Starting phenix.real_space_refine on Sat Oct 24 11:28:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y75_72643/10_2026/9y75_72643.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y75_72643/10_2026/9y75_72643.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9y75_72643/10_2026/9y75_72643.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y75_72643/10_2026/9y75_72643.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9y75_72643/10_2026/9y75_72643.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y75_72643/10_2026/9y75_72643.map" } resolution = 3.47 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= 0.002 sd= 0.045 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: 4 Type Number sf(0) Gaussians S 80 5.16 5 C 8552 2.51 5 N 2056 2.21 5 O 2336 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13024 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3229 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 4, 'TRANS': 395} Chain breaks: 4 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'AQV': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C, B, D Time building chain proxies: 2.96, per 1000 atoms: 0.23 Number of scatterers: 13024 At special positions: 0 Unit cell: (102.837, 102.837, 109.332, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 80 16.00 O 2336 8.00 N 2056 7.00 C 8552 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 164 " - pdb=" SG CYS A 190 " distance=2.04 Simple disulfide: pdb=" SG CYS A 243 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS C 164 " - pdb=" SG CYS C 190 " distance=2.04 Simple disulfide: pdb=" SG CYS C 243 " - pdb=" SG CYS C 274 " distance=2.03 Simple disulfide: pdb=" SG CYS B 164 " - pdb=" SG CYS B 190 " distance=2.04 Simple disulfide: pdb=" SG CYS B 243 " - pdb=" SG CYS B 274 " distance=2.03 Simple disulfide: pdb=" SG CYS D 164 " - pdb=" SG CYS D 190 " distance=2.04 Simple disulfide: pdb=" SG CYS D 243 " - pdb=" SG CYS D 274 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.07 Conformation dependent library (CDL) restraints added in 487.3 milliseconds 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3048 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 8 sheets defined 63.8% alpha, 16.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 65 through 106 removed outlier: 3.900A pdb=" N GLN A 69 " --> pdb=" O LYS A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 140 removed outlier: 3.735A pdb=" N ALA A 134 " --> pdb=" O SER A 130 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE A 135 " --> pdb=" O ILE A 131 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG A 139 " --> pdb=" O ILE A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 201 removed outlier: 3.971A pdb=" N GLU A 201 " --> pdb=" O VAL A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 212 Processing helix chain 'A' and resid 231 through 238 removed outlier: 3.916A pdb=" N ALA A 234 " --> pdb=" O ASP A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 322 removed outlier: 3.969A pdb=" N PHE A 322 " --> pdb=" O LEU A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 371 Processing helix chain 'A' and resid 376 through 392 removed outlier: 3.922A pdb=" N ILE A 380 " --> pdb=" O ASP A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 397 Processing helix chain 'A' and resid 402 through 439 removed outlier: 3.729A pdb=" N MET A 410 " --> pdb=" O LEU A 406 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLN A 411 " --> pdb=" O ILE A 407 " (cutoff:3.500A) Proline residue: A 415 - end of helix Processing helix chain 'A' and resid 448 through 461 Processing helix chain 'A' and resid 464 through 471 Processing helix chain 'A' and resid 476 through 512 removed outlier: 3.899A pdb=" N TRP A 480 " --> pdb=" O SER A 476 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP A 508 " --> pdb=" O ALA A 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 106 Processing helix chain 'C' and resid 123 through 140 removed outlier: 3.735A pdb=" N ALA C 134 " --> pdb=" O SER C 130 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE C 135 " --> pdb=" O ILE C 131 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG C 139 " --> pdb=" O ILE C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 201 removed outlier: 3.971A pdb=" N GLU C 201 " --> pdb=" O VAL C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 212 Processing helix chain 'C' and resid 231 through 238 removed outlier: 3.916A pdb=" N ALA C 234 " --> pdb=" O ASP C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 322 removed outlier: 3.970A pdb=" N PHE C 322 " --> pdb=" O LEU C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 371 Processing helix chain 'C' and resid 376 through 392 removed outlier: 3.921A pdb=" N ILE C 380 " --> pdb=" O ASP C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 397 Processing helix chain 'C' and resid 402 through 439 removed