Starting phenix.real_space_refine on Wed Feb 4 15:54:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9clv_45731/02_2026/9clv_45731.cif Found real_map, /net/cci-nas-00/data/ceres_data/9clv_45731/02_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_45731/02_2026/9clv_45731.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9clv_45731/02_2026/9clv_45731.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9clv_45731/02_2026/9clv_45731.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9clv_45731/02_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-2.0-5952/lib/python3.9/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, 2 Unusual residues: {' K': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 3.53, per 1000 atoms: 0.31 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: 0.70 Conformation dependent library (CDL) restraints added in 658.5 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: 0.34 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: 1.54 Time building geometry restraints manager: 1.01 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.110 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: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 11.300 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 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 covalent geometry : bond 0.00364 (11628) covalent geometry : angle 0.55704 (15756) hydrogen bonds : bond 0.14653 ( 632) hydrogen bonds : angle 5.14415 ( 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 : 0.273 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: 0.1090 time to fit residues: 39.1206 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 : 0.438 ------------------------------------------------------------------------------- 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: 0.7980 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: 0.4232 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4109 r_free = 0.4109 target = 0.200930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.160068 restraints weight = 36266.590| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 6.80 r_work: 0.3060 rms_B_bonded: 5.31 restraints_weight: 2.0000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3134 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3135 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1444 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= 0.116 Angle : 0.488 5.443 15756 Z= 0.260 Chirality : 0.040 0.126 1748 Planarity : 0.005 0.044 2004 Dihedral : 5.263 45.808 1576 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.06 % Allowed : 11.12 % Favored : 87.82 % 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: 0.78 (0.24), residues: 1372 helix: 1.26 (0.19), residues: 848 sheet: -3.92 (0.77), residues: 40 loop : -0.30 (0.31), 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 161 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 covalent geometry : bond 0.00261 (11628) covalent geometry : angle 0.48766 (15756) hydrogen bonds : bond 0.04014 ( 632) hydrogen bonds : angle 3.95332 ( 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 185 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 172 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 LEU cc_start: 0.8412 (mt) cc_final: 0.8163 (mt) REVERT: A 346 GLU cc_start: 0.7221 (tp30) cc_final: 0.6583 (mt-10) REVERT: A 420 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7953 (mt-10) REVERT: A 486 PHE cc_start: 0.9099 (m-80) cc_final: 0.8863 (m-80) REVERT: A 489 ARG cc_start: 0.8302 (mtp-110) cc_final: 0.8067 (mtm110) REVERT: B 222 LEU cc_start: 0.8401 (mt) cc_final: 0.8154 (mt) REVERT: B 346 GLU cc_start: 0.7214 (tp30) cc_final: 0.6568 (mt-10) REVERT: B 486 PHE cc_start: 0.9102 (m-80) cc_final: 0.8860 (m-80) REVERT: B 489 ARG cc_start: 0.8296 (mtp-110) cc_final: 0.8070 (mtm110) REVERT: C 222 LEU cc_start: 0.8401 (mt) cc_final: 0.8144 (mt) REVERT: C 346 GLU cc_start: 0.7208 (tp30) cc_final: 0.6568 (mt-10) REVERT: C 420 