT: D 150 ASP cc_start: 0.8872 (OUTLIER) cc_final: 0.8576 (t70) REVERT: D 188 GLN cc_start: 0.7915 (mm-40) cc_final: 0.7604 (mm110) REVERT: D 196 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7761 (ptmt) REVERT: D 332 ASP cc_start: 0.8005 (m-30) cc_final: 0.7708 (m-30) REVERT: D 486 PHE cc_start: 0.9006 (m-80) cc_final: 0.8743 (m-80) outliers start: 10 outliers final: 5 residues processed: 142 average time/residue: 0.1275 time to fit residues: 25.4617 Evaluate side-chains 142 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 132 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 364 ARG Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 364 ARG Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 196 LYS Chi-restraints excluded: chain D residue 364 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 32 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 52 optimal weight: 7.9990 chunk 85 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 100 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.201728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.159763 restraints weight = 41744.885| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 4.21 r_work: 0.2995 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2829 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2829 r_free = 0.2829 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2829 r_free = 0.2829 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2829 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11628 Z= 0.120 Angle : 0.475 6.378 15756 Z= 0.254 Chirality : 0.040 0.122 1748 Planarity : 0.005 0.047 2004 Dihedral : 4.569 41.193 1560 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.81 % Allowed : 13.47 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.24), residues: 1372 helix: 1.47 (0.19), residues: 872 sheet: -4.51 (0.58), residues: 40 loop : -0.51 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 489 TYR 0.015 0.002 TYR B 162 PHE 0.022 0.001 PHE B 314 TRP 0.004 0.001 TRP C 221 HIS 0.001 0.001 HIS D 380 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 (11628) covalent geometry : angle 0.47534 / 0.25 (15756) hydrogen bonds : bond 0.03471 / 2.30 ( 632) hydrogen bonds : angle 3.62159 / 2.53 ( 1848) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 140 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 ASP cc_start: 0.8869 (OUTLIER) cc_final: 0.8572 (t70) REVERT: A 188 GLN cc_start: 0.7959 (mm-40) cc_final: 0.7649 (mm110) REVERT: A 332 ASP cc_start: 0.8030 (m-30) cc_final: 0.7710 (m-30) REVERT: A 486 PHE cc_start: 0.8997 (m-80) cc_final: 0.8788 (m-80) REVERT: B 150 ASP cc_start: 0.8887 (OUTLIER) cc_final: 0.8592 (t70) REVERT: B 188 GLN cc_start: 0.7948 (mm-40) cc_final: 0.7639 (mm110) REVERT: B 332 ASP cc_start: 0.8025 (m-30) cc_final: 0.7708 (m-30) REVERT: B 486 PHE cc_start: 0.8999 (m-80) cc_final: 0.8790 (m-80) REVERT: C 150 ASP cc_start: 0.8881 (OUTLIER) cc_final: 0.8592 (t70) REVERT: C 188 GLN cc_start: 0.7956 (mm-40) cc_final: 0.7648 (mm110) REVERT: C 226 TYR cc_start: 0.8282 (m-80) cc_final: 0.7898 (m-80) REVERT: C 332 ASP cc_start: 0.7996 (m-30) cc_final: 0.7675 (m-30) REVERT: C 486 PHE cc_start: 0.9002 (m-80) cc_final: 0.8726 (m-80) REVERT: D 150 ASP cc_start: 0.8868 (OUTLIER) cc_final: 0.8563 (t70) REVERT: D 188 GLN cc_start: 0.7937 (mm-40) cc_final: 0.7621 (mm110) REVERT: D 332 ASP cc_start: 0.8020 (m-30) cc_final: 0.7740 (m-30) REVERT: D 486 PHE cc_start: 0.9007 (m-80) cc_final: 0.8734 (m-80) outliers start: 10 outliers final: 4 residues processed: 148 average time/residue: 0.1246 time to fit residues: 26.0941 Evaluate side-chains 142 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 134 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 364 ARG Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 364 ARG Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 364 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 chunk 127 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 135 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 52 optimal weight: 9.9990 chunk 71 