outlier: 3.729A pdb=" N MET C 410 " --> pdb=" O LEU C 406 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLN C 411 " --> pdb=" O ILE C 407 " (cutoff:3.500A) Proline residue: C 415 - end of helix Processing helix chain 'C' and resid 448 through 461 Processing helix chain 'C' and resid 464 through 471 Processing helix chain 'C' and resid 476 through 512 removed outlier: 3.899A pdb=" N TRP C 480 " --> pdb=" O SER C 476 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP C 508 " --> pdb=" O ALA C 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 106 Processing helix chain 'B' and resid 123 through 140 removed outlier: 3.735A pdb=" N ALA B 134 " --> pdb=" O SER B 130 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE B 135 " --> pdb=" O ILE B 131 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG B 139 " --> pdb=" O ILE B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 201 removed outlier: 3.970A pdb=" N GLU B 201 " --> pdb=" O VAL B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 212 Processing helix chain 'B' and resid 231 through 238 removed outlier: 3.916A pdb=" N ALA B 234 " --> pdb=" O ASP B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 322 removed outlier: 3.970A pdb=" N PHE B 322 " --> pdb=" O LEU B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 371 Processing helix chain 'B' and resid 376 through 392 removed outlier: 3.921A pdb=" N ILE B 380 " --> pdb=" O ASP B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 397 Processing helix chain 'B' and resid 402 through 439 removed outlier: 3.729A pdb=" N MET B 410 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLN B 411 " --> pdb=" O ILE B 407 " (cutoff:3.500A) Proline residue: B 415 - end of helix Processing helix chain 'B' and resid 448 through 461 Processing helix chain 'B' and resid 464 through 471 Processing helix chain 'B' and resid 476 through 512 removed outlier: 3.899A pdb=" N TRP B 480 " --> pdb=" O SER B 476 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP B 508 " --> pdb=" O ALA B 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 106 Processing helix chain 'D' and resid 123 through 140 removed outlier: 3.734A pdb=" N ALA D 134 " --> pdb=" O SER D 130 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE D 135 " --> pdb=" O ILE D 131 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG D 139 " --> pdb=" O ILE D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 201 removed outlier: 3.971A pdb=" N GLU D 201 " --> pdb=" O VAL D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 212 Processing helix chain 'D' and resid 231 through 238 removed outlier: 3.916A pdb=" N ALA D 234 " --> pdb=" O ASP D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 322 removed outlier: 3.968A pdb=" N PHE D 322 " --> pdb=" O LEU D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 371 Processing helix chain 'D' and resid 376 through 392 removed outlier: 3.921A pdb=" N ILE D 380 " --> pdb=" O ASP D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 397 Processing helix chain 'D' and resid 402 through 439 removed outlier: 3.729A pdb=" N MET D 410 " --> pdb=" O LEU D 406 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLN D 411 " --> pdb=" O ILE D 407 " (cutoff:3.500A) Proline residue: D 415 - end of helix Processing helix chain 'D' and resid 448 through 461 Processing helix chain 'D' and resid 464 through 471 Processing helix chain 'D' and resid 476 through 512 removed outlier: 3.899A pdb=" N TRP D 480 " --> pdb=" O SER D 476 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP D 508 " --> pdb=" O ALA D 504 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 119 through 121 removed outlier: 3.725A pdb=" N CYS A 119 " --> pdb=" O ILE A 263 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS A 262 " --> pdb=" O ASP A 253 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL A 221 " --> pdb=" O PHE A 252 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU A 218 " --> pdb=" O TYR A 168 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N TYR A 168 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN A 220 " --> pdb=" O GLN A 166 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ALA A 226 " --> pdb=" O GLY A 160 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLY A 160 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 163 " --> pdb=" O ILE A 191 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE A 191 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LYS A 165 " --> pdb=" O ASP A 189 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ASP A 189 " --> pdb=" O LYS A 165 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 150 through 151 removed outlier: 3.507A pdb=" N GLY A 150 " --> pdb=" O LYS A 228 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL A 221 " --> pdb=" O PHE A 252 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N CYS A 243 " --> pdb=" O