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7944 (mt-10) REVERT: C 486 PHE cc_start: 0.9109 (m-80) cc_final: 0.8883 (m-80) REVERT: D 222 LEU cc_start: 0.8391 (mt) cc_final: 0.8169 (mt) REVERT: D 346 GLU cc_start: 0.7196 (tp30) cc_final: 0.6533 (mt-10) REVERT: D 486 PHE cc_start: 0.9098 (m-80) cc_final: 0.8893 (m-80) REVERT: D 489 ARG cc_start: 0.8272 (mtp-110) cc_final: 0.8037 (mtm110) outliers start: 13 outliers final: 8 residues processed: 184 average time/residue: 0.1064 time to fit residues: 26.9962 Evaluate side-chains 145 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 137 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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: 10.0000 chunk 62 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 75 optimal weight: 0.0570 chunk 54 optimal weight: 4.9990 chunk 89 optimal weight: 9.9990 chunk 50 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 126 optimal weight: 2.9990 chunk 83 optimal weight: 0.4980 chunk 65 optimal weight: 2.9990 overall best weight: 1.5102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.197582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.154777 restraints weight = 35184.259| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 7.11 r_work: 0.2928 rms_B_bonded: 5.33 restraints_weight: 2.0000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2890 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2890 r_free = 0.2890 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2890 r_free = 0.2890 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2890 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11628 Z= 0.183 Angle : 0.520 5.291 15756 Z= 0.276 Chirality : 0.042 0.130 1748 Planarity : 0.005 0.047 2004 Dihedral : 5.203 41.645 1572 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.81 % Allowed : 11.77 % Favored : 87.42 % 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: 0.79 (0.24), residues: 1372 helix: 1.23 (0.19), residues: 872 sheet: -4.27 (0.67), residues: 40 loop : -0.26 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 144 TYR 0.009 0.002 TYR B 187 PHE 0.009 0.001 PHE C 406 TRP 0.005 0.001 TRP B 436 HIS 0.003 0.001 HIS D 380 Details of bonding type rmsd covalent geometry : bond 0.00449 (11628) covalent geometry : angle 0.51979 (15756) hydrogen bonds : bond 0.04150 ( 632) hydrogen bonds : angle 3.94752 ( 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 148 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 138 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 GLN cc_start: 0.7890 (mm-40) cc_final: 0.7559 (mm110) REVERT: A 196 LYS cc_start: 0.8297 (mtpp) cc_final: 0.8001 (mtmm) REVERT: A 222 LEU cc_start: 0.8333 (mt) cc_final: 0.8032 (mt) REVERT: A 332 ASP cc_start: 0.8286 (m-30) cc_final: 0.8018 (m-30) REVERT: A 486 PHE cc_start: 0.9179 (m-80) cc_final: 0.8932 (m-80) REVERT: B 188 GLN cc_start: 0.7887 (mm-40) cc_final: 0.7553 (mm110) REVERT: B 196 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7986 (ttpt) REVERT: B 222 LEU cc_start: 0.8337 (mt) cc_final: 0.8039 (mt) REVERT: B 332 ASP cc_start: 0.8261 (m-30) cc_final: 0.8003 (m-30) REVERT: B 486 PHE cc_start: 0.9185 (m-80) cc_final: 0.8939 (m-80) REVERT: C 188 GLN cc_start: 0.7870 (mm-40) cc_final: 0.7531 (mm110) REVERT: C 196 LYS cc_start: 0.8307 (mtpp) cc_final: 0.8034 (mtmm) REVERT: C 222 LEU cc_start: 0.8329 (mt) cc_final: 0.7995 (mt) REVERT: C 332 ASP cc_start: 0.8291 (m-30) cc_final: 0.8034 (m-30) REVERT: C 486 PHE cc_start: 0.9176 (m-80) cc_final: 0.8932 (m-80) REVERT: D 188 GLN cc_start: 0.7905 (mm-40) cc_final: 0.7560 (mm110) REVERT: D 196 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.8002 (ttpt) REVERT: D 222 LEU cc_start: 0.8367 (mt) cc_final: 0.8073 (mt) REVERT: D 346 GLU cc_start: 0.7098 (tp30) cc_final: 0.6363 (mt-10) REVERT: D 486 PHE cc_start: 0.9171 (m-80) cc_final: 0.8924 (m-80) outliers start: 10 outliers final: 8 residues processed: 146 average time/residue: 0.1016 time to fit residues: 20.8298 Evaluate side-chains 141 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 