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.199871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.157788 restraints weight = 38746.992| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 4.15 r_work: 0.2964 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2796 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2796 r_free = 0.2796 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2796 r_free = 0.2796 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2796 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 11628 Z= 0.182 Angle : 0.509 5.303 15756 Z= 0.272 Chirality : 0.042 0.129 1748 Planarity : 0.005 0.048 2004 Dihedral : 4.647 41.662 1560 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.46 % Allowed : 12.50 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.24), residues: 1372 helix: 1.42 (0.19), residues: 888 sheet: -4.80 (0.51), residues: 40 loop : -0.51 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 489 TYR 0.021 0.002 TYR D 161 PHE 0.012 0.001 PHE C 224 TRP 0.003 0.001 TRP A 437 HIS 0.003 0.001 HIS B 380 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.18 (11628) covalent geometry : angle 0.50851 / 0.27 (15756) hydrogen bonds : bond 0.03854 / 2.57 ( 632) hydrogen bonds : angle 3.75434 / 2.63 ( 1848) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 136 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 ASP cc_start: 0.8812 (OUTLIER) cc_final: 0.8508 (t70) REVERT: A 188 GLN cc_start: 0.8028 (mm-40) cc_final: 0.7715 (mm110) REVERT: A 332 ASP cc_start: 0.8060 (m-30) cc_final: 0.7782 (m-30) REVERT: A 396 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.7501 (ttt90) REVERT: A 486 PHE cc_start: 0.9021 (m-80) cc_final: 0.8768 (m-80) REVERT: B 150 ASP cc_start: 0.8827 (OUTLIER) cc_final: 0.8526 (t70) REVERT: B 188 GLN cc_start: 0.8047 (mm-40) cc_final: 0.7732 (mm110) REVERT: B 332 ASP cc_start: 0.8037 (m-30) cc_final: 0.7778 (m-30) REVERT: B 486 PHE cc_start: 0.9018 (m-80) cc_final: 0.8767 (m-80) REVERT: C 150 ASP cc_start: 0.8822 (OUTLIER) cc_final: 0.8514 (t70) REVERT: C 188 GLN cc_start: 0.8033 (mm-40) cc_final: 0.7727 (mm110) REVERT: C 332 ASP cc_start: 0.8042 (m-30) cc_final: 0.7775 (m-30) REVERT: C 396 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.7505 (ttt90) REVERT: C 486 PHE cc_start: 0.9015 (m-80) cc_final: 0.8762 (m-80) REVERT: D 150 ASP cc_start: 0.8821 (OUTLIER) cc_final: 0.8515 (t70) REVERT: D 188 GLN cc_start: 0.8045 (mm-40) cc_final: 0.7724 (mm110) REVERT: D 332 ASP cc_start: 0.8073 (m-30) cc_final: 0.7817 (m-30) REVERT: D 396 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.7485 (ttt90) REVERT: D 486 PHE cc_start: 0.9016 (m-80) cc_final: 0.8760 (m-80) outliers start: 18 outliers final: 8 residues processed: 150 average time/residue: 0.1138 time to fit residues: 23.5381 Evaluate side-chains 148 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 133 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 396 ARG Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 364 ARG Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 364 ARG Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 396 ARG Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 364 ARG Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 396 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 117 optimal weight: 4.9990 chunk 96 optimal weight: 0.0980 chunk 92 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 19 optimal weight: 0.0970 chunk 132 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 62 optimal weight: 0.0020 chunk 99 optimal weight: 0.9990 overall best weight: 0.