GLU A 272 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU A 268 " --> pdb=" O GLN A 247 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 119 through 121 removed outlier: 3.725A pdb=" N CYS C 119 " --> pdb=" O ILE C 263 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS C 262 " --> pdb=" O ASP C 253 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL C 221 " --> pdb=" O PHE C 252 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU C 218 " --> pdb=" O TYR C 168 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N TYR C 168 " --> pdb=" O LEU C 218 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN C 220 " --> pdb=" O GLN C 166 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ALA C 226 " --> pdb=" O GLY C 160 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLY C 160 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL C 163 " --> pdb=" O ILE C 191 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE C 191 " --> pdb=" O VAL C 163 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LYS C 165 " --> pdb=" O ASP C 189 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ASP C 189 " --> pdb=" O LYS C 165 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 150 through 151 removed outlier: 3.507A pdb=" N GLY C 150 " --> pdb=" O LYS C 228 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL C 221 " --> pdb=" O PHE C 252 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N CYS C 243 " --> pdb=" O GLU C 272 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU C 268 " --> pdb=" O GLN C 247 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 119 through 121 removed outlier: 3.725A pdb=" N CYS B 119 " --> pdb=" O ILE B 263 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS B 262 " --> pdb=" O ASP B 253 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL B 221 " --> pdb=" O PHE B 252 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU B 218 " --> pdb=" O TYR B 168 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N TYR B 168 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN B 220 " --> pdb=" O GLN B 166 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ALA B 226 " --> pdb=" O GLY B 160 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N GLY B 160 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL B 163 " --> pdb=" O ILE B 191 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE B 191 " --> pdb=" O VAL B 163 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LYS B 165 " --> pdb=" O ASP B 189 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ASP B 189 " --> pdb=" O LYS B 165 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 150 through 151 removed outlier: 3.507A pdb=" N GLY B 150 " --> pdb=" O LYS B 228 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL B 221 " --> pdb=" O PHE B 252 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N CYS B 243 " --> pdb=" O GLU B 272 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU B 268 " --> pdb=" O GLN B 247 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 119 through 121 removed outlier: 3.725A pdb=" N CYS D 119 " --> pdb=" O ILE D 263 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS D 262 " --> pdb=" O ASP D 253 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL D 221 " --> pdb=" O PHE D 252 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU D 218 " --> pdb=" O TYR D 168 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N TYR D 168 " --> pdb=" O LEU D 218 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN D 220 " --> pdb=" O GLN D 166 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ALA D 226 " --> pdb=" O GLY D 160 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLY D 160 " --> pdb=" O ALA D 226 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL D 163 " --> pdb=" O ILE D 191 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE D 191 " --> pdb=" O VAL D 163 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LYS D 165 " --> pdb=" O ASP D 189 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ASP D 189 " --> pdb=" O LYS D 165 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 150 through 151 removed outlier: 3.506A pdb=" N GLY D 150 " --> pdb=" O LYS D 228 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL D 221 " --> pdb=" O PHE D 252 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N CYS D 243 " --> pdb=" O GLU D 272 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU D 268 " --> pdb=" O GLN D 247 " (cutoff:3.500A) 904 hydrogen bonds defined for protein. 