131 time to evaluate : 0.437 ------------------------------------------------------------------------------- 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 196 LYS 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 196 LYS 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: 8.9990 chunk 14 optimal weight: 0.8980 chunk 119 optimal weight: 3.9990 chunk 132 optimal weight: 0.0270 chunk 57 optimal weight: 0.9980 chunk 47 optimal weight: 6.9990 chunk 96 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 55 optimal weight: 10.0000 chunk 118 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.201471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.161058 restraints weight = 33091.907| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 6.22 r_work: 0.2930 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2917 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2917 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1860 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= 0.117 Angle : 0.464 5.442 15756 Z= 0.244 Chirality : 0.040 0.124 1748 Planarity : 0.004 0.046 2004 Dihedral : 4.931 40.732 1572 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.14 % Allowed : 12.01 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.24), residues: 1372 helix: 1.34 (0.19), residues: 888 sheet: None (None), residues: 0 loop : -0.52 (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 0.008 0.001 PHE C 156 TRP 0.004 0.001 TRP D 305 HIS 0.001 0.001 HIS C 380 Details of bonding type rmsd covalent geometry : bond 0.00277 (11628) covalent geometry : angle 0.46442 (15756) hydrogen bonds : bond 0.03611 ( 632) hydrogen bonds : angle 3.72096 ( 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 151 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 LEU cc_start: 0.8282 (mt) cc_final: 0.7983 (mt) REVERT: A 332 ASP cc_start: 0.8087 (m-30) cc_final: 0.7787 (m-30) REVERT: A 486 PHE cc_start: 0.9142 (m-80) cc_final: 0.8878 (m-80) REVERT: A 489 ARG cc_start: 0.8297 (mtp-110) cc_final: 0.8051 (mtp-110) REVERT: B 222 LEU cc_start: 0.8284 (mt) cc_final: 0.7994 (mt) REVERT: B 332 ASP cc_start: 0.8071 (m-30) cc_final: 0.7774 (m-30) REVERT: B 486 PHE cc_start: 0.9146 (m-80) cc_final: 0.8887 (m-80) REVERT: C 222 LEU cc_start: 0.8224 (mt) cc_final: 0.7899 (mt) REVERT: C 332 ASP cc_start: 0.8071 (m-30) cc_final: 0.7775 (m-30) REVERT: C 486 PHE cc_start: 0.9141 (m-80) cc_final: 0.8883 (m-80) REVERT: D 222 LEU cc_start: 0.8256 (mt) cc_final: 0.7964 (mt) REVERT: D 486 PHE cc_start: 0.9135 (m-80) cc_final: 0.8903 (m-80) outliers start: 14 outliers final: 4 residues processed: 149 average time/residue: 0.0922 time to fit residues: 19.7985 Evaluate side-chains 135 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 131 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain B residue 364 ARG Chi-restraints excluded: chain C residue 364 ARG 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: 0.9980 chunk 2 optimal weight: 10.0000 chunk 65 optimal weight: 0.7980 chunk 98 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 chunk 67 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.202199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.160232 restraints weight = 38514.866| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 7.32 r_work: 0.2962 rms_B_bonded: 5.56 restraints_weight: 2.0000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3000 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 11628 Z= 0.134 Angle : 0.480 6.241 15756 Z= 0.253 Chirality : 0.041 0.122 1748 Planarity : 0.004 0.047 2004 Dihedral : 4.468 41.058 1560 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.97 % Allowed : 13.15 % Favored : 85.88 % 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: 0.81 (0.24), residues: 1372 helix: 1.35 (0.19), residues: 872 sheet: -4.46 (0.60), residues: 40 loop : -0.46 (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 0.022 0.001 PHE B 314 TRP 0.003 0.001 TRP D 305 HIS 0.002 0.001 HIS B 380 Details of