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.203813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.160822 restraints weight = 35602.974| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 4.21 r_work: 0.3025 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2875 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2875 r_free = 0.2875 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2875 r_free = 0.2875 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2875 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 11628 Z= 0.105 Angle : 0.477 7.166 15756 Z= 0.254 Chirality : 0.040 0.126 1748 Planarity : 0.005 0.047 2004 Dihedral : 4.514 41.512 1560 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.22 % Allowed : 13.39 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.24), residues: 1372 helix: 1.56 (0.19), residues: 872 sheet: -4.65 (0.50), residues: 40 loop : -0.55 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 489 TYR 0.023 0.002 TYR D 161 PHE 0.010 0.001 PHE D 148 TRP 0.005 0.001 TRP C 221 HIS 0.000 0.000 HIS D 380 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (11628) covalent geometry : angle 0.47669 / 0.25 (15756) hydrogen bonds : bond 0.03338 / 2.21 ( 632) hydrogen bonds : angle 3.54840 / 2.48 ( 1848) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 ASP cc_start: 0.8854 (OUTLIER) cc_final: 0.8554 (t70) REVERT: A 188 GLN cc_start: 0.8000 (mm-40) cc_final: 0.7700 (mm110) REVERT: A 332 ASP cc_start: 0.8052 (m-30) cc_final: 0.7736 (m-30) REVERT: A 364 ARG cc_start: 0.4576 (OUTLIER) cc_final: 0.3705 (tpt-90) REVERT: A 396 ARG cc_start: 0.7926 (OUTLIER) cc_final: 0.7542 (ttt90) REVERT: A 486 PHE cc_start: 0.9048 (m-80) cc_final: 0.8771 (m-80) REVERT: B 150 ASP cc_start: 0.8833 (OUTLIER) cc_final: 0.8537 (t70) REVERT: B 188 GLN cc_start: 0.7999 (mm-40) cc_final: 0.7702 (mm110) REVERT: B 332 ASP cc_start: 0.8031 (m-30) cc_final: 0.7718 (m-30) REVERT: B 364 ARG cc_start: 0.4573 (OUTLIER) cc_final: 0.3712 (tpt-90) REVERT: B 396 ARG cc_start: 0.7917 (OUTLIER) cc_final: 0.7537 (ttt90) REVERT: B 486 PHE cc_start: 0.9038 (m-80) cc_final: 0.8763 (m-80) REVERT: C 150 ASP cc_start: 0.8870 (OUTLIER) cc_final: 0.8580 (t70) REVERT: C 188 GLN cc_start: 0.7997 (mm-40) cc_final: 0.7699 (mm110) REVERT: C 332 ASP cc_start: 0.8019 (m-30) cc_final: 0.7708 (m-30) REVERT: C 364 ARG cc_start: 0.4564 (OUTLIER) cc_final: 0.3685 (tpt-90) REVERT: C 396 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.7528 (ttt90) REVERT: C 486 PHE cc_start: 0.9039 (m-80) cc_final: 0.8745 (m-80) REVERT: D 150 ASP cc_start: 0.8848 (OUTLIER) cc_final: 0.8540 (t70) REVERT: D 188 GLN cc_start: 0.7997 (mm-40) cc_final: 0.7694 (mm110) REVERT: D 332 ASP cc_start: 0.8057 (m-30) cc_final: 0.7763 (m-30) REVERT: D 364 ARG cc_start: 0.4508 (OUTLIER) cc_final: 0.3632 (tpt-90) REVERT: D 396 ARG cc_start: 0.7924 (OUTLIER) cc_final: 0.7538 (ttt90) REVERT: D 486 PHE cc_start: 0.9037 (m-80) cc_final: 0.8743 (m-80) outliers start: 15 outliers final: 0 residues processed: 152 average time/residue: 0.1058 time to fit residues: 22.5650 Evaluate side-chains 144 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 396 ARG Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 364 ARG Chi-restraints excluded: chain B residue 396 ARG Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 364 ARG Chi-restraints excluded: chain C residue 396 ARG Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 364 ARG Chi-restraints excluded: chain D residue 396 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 54 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 chunk 113 optimal weight: 0.0270 chunk 131 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.202160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.159708 restraints weight = 41145.404| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 4.20 r_work: 0.3034 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2849 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2849 r_free = 0.2849 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2849 r_free = 0.2849 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2849 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 11628 Z= 0.126 Angle : 0.500 7.056 15756 Z= 0.265 Chirality : 0.041 0.159 1748 Planarity : 0.005 0.047 2004 Dihedral : 4.538 41.661 1560 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.06 % Allowed : 13.88 % Favored : 85.06 % 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: 1.05 (0.24), residues: 1372 helix: 1.64 (0.19), residues: 872 sheet: -4.63 (0.50), residues: 40 loop : -0.59 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 209 TYR 0.025 0.002 TYR C 161 PHE 0.021 0.001 PHE D 186 TRP 0.005 0.001 TRP C 221 HIS 0.002 0.001 HIS D 380 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (11628) covalent geometry : angle 0.49995 / 0.26 (15756) hydrogen bonds : bond 0.03406 / 2.26 ( 632) hydrogen bonds : angle 3.56764 / 2.50 ( 1848) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 138 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 ASP cc_start: 0.8814 (OUTLIER) cc_final: 0.8503 (t70) REVERT: A 188 GLN cc_start: 0.7999 (mm-40) cc_final: 0.7700 (mm110) REVERT: A 226 TYR cc_start: 0.8363 (m-80) cc_final: 0.7948 (m-80) REVERT: A 332 ASP cc_start: 0.8116 (m-30) cc_final: 0.7804 (m-30) REVERT: A 364 ARG cc_start: 0.4661 (OUTLIER) cc_final: 0.3719 (tpt-90) REVERT: A 396 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.7540 (ttt90) REVERT: A 486 PHE cc_start: 0.9049 (m-80) cc_final: 0.8758 (m-80) REVERT: B 150 ASP cc_start: 0.8814 (OUTLIER) cc_final: 0.8508 (t70) REVERT: B 188 GLN cc_start: 0.7994 (mm-40) cc_final: 0.7694 (mm110) REVERT: B 226 TYR cc_start: 0.8429 (m-80) cc_final: 0.8089 (m-80) REVERT: B 332 ASP cc_start: 0.8086 (m-30) cc_final: 0.7783 (m-30) REVERT: B 364 ARG cc_start: 0.4648 (OUTLIER) cc_final: 0.3714 (tpt-90) REVERT: B 396 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7554 (ttt90) REVERT: B 486 PHE cc_start: 0.9049 (m-80) cc_final: 0.8760 (m-80) REVERT: C 150 ASP cc_start: 0.8828 (OUTLIER) cc_final: 0.8518 (t70) REVERT: C 188 GLN cc_start: 0.8014 (mm-40) cc_final: 0.7708 (mm110) REVERT: C 332 ASP cc_start: 0.8080 (m-30) cc_final: 0.7783 (m-30) REVERT: C 364 ARG cc_start: 0.4704 (OUTLIER) cc_final: 0.3755 (tpt-90) REVERT: C 396 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7621 (ttt90) REVERT: C 486 PHE cc_start: 0.9038 (m-80) cc_final: 0.8776 (m-80) REVERT: D 150 ASP cc_start: 0.8806 (OUTLIER) cc_final: 0.8491 (t70) REVERT: D 188 GLN cc_start: 0.8000 (mm-40) cc_final: 0.7701 (mm110) REVERT: D 226 TYR cc_start: 0.8434 (m-80) cc_final: 0.8039 (m-80) REVERT: D 332 ASP cc_start: 0.8111 (m-30) cc_final: 0.7840 (m-30) REVERT: D 364 ARG cc_start: 0.4647 (OUTLIER) cc_final: 0.3745 (tpt-90) REVERT: D 396 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7542 (ttt90) REVERT: D 486 PHE cc_start: 0.9033 (m-80) cc_final: 0.8772 (m-80) outliers start: 13 outliers final: 1 residues processed: 150 average time/residue: 0.1001 time to fit residues: 20.7208 Evaluate side-chains 145 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 396 ARG Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 364 ARG Chi-restraints excluded: chain B residue 396 ARG Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 196 LYS Chi-restraints excluded: chain C residue 364 ARG Chi-restraints excluded: chain C residue 396 ARG Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 364 ARG Chi-restraints excluded: chain D residue 396 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 89 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 56 optimal weight: 7.9990 chunk 130 optimal weight: 0.6980 chunk 21 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 79 optimal weight: 0.2980 chunk 86 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.202457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.158796 restraints weight = 44688.522| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 4.31 r_work: 0.2978 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2811 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2811 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11628 Z= 0.125 Angle : 0.498 7.451 15756 Z= 0.263 Chirality : 0.042 0.183 1748 Planarity : 0.005 0.047 2004 Dihedral : 4.569 41.948 1560 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.14 % Allowed : 13.88 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.24), residues: 1372 helix: 1.62 (0.19), residues: 872 sheet: -4.73 (0.47), residues: 40 loop : -0.65 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 144 TYR 0.027 0.002 TYR D 161 PHE 0.022 0.001 PHE A 186 TRP 0.008 0.001 TRP C 221 