2604 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: 2.40 Time building geometry restraints manager: 1.42 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: 3029 1.33 - 1.45: 2896 1.45 - 1.58: 7255 1.58 - 1.70: 0 1.70 - 1.82: 112 Bond restraints: 13292 Sorted by residual: bond pdb=" C10 AQV B 601 " pdb=" N2 AQV B 601 " ideal model delta sigma weight residual 1.367 1.447 -0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" C10 AQV A 601 " pdb=" N2 AQV A 601 " ideal model delta sigma weight residual 1.367 1.447 -0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" C10 AQV C 601 " pdb=" N2 AQV C 601 " ideal model delta sigma weight residual 1.367 1.447 -0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" C10 AQV D 601 " pdb=" N2 AQV D 601 " ideal model delta sigma weight residual 1.367 1.447 -0.080 2.00e-02 2.50e+03 1.58e+01 bond pdb=" C15 AQV C 601 " pdb=" N2 AQV C 601 " ideal model delta sigma weight residual 1.423 1.497 -0.074 2.00e-02 2.50e+03 1.38e+01 ... (remaining 13287 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 17767 2.09 - 4.18: 181 4.18 - 6.27: 36 6.27 - 8.37: 20 8.37 - 10.46: 8 Bond angle restraints: 18012 Sorted by residual: angle pdb=" N GLU C 454 " pdb=" CA GLU C 454 " pdb=" CB GLU C 454 " ideal model delta sigma weight residual 110.28 116.01 -5.73 1.55e+00 4.16e-01 1.36e+01 angle pdb=" C9 AQV B 601 " pdb=" C10 AQV B 601 " pdb=" N2 AQV B 601 " ideal model delta sigma weight residual 119.50 129.96 -10.46 3.00e+00 1.11e-01 1.21e+01 angle pdb=" C9 AQV C 601 " pdb=" C10 AQV C 601 " pdb=" N2 AQV C 601 " ideal model delta sigma weight residual 119.50 129.92 -10.42 3.00e+00 1.11e-01 1.21e+01 angle pdb=" C9 AQV A 601 " pdb=" C10 AQV A 601 " pdb=" N2 AQV A 601 " ideal model delta sigma weight residual 119.50 129.92 -10.42 3.00e+00 1.11e-01 1.21e+01 angle pdb=" C9 AQV D 601 " pdb=" C10 AQV D 601 " pdb=" N2 AQV D 601 " ideal model delta sigma weight residual 119.50 129.89 -10.39 3.00e+00 1.11e-01 1.20e+01 ... (remaining 18007 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.46: 7592 34.46 - 68.92: 196 68.92 - 103.38: 36 103.38 - 137.84: 8 137.84 - 172.30: 12 Dihedral angle restraints: 7844 sinusoidal: 3136 harmonic: 4708 Sorted by residual: dihedral pdb=" C13 AQV B 601 " pdb=" C11 AQV B 601 " pdb=" C12 AQV B 601 " pdb=" C21 AQV B 601 " ideal model delta sinusoidal sigma weight residual 93.84 -93.86 -172.30 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C13 AQV A 601 " pdb=" C11 AQV A 601 " pdb=" C12 AQV A 601 " pdb=" C21 AQV A 601 " ideal model delta sinusoidal sigma weight residual 93.84 -93.88 -172.28 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C13 AQV C 601 " pdb=" C11 AQV C 601 " pdb=" C12 AQV C 601 " pdb=" C21 AQV C 601 " ideal model delta sinusoidal sigma weight residual 93.84 -93.92 -172.24 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 7841 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1540 0.038 - 0.076: 459 0.076 - 0.114: 88 0.114 - 0.152: 29 0.152 - 0.190: 4 Chirality restraints: 2120 Sorted by residual: chirality pdb=" CA PHE A 494 " pdb=" N PHE A 494 " pdb=" C PHE A 494 " pdb=" CB PHE A 494 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.01e-01 chirality pdb=" CA PHE C 494 " pdb=" N PHE C 494 " pdb=" C PHE C 494 " pdb=" CB PHE C 494 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.01e-01 chirality pdb=" CA PHE D 494 " pdb=" N PHE D 494 " pdb=" C PHE D 494 " pdb=" CB PHE D 494 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.93e-01 ... (remaining 2117 not shown) Planarity restraints: 2176 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU C 201 " -0.042 5.00e-02 4.00e+02 6.34e-02 6.42e+00 pdb=" N PRO C 202 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO C 202 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 202 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 201 " -0.042 5.00e-02 4.00e+02 6.32e-02 6.39e+00 pdb=" N PRO A 202 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 202 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 202 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 201 " -0.042 5.00e-02 4.00e+02 6.31e-02 6.38e+00 pdb=" N PRO D 202 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO D 202 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 202 " -0.034 5.00e-02 4.00e+02 ... (remaining 2173 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 256 2.69 - 3.24: 12702 3.24 - 3.80: 19798 3.80 - 4.35: 25132 4.35 - 4.90: 43800 Nonbonded interactions: 101688 Sorted by model distance: nonbonded pdb=" OG1 THR A 357 " pdb=" OG SER A 385 " model vdw 2.141 3.040 nonbonded pdb=" OG1 THR B 357 " pdb=" OG SER B 385 " model vdw 2.141 3.040 nonbonded pdb=" OG1 THR D 357 " pdb=" OG SER D 385 " model vdw 2.141 3.040 nonbonded pdb=" OG1 THR C 357 " pdb=" OG SER C 385 " model vdw 2.141 3.040 nonbonded pdb=" OH TYR D 428 " pdb=" O ALA D 453 " model vdw 2.188 3.040 ... (remaining 101683 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 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: 0.020 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.390 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 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 : 0.003 0.080 13300 Z= 0.173 Angle : 0.626 10.456 18028 Z= 0.316 Chirality : 