bonding type rmsd covalent geometry : bond 0.00333 (11628) covalent geometry : angle 0.47994 (15756) hydrogen bonds : bond 0.03673 ( 632) hydrogen bonds : angle 3.72716 ( 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 147 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 135 time to evaluate : 0.417 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 150 ASP cc_start: 0.8744 (OUTLIER) cc_final: 0.8535 (t70) REVERT: A 188 GLN cc_start: 0.7949 (mm-40) cc_final: 0.7628 (mm110) REVERT: A 222 LEU cc_start: 0.8286 (mt) cc_final: 0.8003 (mt) REVERT: A 332 ASP cc_start: 0.8273 (m-30) cc_final: 0.7985 (m-30) REVERT: A 486 PHE cc_start: 0.9166 (m-80) cc_final: 0.8926 (m-80) REVERT: B 150 ASP cc_start: 0.8737 (OUTLIER) cc_final: 0.8525 (t70) REVERT: B 188 GLN cc_start: 0.7913 (mm-40) cc_final: 0.7585 (mm110) REVERT: B 196 LYS cc_start: 0.8064 (ttpt) cc_final: 0.7846 (ttpp) REVERT: B 222 LEU cc_start: 0.8290 (mt) cc_final: 0.8009 (mt) REVERT: B 332 ASP cc_start: 0.8250 (m-30) cc_final: 0.7960 (m-30) REVERT: B 486 PHE cc_start: 0.9173 (m-80) cc_final: 0.8927 (m-80) REVERT: C 137 MET cc_start: 0.8159 (mmm) cc_final: 0.7955 (mmt) REVERT: C 188 GLN cc_start: 0.7901 (mm-40) cc_final: 0.7562 (mm110) REVERT: C 222 LEU cc_start: 0.8284 (mt) cc_final: 0.7981 (mt) REVERT: C 332 ASP cc_start: 0.8250 (m-30) cc_final: 0.7971 (m-30) REVERT: C 486 PHE cc_start: 0.9176 (m-80) cc_final: 0.8935 (m-80) REVERT: D 150 ASP cc_start: 0.8731 (OUTLIER) cc_final: 0.8515 (t70) REVERT: D 188 GLN cc_start: 0.7925 (mm-40) cc_final: 0.7606 (mm110) REVERT: D 196 LYS cc_start: 0.8078 (ttpt) cc_final: 0.7872 (ttpp) REVERT: D 222 LEU cc_start: 0.8295 (mt) cc_final: 0.8009 (mt) REVERT: D 486 PHE cc_start: 0.9159 (m-80) cc_final: 0.8913 (m-80) outliers start: 12 outliers final: 7 residues processed: 144 average time/residue: 0.1130 time to fit residues: 22.7277 Evaluate side-chains 140 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 0.439 ------------------------------------------------------------------------------- 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 150 ASP Chi-restraints excluded: chain B residue 364 ARG Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain C residue 364 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 32 optimal weight: 0.8980 chunk 13 optimal weight: 6.9990 chunk 19 optimal weight: 0.1980 chunk 37 optimal weight: 0.1980 chunk 52 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 100 optimal weight: 0.7980 chunk 53 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4115 r_free = 0.4115 target = 0.201210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.164905 restraints weight = 41927.444| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 4.77 r_work: 0.3044 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3094 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3094 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11628 Z= 0.126 Angle : 0.471 5.207 15756 Z= 0.250 Chirality : 0.040 0.121 1748 Planarity : 0.004 0.046 2004 Dihedral : 4.452 41.350 1560 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.81 % Allowed : 12.91 % Favored : 86.28 % 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: 0.88 (0.24), residues: 1372 helix: 1.39 (0.19), residues: 872 sheet: -4.48 (0.59), residues: 40 loop : -0.40 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 489 TYR 0.015 0.002 TYR D 161 PHE 0.019 0.001 PHE D 314 TRP 0.003 0.001 TRP D 305 HIS 0.002 0.001 HIS B 380 Details of bonding type rmsd covalent geometry : bond 0.00309 (11628) covalent geometry : angle 0.47064 (15756) hydrogen bonds : bond 0.03566 ( 632) hydrogen bonds : angle 3.67809 ( 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 146 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 136 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 ASP cc_start: 0.8669 (OUTLIER) cc_final: 0.8450 (t70) REVERT: A 188 GLN cc_start: 0.7934 (mm-40) cc_final: 0.7614 (mm110) REVERT: A 222 LEU cc_start: 0.8226 (mt) cc_final: 0.7932 (mt) REVERT: A 332 ASP cc_start: 