HIS 0.002 0.001 HIS D 380 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (11628) covalent geometry : angle 0.49760 / 0.26 (15756) hydrogen bonds : bond 0.03394 / 2.26 ( 632) hydrogen bonds : angle 3.54468 / 2.48 ( 1848) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 144 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 ASP cc_start: 0.8787 (OUTLIER) cc_final: 0.8462 (t70) REVERT: A 188 GLN cc_start: 0.8012 (mm-40) cc_final: 0.7713 (mm110) REVERT: A 226 TYR cc_start: 0.8315 (m-80) cc_final: 0.7863 (m-80) REVERT: A 332 ASP cc_start: 0.8077 (m-30) cc_final: 0.7789 (m-30) REVERT: A 396 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7430 (ttt90) REVERT: A 486 PHE cc_start: 0.8993 (m-80) cc_final: 0.8739 (m-80) REVERT: B 150 ASP cc_start: 0.8788 (OUTLIER) cc_final: 0.8468 (t70) REVERT: B 188 GLN cc_start: 0.8005 (mm-40) cc_final: 0.7707 (mm110) REVERT: B 332 ASP cc_start: 0.8047 (m-30) cc_final: 0.7769 (m-30) REVERT: B 396 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.7440 (ttt90) REVERT: B 486 PHE cc_start: 0.8997 (m-80) cc_final: 0.8745 (m-80) REVERT: C 150 ASP cc_start: 0.8791 (OUTLIER) cc_final: 0.8474 (t70) REVERT: C 188 GLN cc_start: 0.7997 (mm-40) cc_final: 0.7716 (mm110) REVERT: C 226 TYR cc_start: 0.8314 (m-80) cc_final: 0.7877 (m-80) REVERT: C 332 ASP cc_start: 0.8038 (m-30) cc_final: 0.7768 (m-30) REVERT: C 396 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.7512 (ttt90) REVERT: C 486 PHE cc_start: 0.8985 (m-80) cc_final: 0.8714 (m-80) REVERT: D 150 ASP cc_start: 0.8787 (OUTLIER) cc_final: 0.8470 (t70) REVERT: D 188 GLN cc_start: 0.8008 (mm-40) cc_final: 0.7707 (mm110) REVERT: D 332 ASP cc_start: 0.8051 (m-30) cc_final: 0.7796 (m-30) REVERT: D 364 ARG cc_start: 0.4698 (OUTLIER) cc_final: 0.3766 (tpt-90) REVERT: D 396 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.7423 (ttt90) REVERT: D 486 PHE cc_start: 0.8977 (m-80) cc_final: 0.8707 (m-80) outliers start: 14 outliers final: 5 residues processed: 157 average time/residue: 0.1075 time to fit residues: 23.3509 Evaluate side-chains 157 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 143 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 396 ARG Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 364 ARG Chi-restraints excluded: chain B residue 396 ARG Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 196 LYS Chi-restraints excluded: chain C residue 364 ARG Chi-restraints excluded: chain C residue 396 ARG Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 364 ARG Chi-restraints excluded: chain D residue 396 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 100 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 44 optimal weight: 0.4980 chunk 12 optimal weight: 0.7980 chunk 115 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 127 optimal weight: 0.5980 chunk 114 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.202063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.158822 restraints weight = 45739.002| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 4.27 r_work: 0.2995 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2832 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2832 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11628 Z= 0.118 Angle : 0.502 8.297 15756 Z= 0.262 Chirality : 0.041 0.189 1748 Planarity : 0.005 0.047 2004 Dihedral : 4.552 42.031 1560 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.38 % Allowed : 13.47 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.24), residues: 1372 helix: 1.62 (0.19), residues: 872 sheet: -4.73 (0.45), residues: 40 loop : -0.65 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 144 TYR 0.026 0.002 TYR C 161 PHE 0.022 0.001 PHE C 186 TRP 0.008 0.001 TRP C 221 HIS 0.001 0.001 HIS D 380 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 (11628) covalent geometry : angle 0.50166 / 0.26 (15756) hydrogen bonds : bond 0.03321 / 2.21 ( 632) hydrogen bonds : angle 3.51783 / 2.46 ( 1848) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3300.48 seconds wall clock time: 57 minutes 2.63 seconds (3422.63 seconds total)