0.039 0.190 2120 Planarity : 0.003 0.063 2176 Dihedral : 18.864 172.301 4772 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % 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: 1.28 (0.22), residues: 1560 helix: 2.34 (0.17), residues: 936 sheet: -0.33 (0.40), residues: 160 loop : -1.99 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 484 TYR 0.016 0.001 TYR C 486 PHE 0.024 0.001 PHE B 494 TRP 0.029 0.002 TRP C 480 HIS 0.002 0.001 HIS B 236 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.17 (13292) covalent geometry : angle 0.62530 / 0.32 (18012) SS BOND : bond 0.00590 / 0.32 ( 8) SS BOND : angle 1.14756 / 0.63 ( 16) hydrogen bonds : bond 0.15305 / 10.54 ( 876) hydrogen bonds : angle 5.26733 / 3.83 ( 2604) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 442 TYR cc_start: 0.7673 (m-80) cc_final: 0.6934 (m-80) REVERT: C 359 ILE cc_start: 0.8711 (mt) cc_final: 0.8373 (mt) REVERT: B 359 ILE cc_start: 0.8750 (mt) cc_final: 0.8380 (mt) REVERT: D 442 TYR cc_start: 0.7592 (m-80) cc_final: 0.6981 (m-80) outliers start: 0 outliers final: 0 residues processed: 217 average time/residue: 0.0744 time to fit residues: 27.1600 Evaluate side-chains 158 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 8.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.187760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.153937 restraints weight = 14276.936| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 1.88 r_work: 0.3317 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 13300 Z= 0.214 Angle : 0.637 7.696 18028 Z= 0.329 Chirality : 0.042 0.212 2120 Planarity : 0.004 0.072 2176 Dihedral : 20.496 174.796 1804 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.38 % Allowed : 10.36 % Favored : 86.26 % 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: 1.27 (0.22), residues: 1560 helix: 2.21 (0.17), residues: 968 sheet: -0.25 (0.41), residues: 180 loop : -2.11 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 484 TYR 0.021 0.002 TYR C 510 PHE 0.028 0.002 PHE D 296 TRP 0.024 0.002 TRP D 480 HIS 0.003 0.001 HIS A 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.21 (13292) covalent geometry : angle 0.63594 / 0.33 (18012) SS BOND : bond 0.00683 / 0.30 ( 8) SS BOND : angle 1.61601 / 0.88 ( 16) hydrogen bonds : bond 0.04336 / 2.84 ( 876) hydrogen bonds : angle 4.27819 / 3.06 ( 2604) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 175 time to evaluate : 0.479 Fit side-chains REVERT: A 207 GLN cc_start: 0.8562 (mp10) cc_final: 0.7777 (mp-120) REVERT: A 296 PHE cc_start: 0.6529 (m-80) cc_final: 0.6295 (m-80) REVERT: A 442 TYR cc_start: 0.8319 (m-80) cc_final: 0.7740 (m-80) REVERT: A 469 PHE cc_start: 0.7377 (m-80) cc_final: 0.7146 (m-80) REVERT: A 480 TRP cc_start: 0.6500 (m100) cc_final: 0.5740 (m100) REVERT: C 296 PHE cc_start: 0.6580 (m-80) cc_final: 0.6358 (m-80) REVERT: C 359 ILE cc_start: 0.8605 (mt) cc_final: 0.8343 (mt) REVERT: C 426 MET cc_start: 0.7683 (mmt) cc_final: 0.7121 (mmt) REVERT: C 469 PHE cc_start: 0.7495 (m-80) cc_final: 0.7271 (m-80) REVERT: C 494 PHE cc_start: 0.6648 (OUTLIER) cc_final: 0.5879 (t80) REVERT: B 296 PHE cc_start: 0.6480 (m-80) cc_final: 0.6266 (m-80) REVERT: B 359 ILE cc_start: 0.8618 (mt) cc_final: 0.8353 (mt) REVERT: B 469 PHE cc_start: 0.7488 (m-80) cc_final: 0.7272 (m-80) REVERT: B 480 TRP cc_start: 0.6317 (m100) cc_final: 0.5713 (m100) REVERT: D 207 GLN cc_start: 0.8364 (mp10) cc_final: 0.7648 (mp-120) REVERT: D 296 PHE cc_start: 0.6585 (m-80) cc_final: 0.6361 (m-80) REVERT: D 442 TYR cc_start: 0.8161 (m-80) cc_final: 0.7675 (m-80) REVERT: D 469 PHE cc_start: 0.7451 (m-80) cc_final: 0.7236 (m-80) REVERT: D 491 ILE cc_start: 0.6620 (OUTLIER) cc_final: 0.6348 (mt) outliers start: 49 outliers final: 34 residues processed: 193 average time/residue: 0.0727 time to fit residues: 23.7805 Evaluate side-chains 198 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 162 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain D residue 458 SER Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 494 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [58, 5, 127, 121, 137, 94, 89, 129, 149, 148, 117] chunk 58 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 127 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 chunk 149 optimal weight: 8.9990 chunk 148 optimal weight: 0.9980 chunk 117 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 461 ASN D 461 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.190715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.159360 restraints weight = 14334.586| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 1.75 r_work: 0.3390 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13300 Z= 0.137 Angle : 0.557 7.954 18028 Z= 0.278 Chirality : 0.038 0.148 2120 Planarity : 0.004 0.072 2176 Dihedral : 20.467 175.565 1804 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.62 % Allowed : 