0.8200 (m-30) cc_final: 0.7889 (m-30) REVERT: A 486 PHE cc_start: 0.9079 (m-80) cc_final: 0.8824 (m-80) REVERT: B 150 ASP cc_start: 0.8659 (OUTLIER) cc_final: 0.8439 (t70) REVERT: B 188 GLN cc_start: 0.7890 (mm-40) cc_final: 0.7561 (mm110) REVERT: B 222 LEU cc_start: 0.8217 (mt) cc_final: 0.7917 (mt) REVERT: B 332 ASP cc_start: 0.8209 (m-30) cc_final: 0.7915 (m-30) REVERT: B 486 PHE cc_start: 0.9088 (m-80) cc_final: 0.8864 (m-80) REVERT: C 188 GLN cc_start: 0.7862 (mm-40) cc_final: 0.7526 (mm110) REVERT: C 222 LEU cc_start: 0.8239 (mt) cc_final: 0.7915 (mt) REVERT: C 332 ASP cc_start: 0.8175 (m-30) cc_final: 0.7873 (m-30) REVERT: C 486 PHE cc_start: 0.9092 (m-80) cc_final: 0.8872 (m-80) REVERT: D 150 ASP cc_start: 0.8640 (OUTLIER) cc_final: 0.8418 (t70) REVERT: D 188 GLN cc_start: 0.7895 (mm-40) cc_final: 0.7575 (mm110) REVERT: D 222 LEU cc_start: 0.8251 (mt) cc_final: 0.7957 (mt) REVERT: D 486 PHE cc_start: 0.9077 (m-80) cc_final: 0.8821 (m-80) outliers start: 10 outliers final: 7 residues processed: 143 average time/residue: 0.1086 time to fit residues: 21.9185 Evaluate side-chains 138 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 128 time to evaluate : 0.422 ------------------------------------------------------------------------------- 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 150 ASP Chi-restraints excluded: chain B residue 364 ARG Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain C residue 364 ARG Chi-restraints excluded: chain C residue 374 ILE 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: 0.7980 chunk 8 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 6 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 chunk 127 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 135 optimal weight: 0.0010 chunk 23 optimal weight: 3.9990 chunk 52 optimal weight: 8.9990 chunk 71 optimal weight: 0.7980 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4135 r_free = 0.4135 target = 0.203403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.169018 restraints weight = 39043.401| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 4.33 r_work: 0.3144 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3212 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3212 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 11628 Z= 0.114 Angle : 0.459 6.119 15756 Z= 0.242 Chirality : 0.040 0.121 1748 Planarity : 0.004 0.046 2004 Dihedral : 4.400 41.449 1560 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 0.89 % Allowed : 13.23 % Favored : 85.88 % 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: 0.97 (0.25), residues: 1372 helix: 1.46 (0.19), residues: 872 sheet: -4.52 (0.56), residues: 40 loop : -0.35 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 489 TYR 0.023 0.002 TYR D 161 PHE 0.023 0.001 PHE A 314 TRP 0.003 0.001 TRP C 305 HIS 0.001 0.000 HIS B 380 Details of bonding type rmsd covalent geometry : bond 0.00278 (11628) covalent geometry : angle 0.45945 (15756) hydrogen bonds : bond 0.03468 ( 632) hydrogen bonds : angle 3.62921 ( 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 153 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 142 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 GLN cc_start: 0.7708 (mm-40) cc_final: 0.7410 (mm110) REVERT: A 222 LEU cc_start: 0.8155 (mt) cc_final: 0.7929 (mt) REVERT: A 332 ASP cc_start: 0.8037 (m-30) cc_final: 0.7808 (m-30) REVERT: A 364 ARG cc_start: 0.4929 (OUTLIER) cc_final: 0.3988 (tpt-90) REVERT: A 486 PHE cc_start: 0.9039 (m-80) cc_final: 0.8832 (m-80) REVERT: B 188 GLN cc_start: 0.7662 (mm-40) cc_final: 0.7363 (mm110) REVERT: B 222 LEU cc_start: 0.8171 (mt) cc_final: 0.7943 (mt) REVERT: B 332 ASP cc_start: 0.8026 (m-30) cc_final: 0.7781 (m-30) REVERT: B 364 ARG cc_start: 0.4916 (OUTLIER) cc_final: 0.4009 (tpt-90) REVERT: C 222 LEU cc_start: 0.8189 (mt) cc_final: 0.7909 (mt) REVERT: C 332 ASP cc_start: 0.8068 (m-30) cc_final: 0.7813 (m-30) REVERT: C 364 ARG cc_start: 0.4926 (OUTLIER) cc_final: 0.3968 (tpt-90) REVERT: C 486 PHE cc_start: 0.9043 (m-80) cc_final: 0.8805 (m-80) REVERT: D 188 GLN cc_start: 0.7694 (mm-40) cc_final: 0.7390 (mm110) REVERT: D 222 LEU cc_start: 0.8194 (mt) cc_final: 0.7973 (mt) REVERT: D 486 PHE cc_start: 0.9028 (m-80) cc_final: 0.8793 (m-80) outliers start: 11 outliers final: 3 residues processed: 149 average time/residue: 0.1052 time to fit residues: 22.1283 Evaluate side-chains 141 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 135 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain B residue 364 ARG Chi-restraints excluded: chain C residue 196 LYS Chi-restraints excluded: chain C residue 364 ARG Chi-restraints excluded: chain D residue 364 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: 2.9990 chunk 92 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.201535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.153249 restraints weight = 35630.612| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 4.33 r_work: 0.2944 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2785 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2785 r_free = 0.2785 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2784 r_free = 0.2784 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2784 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 11628 Z= 0.147 Angle : 0.500 7.773 15756 Z= 0.266 Chirality : 0.041 0.124 1748 Planarity : 0.005 0.047 2004 Dihedral : 4.504 41.780 1560 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.14 % Allowed : 13.64 % Favored : 85.23 % 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: 0.92 (0.24), residues: 1372 helix: 1.44 (0.19), residues: 872 sheet: -4.66 (0.52), residues: 40 loop : -0.39 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 136 TYR 0.025 0.002 TYR A 161 PHE 0.008 0.001 PHE A 156 TRP 0.003 0.001 TRP B 437 HIS 0.002 0.001 HIS D 380 Details of bonding type rmsd covalent geometry : bond 0.00366 (11628) covalent geometry : angle 0.50001 (15756) hydrogen bonds : bond 0.03613 ( 632) hydrogen bonds : angle 3.67331 ( 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 149 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 135 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 GLN cc_start: 0.7982 (mm-40) cc_final: 0.7672 (mm110) REVERT: A 222 LEU cc_start: 0.7979 (mt) cc_final: 0.7646 (mt) REVERT: A 332 ASP cc_start: 0.8091 (m-30) cc_final: 0.7795 (m-30) REVERT: A 396 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7410 (ttt90) REVERT: A 486 PHE cc_start: 0.8973 (m-80) cc_final: 0.8714 (m-80) REVERT: B 188 GLN cc_start: 0.7981 (mm-40) cc_final: 0.7673 (mm110) REVERT: B 222 LEU cc_start: 0.8014 (mt) cc_final: 0.7689 (mt) REVERT: B 332 ASP cc_start: 0.8093 (m-30) cc_final: 0.7800 (m-30) REVERT: B 396 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.7414 (ttt90) REVERT: B 486 PHE cc_start: 0.8928 (m-80) cc_final: 0.8696 (m-80) REVERT: C 137 MET cc_start: 0.8094 (mmm) cc_final: 0.7827 (mmt) REVERT: C 188 GLN cc_start: 0.7954 (mm-40) cc_final: 0.7628 (mm110) REVERT: C 222 LEU cc_start: 0.7952 (mt) cc_final: 0.7606 (mt) REVERT: C 332 ASP cc_start: 0.8061 (m-30) cc_final: 0.7773 (m-30) REVERT: C 396 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.7431 (ttt90) REVERT: C 486 PHE cc_start: 0.8971 (m-80) cc_final: 0.8716 (m-80) REVERT: D 188 GLN cc_start: 0.8014 (mm-40) cc_final: 0.7709 (mm110) REVERT: D 222 LEU cc_start: 0.7989 (mt) cc_final: 0.7661 (mt) REVERT: D 486 PHE cc_start: 0.8973 (m-80) cc_final: 0.8716 (m-80) outliers start: 14 outliers final: 10 residues processed: 143 average time/residue: 0.1181 time to fit residues: 23.0997 Evaluate side-chains 144 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 131 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 LYS 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 364 ARG Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 396 ARG Chi-restraints excluded: chain C residue 196 LYS 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 364 ARG Chi-restraints excluded: chain D residue 374 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 54 optimal weight: 0.8980 chunk 12 optimal weight: 0.1980 chunk 101 optimal weight: 1.9990 chunk 113 optimal weight: 0.5980 chunk 131 optimal weight: 1.9990 chunk 120 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.204555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.169148 restraints weight = 41385.983| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 4.62 r_work: 0.3110 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3161 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3161 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 11628 Z= 0.115 Angle : 0.468 7.228 15756 Z= 0.248 Chirality : 0.040 0.122 1748 Planarity : 0.005 0.046 2004 Dihedral : 4.427 41.931 1560 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.14 % Allowed : 13.56 % Favored : 85.31 % 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: 1.02 (0.24), residues: 1372 helix: 1.53 (0.19), residues: 872 sheet: -4.57 (0.52), residues: 40 loop : -0.40 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 489 TYR 0.028 0.002 TYR C 161 PHE 0.023 0.001 PHE A 314 TRP 0.003 0.001 TRP C 305 HIS 0.001 0.000 HIS C 380 Details of bonding type rmsd covalent geometry : bond 0.00282 (11628) covalent geometry : angle 0.46791 (15756) hydrogen bonds : bond 0.03418 ( 632) hydrogen bonds : angle 3.59592 ( 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 154 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 140 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 GLN cc_start: 0.7824 (mm-40) cc_final: 0.7529 (mm110) REVERT: A 222 LEU cc_start: 0.8207 (mt) cc_final: 0.7944 (mt) REVERT: A 332 ASP cc_start: 0.8089 (m-30) cc_final: 0.7845 (m-30) REVERT: A 364 ARG cc_start: 0.4952 (OUTLIER) cc_final: 0.4040 (tpt-90) REVERT: A 486 PHE cc_start: 0.9055 (m-80) cc_final: 0.8836 (m-80) REVERT: B 188 GLN cc_start: 0.7770 (mm-40) cc_final: 0.7463 (mm110) REVERT: B 222 LEU cc_start: 0.8220 (mt) cc_final: 0.7954 (mt) REVERT: B 332 ASP cc_start: 0.8099 (m-30) cc_final: 0.7845 (m-30) REVERT: B 364 ARG cc_start: 0.4895 (OUTLIER) cc_final: 0.3984 (tpt-90) REVERT: C 188 GLN cc_start: 0.7777 (mm-40) cc_final: 0.7461 (mm110) REVERT: C 222 LEU cc_start: 0.8206 (mt) cc_final: 0.7930 (mt) REVERT: C 332 ASP cc_start: 0.8136 (m-30) cc_final: 0.7879 (m-30) REVERT: C 364 ARG cc_start: 0.5041 (OUTLIER) cc_final: 0.4086 (tpt-90) REVERT: C 486 PHE cc_start: 0.9067 (m-80) cc_final: 0.8819 (m-80) REVERT: D 188 GLN cc_start: 0.7862 (mm-40) cc_final: 0.7557 (mm110) REVERT: D 222 LEU cc_start: 0.8221 (mt) cc_final: 0.7950 (mt) REVERT: D 364 ARG cc_start: 0.4914 (OUTLIER) cc_final: 0.3988 (tpt-90) REVERT: D 486 PHE cc_start: 0.9057 (m-80) cc_final: 0.8807 (m-80) outliers start: 14 outliers final: 5 residues processed: 149 average time/residue: 0.1161 time to fit residues: 23.7145 Evaluate side-chains 140 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 131 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain B residue 364 ARG Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain C residue 196 LYS Chi-restraints excluded: chain C residue 364 ARG Chi-restraints excluded: chain D residue 364 ARG Chi-restraints excluded: chain D residue 374 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 89 optimal weight: 8.9990 chunk 103 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 85 optimal weight: 0.7980 chunk 56 optimal weight: 0.2980 chunk 130 optimal weight: 0.0050 chunk 21 optimal weight: 10.0000 chunk 17 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 98 optimal weight: 0.1980 overall best weight: 0.