13.67 % Favored : 83.70 % 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: 1.55 (0.22), residues: 1560 helix: 2.45 (0.17), residues: 968 sheet: -0.13 (0.42), residues: 160 loop : -1.98 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 238 TYR 0.019 0.001 TYR B 442 PHE 0.019 0.001 PHE D 296 TRP 0.014 0.001 TRP D 480 HIS 0.002 0.000 HIS D 443 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (13292) covalent geometry : angle 0.55603 / 0.28 (18012) SS BOND : bond 0.00836 / 0.41 ( 8) SS BOND : angle 1.41174 / 0.73 ( 16) hydrogen bonds : bond 0.03681 / 2.43 ( 876) hydrogen bonds : angle 3.98546 / 2.87 ( 2604) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 181 time to evaluate : 0.413 Fit side-chains REVERT: A 190 CYS cc_start: 0.5819 (t) cc_final: 0.5465 (t) REVERT: A 296 PHE cc_start: 0.6545 (m-80) cc_final: 0.6297 (m-80) REVERT: A 442 TYR cc_start: 0.8137 (m-80) cc_final: 0.7514 (m-80) REVERT: A 480 TRP cc_start: 0.6297 (m100) cc_final: 0.5487 (m100) REVERT: C 207 GLN cc_start: 0.8025 (mp10) cc_final: 0.7477 (mp-120) REVERT: C 296 PHE cc_start: 0.6517 (m-80) cc_final: 0.6226 (m-80) REVERT: C 359 ILE cc_start: 0.8536 (mt) cc_final: 0.8247 (mt) REVERT: C 426 MET cc_start: 0.7422 (mmt) cc_final: 0.6921 (mmt) REVERT: C 480 TRP cc_start: 0.5901 (t-100) cc_final: 0.5561 (m-90) REVERT: C 494 PHE cc_start: 0.6522 (OUTLIER) cc_final: 0.5765 (t80) REVERT: B 296 PHE cc_start: 0.6532 (m-80) cc_final: 0.6314 (m-80) REVERT: B 359 ILE cc_start: 0.8560 (mt) cc_final: 0.8286 (mt) REVERT: B 480 TRP cc_start: 0.6127 (m100) cc_final: 0.5465 (m100) REVERT: D 207 GLN cc_start: 0.8129 (mp10) cc_final: 0.7541 (mp-120) REVERT: D 296 PHE cc_start: 0.6592 (m-80) cc_final: 0.6309 (m-80) REVERT: D 299 MET cc_start: 0.7179 (OUTLIER) cc_final: 0.6951 (ttp) REVERT: D 442 TYR cc_start: 0.8004 (m-80) cc_final: 0.7551 (m-80) REVERT: D 480 TRP cc_start: 0.6034 (t-100) cc_final: 0.5684 (m-90) outliers start: 38 outliers final: 30 residues processed: 195 average time/residue: 0.0791 time to fit residues: 25.5972 Evaluate side-chains 204 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 172 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 421 CYS Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 454 GLU Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 421 CYS Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 421 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [126, 125, 30, 158, 49, 103, 44, 38, 21, 134, 60] chunk 126 optimal weight: 1.9990 chunk 125 optimal weight: 0.7980 chunk 30 optimal weight: 7.9990 chunk 158 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 44 optimal weight: 0.4980 chunk 38 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 474 GLN ** 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 = 0.4074 r_free = 0.4074 target = 0.190710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.161917 restraints weight = 14283.288| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 1.40 r_work: 0.3456 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13300 Z= 0.133 Angle : 0.544 8.408 18028 Z= 0.272 Chirality : 0.038 0.148 2120 Planarity : 0.004 0.072 2176 Dihedral : 20.400 175.396 1804 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.18 % Allowed : 16.23 % Favored : 80.59 % 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: 1.66 (0.22), residues: 1560 helix: 2.65 (0.17), residues: 956 sheet: -0.15 (0.42), residues: 160 loop : -2.06 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 317 TYR 0.015 0.001 TYR B 442 PHE 0.022 0.001 PHE C 469 TRP 0.014 0.001 TRP A 480 HIS 0.002 0.001 HIS B 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (13292) covalent geometry : angle 0.54182 / 0.27 (18012) SS BOND : bond 0.00547 / 0.28 ( 8) SS BOND : angle 1.84981 / 0.93 ( 16) hydrogen bonds : bond 0.03534 / 2.32 ( 876) hydrogen bonds : angle 3.87576 / 2.78 ( 2604) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 183 time to evaluate : 0.383 Fit side-chains REVERT: A 296 PHE cc_start: 0.6520 (m-80) cc_final: 0.6232 (m-80) REVERT: A 442 TYR cc_start: 0.8209 (m-80) cc_final: 0.7575 (m-80) REVERT: A 480 TRP cc_start: 0.6635 (m100) cc_final: 0.5586 (m100) REVERT: C 207 GLN cc_start: 0.8217 (mp10) cc_final: 0.7547 (mp-120) REVERT: C 296 PHE cc_start: 0.6824 (m-80) cc_final: 0.6387 (m-80) REVERT: C 359 ILE cc_start: 0.8491 (mt) cc_final: 0.8212 (mt) REVERT: C 480 TRP cc_start: 0.6069 (t-100) cc_final: 0.5764 (m-90) REVERT: B 296 PHE cc_start: 0.6775 (m-80) cc_final: 0.6427 (m-80) REVERT: B 309 THR cc_start: 0.7348 (m) cc_final: 0.7134 (p) REVERT: B 359 ILE cc_start: 0.8597 (mt) cc_final: 0.8316 (mt) REVERT: B 480 TRP cc_start: 0.6489 (m100) cc_final: 0.5586 (m100) REVERT: D 296 PHE cc_start: 0.6650 (m-80) cc_final: 0.6303 (m-80) REVERT: D 299 MET cc_start: 0.7237 (OUTLIER) cc_final: 0.7030 (ttp) REVERT: D 365 MET cc_start: 0.8371 (mmm) cc_final: 0.8168 (mmm) REVERT: D 442 TYR cc_start: 0.8115 (m-80) cc_final: 0.7656 (m-80) REVERT: D 480 TRP cc_start: 0.6098 (t-100) cc_final: 0.5779 (m-90) REVERT: D 497 MET cc_start: 0.7978 (mtp) cc_final: 0.7106 (mmm) outliers start: 46 outliers final: 41 residues processed: 203 average time/residue: 0.0784 time to fit residues: 26.5905 Evaluate side-chains 216 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 174 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 421 CYS Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 421 CYS Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 454 GLU Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 421 CYS Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 421 CYS Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 458 SER Chi-restraints excluded: chain D residue 494 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [50, 110, 0, 104, 63, 94, 36, 130, 14, 87, 111] chunk 50 optimal weight: 3.9990 chunk 110 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 104 optimal weight: 2.9990 chunk 63 optimal weight: 9.9990 chunk 94 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 87 optimal weight: 0.0770 chunk 111 optimal weight: 4.9990 overall best weight: 1.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.188008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.160553 restraints weight = 14287.549| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 1.38 r_work: 0.3403 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 13300 Z= 0.209 Angle : 0.616 8.349 18028 Z= 0.311 Chirality : 0.040 0.146 2120 Planarity : 0.004 0.073 2176 Dihedral : 20.449 175.706 1804 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.59 % Allowed : 17.40 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.22), residues: 1560 helix: 2.43 (0.17), residues: 956 sheet: -0.42 (0.41), residues: 180 loop : -1.99 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 317 TYR 0.020 0.001 TYR B 442 PHE 0.015 0.002 PHE D 469 TRP 0.013 0.001 TRP A 480 HIS 0.004 0.001 HIS D 443 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.21 (13292) covalent geometry : angle 0.61266 / 0.31 (18012) SS BOND : bond 0.00455 / 0.26 ( 8) SS BOND : angle 2.16045 / 1.15 ( 16) hydrogen bonds : bond 0.04066 / 2.67 ( 876) hydrogen bonds : angle 4.09373 / 2.93 ( 2604) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 172 time to evaluate : 0.516 Fit side-chains revert: symmetry clash REVERT: A 296 PHE cc_start: 0.6798 (m-80) cc_final: 0.6391 (m-80) REVERT: A 442 TYR cc_start: 0.8271 (m-80) cc_final: 0.7698 (m-80) REVERT: C 296 PHE cc_start: 0.6919 (m-80) cc_final: 0.6411 (m-80) REVERT: C 309 THR cc_start: 0.7463 (m) cc_final: 0.7229 (p) REVERT: C 359 ILE cc_start: 0.8567 (mt) cc_final: 0.8304 (mt) REVERT: C 426 MET cc_start: 0.7645 (mmt) cc_final: 0.7162 (mmt) REVERT: C 480 TRP cc_start: 0.6067 (t-100) cc_final: 0.5820 (m-90) REVERT: B 296 PHE cc_start: 0.6780 (m-80) cc_final: 0.6372 (m-80) REVERT: B 309 THR cc_start: 0.7401 (m) cc_final: 0.7165 (p) REVERT: B 359 ILE cc_start: 0.8636 (mt) cc_final: 0.8347 (mt) REVERT: D 296 PHE cc_start: 0.6925 (m-80) cc_final: 0.6508 (m-80) REVERT: D 299 MET cc_start: 0.7350 (OUTLIER) cc_final: 0.7113 (ttp) REVERT: D 442 TYR cc_start: 0.8151 (m-80) cc_final: 0.7734 (m-80) REVERT: D 480 TRP cc_start: 0.6413 (t-100) cc_final: 0.6064 (m-90) REVERT: D 497 MET cc_start: 0.7959 (mtp) cc_final: 0.7141 (mmm) outliers start: 52 outliers final: 39 residues processed: 201 average time/residue: 0.0724 time to fit residues: 24.6390 Evaluate side-chains 203 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 163 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 421 CYS Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 421 CYS Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 454 GLU Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 421 CYS Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 421 CYS Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 494 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [90, 59, 159, 98, 84, 18, 21, 104, 26, 77, 148] chunk 90 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 148 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 461 ASN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.189155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.162312 restraints weight = 14227.287| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 1.26 r_work: 0.3432 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13300 Z= 0.167 Angle : 0.583 9.028 18028 Z= 0.292 Chirality : 0.039 0.149 2120 Planarity : 0.004 0.076 2176 Dihedral : 20.447 175.668 1804 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.45 % Allowed : 19.06 % Favored : 77.49 % 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: 1.49 (0.22), residues: 1560 helix: 2.49 (0.17), residues: 956 sheet: -0.56 (0.41), residues: 180 loop : -1.97 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 