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.205521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.169898 restraints weight = 45092.222| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 4.78 r_work: 0.3130 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3204 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3204 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 11628 Z= 0.105 Angle : 0.473 6.998 15756 Z= 0.251 Chirality : 0.040 0.151 1748 Planarity : 0.005 0.046 2004 Dihedral : 4.377 41.980 1560 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.49 % Allowed : 14.45 % 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: 1.17 (0.24), residues: 1372 helix: 1.67 (0.19), residues: 872 sheet: -4.55 (0.52), residues: 40 loop : -0.38 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 135 TYR 0.026 0.002 TYR D 161 PHE 0.022 0.001 PHE B 186 TRP 0.003 0.001 TRP C 305 HIS 0.001 0.000 HIS D 380 Details of bonding type rmsd covalent geometry : bond 0.00247 (11628) covalent geometry : angle 0.47298 (15756) hydrogen bonds : bond 0.03270 ( 632) hydrogen bonds : angle 3.53309 ( 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 145 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 139 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 GLN cc_start: 0.7729 (mm-40) cc_final: 0.7440 (mm110) REVERT: A 222 LEU cc_start: 0.8163 (mt) cc_final: 0.7924 (mt) REVERT: A 332 ASP cc_start: 0.8066 (m-30) cc_final: 0.7852 (m-30) REVERT: A 364 ARG cc_start: 0.4885 (OUTLIER) cc_final: 0.4027 (tpt-90) REVERT: A 486 PHE cc_start: 0.9057 (m-80) cc_final: 0.8814 (m-80) REVERT: B 188 GLN cc_start: 0.7691 (mm-40) cc_final: 0.7406 (mm110) REVERT: B 222 LEU cc_start: 0.8197 (mt) cc_final: 0.7947 (mt) REVERT: B 332 ASP cc_start: 0.8080 (m-30) cc_final: 0.7861 (m-30) REVERT: B 364 ARG cc_start: 0.4858 (OUTLIER) cc_final: 0.3495 (mmm-85) REVERT: C 188 GLN cc_start: 0.7694 (mm-40) cc_final: 0.7394 (mm110) REVERT: C 222 LEU cc_start: 0.8201 (mt) cc_final: 0.7931 (mt) REVERT: C 332 ASP cc_start: 0.8094 (m-30) cc_final: 0.7885 (m-30) REVERT: C 364 ARG cc_start: 0.4859 (OUTLIER) cc_final: 0.3972 (tpt-90) REVERT: C 486 PHE cc_start: 0.9062 (m-80) cc_final: 0.8830 (m-80) REVERT: D 188 GLN cc_start: 0.7748 (mm-40) cc_final: 0.7450 (mm110) REVERT: D 222 LEU cc_start: 0.8194 (mt) cc_final: 0.7936 (mt) REVERT: D 364 ARG cc_start: 0.4919 (OUTLIER) cc_final: 0.3965 (tpt-90) REVERT: D 486 PHE cc_start: 0.9056 (m-80) cc_final: 0.8815 (m-80) outliers start: 6 outliers final: 2 residues processed: 143 average time/residue: 0.1163 time to fit residues: 23.2743 Evaluate side-chains 137 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 131 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain B residue 364 ARG Chi-restraints excluded: chain C residue 196 LYS Chi-restraints excluded: chain C residue 364 ARG Chi-restraints excluded: chain D residue 364 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 100 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 44 optimal weight: 0.1980 chunk 12 optimal weight: 0.4980 chunk 115 optimal weight: 6.9990 chunk 5 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 127 optimal weight: 0.6980 chunk 114 optimal weight: 0.5980 chunk 67 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.203003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.168346 restraints weight = 45164.166| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 4.91 r_work: 0.2999 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2933 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2933 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11628 Z= 0.111 Angle : 0.471 6.622 15756 Z= 0.250 Chirality : 0.040 0.162 1748 Planarity : 0.005 0.047 2004 Dihedral : 4.384 41.681 1560 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.49 % Allowed : 14.29 % Favored : 85.23 % 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: 1.22 (0.24), residues: 1372 helix: 1.73 (0.19), residues: 872 sheet: -4.62 (0.49), residues: 40 loop : -0.41 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 489 TYR 0.028 0.002 TYR B 161 PHE 0.029 0.001 PHE C 314 TRP 0.002 0.001 TRP C 305 HIS 0.001 0.001 HIS C 380 Details of bonding type rmsd covalent geometry : bond 0.00267 (11628) covalent geometry : angle 0.47113 (15756) hydrogen bonds : bond 0.03224 ( 632) hydrogen bonds : angle 3.51656 ( 1848) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2772.93 seconds wall clock time: 48 minutes 5.49 seconds (2885.49 seconds total)