317 TYR 0.024 0.001 TYR B 442 PHE 0.013 0.002 PHE B 469 TRP 0.019 0.001 TRP A 480 HIS 0.002 0.001 HIS C 443 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (13292) covalent geometry : angle 0.58031 / 0.29 (18012) SS BOND : bond 0.00697 / 0.37 ( 8) SS BOND : angle 1.92121 / 0.97 ( 16) hydrogen bonds : bond 0.03803 / 2.49 ( 876) hydrogen bonds : angle 3.99400 / 2.87 ( 2604) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 175 time to evaluate : 0.459 Fit side-chains revert: symmetry clash REVERT: A 127 THR cc_start: 0.8531 (OUTLIER) cc_final: 0.8093 (m) REVERT: A 296 PHE cc_start: 0.6740 (m-80) cc_final: 0.6326 (m-80) REVERT: A 442 TYR cc_start: 0.8260 (m-80) cc_final: 0.7699 (m-80) REVERT: A 480 TRP cc_start: 0.6413 (m100) cc_final: 0.5502 (m100) REVERT: C 127 THR cc_start: 0.8541 (OUTLIER) cc_final: 0.8270 (m) REVERT: C 296 PHE cc_start: 0.6750 (m-80) cc_final: 0.6279 (m-80) REVERT: C 309 THR cc_start: 0.7450 (m) cc_final: 0.7210 (p) REVERT: B 296 PHE cc_start: 0.6760 (m-80) cc_final: 0.6324 (m-80) REVERT: B 309 THR cc_start: 0.7384 (m) cc_final: 0.7156 (p) REVERT: B 359 ILE cc_start: 0.8614 (mt) cc_final: 0.8345 (mt) REVERT: B 480 TRP cc_start: 0.6440 (m100) cc_final: 0.5505 (m100) REVERT: D 127 THR cc_start: 0.8532 (OUTLIER) cc_final: 0.8246 (m) REVERT: D 296 PHE cc_start: 0.6827 (m-80) cc_final: 0.6396 (m-80) REVERT: D 299 MET cc_start: 0.7288 (OUTLIER) cc_final: 0.7051 (ttp) REVERT: D 365 MET cc_start: 0.8448 (mmm) cc_final: 0.8185 (mmm) REVERT: D 442 TYR cc_start: 0.8177 (m-80) cc_final: 0.7666 (m-80) REVERT: D 480 TRP cc_start: 0.6364 (t-100) cc_final: 0.6070 (m-90) REVERT: D 497 MET cc_start: 0.7917 (mtp) cc_final: 0.7167 (mmm) outliers start: 50 outliers final: 43 residues processed: 200 average time/residue: 0.0754 time to fit residues: 25.4350 Evaluate side-chains 216 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 169 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 421 CYS Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 421 CYS Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 454 GLU Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 421 CYS Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 421 CYS Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 465 MET Chi-restraints excluded: chain D residue 494 PHE Chi-restraints excluded: chain D residue 495 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [21, 84, 89, 143, 57, 13, 44, 95, 96, 10, 104] chunk 21 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 89 optimal weight: 0.0770 chunk 143 optimal weight: 8.9990 chunk 57 optimal weight: 0.5980 chunk 13 optimal weight: 0.0370 chunk 44 optimal weight: 0.0570 chunk 95 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 overall best weight: 0.3134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 474 GLN ** 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 = 0.4099 r_free = 0.4099 target = 0.193639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.164852 restraints weight = 14223.567| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 1.34 r_work: 0.3507 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13300 Z= 0.110 Angle : 0.546 10.483 18028 Z= 0.265 Chirality : 0.037 0.202 2120 Planarity : 0.004 0.076 2176 Dihedral : 20.365 175.633 1804 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.38 % Allowed : 19.61 % Favored : 77.00 % 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: 1.82 (0.22), residues: 1560 helix: 2.77 (0.17), residues: 956 sheet: -0.16 (0.42), residues: 160 loop : -1.97 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 317 TYR 0.016 0.001 TYR B 442 PHE 0.013 0.001 PHE D 469 TRP 0.018 0.001 TRP A 480 HIS 0.002 0.000 HIS D 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.11 (13292) covalent geometry : angle 0.54504 / 0.27 (18012) SS BOND : bond 0.00838 / 0.44 ( 8) SS BOND : angle 1.04699 / 0.56 ( 16) hydrogen bonds : bond 0.03201 / 2.11 ( 876) hydrogen bonds : angle 3.70756 / 2.67 ( 2604) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 178 time to evaluate : 0.312 Fit side-chains REVERT: A 296 PHE cc_start: 0.6691 (m-80) cc_final: 0.6285 (m-80) REVERT: A 442 TYR cc_start: 0.8264 (m-80) cc_final: 0.7737 (m-80) REVERT: A 480 TRP cc_start: 0.6504 (m100) cc_final: 0.5567 (m100) REVERT: C 296 PHE cc_start: 0.6771 (m-80) cc_final: 0.6316 (m-80) REVERT: C 309 THR cc_start: 0.7387 (m) cc_final: 0.7158 (p) REVERT: C 426 MET cc_start: 0.7430 (mmt) cc_final: 0.7010 (mmt) REVERT: B 127 THR cc_start: 0.8437 (OUTLIER) cc_final: 0.7918 (m) REVERT: B 296 PHE cc_start: 0.6662 (m-80) cc_final: 0.6282 (m-80) REVERT: B 480 TRP cc_start: 0.6441 (m100) cc_final: 0.5596 (m100) REVERT: D 127 THR cc_start: 0.8450 (OUTLIER) cc_final: 0.7926 (m) REVERT: D 296 PHE cc_start: 0.6787 (m-80) cc_final: 0.6383 (m-80) REVERT: D 299 MET cc_start: 0.7279 (OUTLIER) cc_final: 0.7035 (ttp) REVERT: D 365 MET cc_start: 0.8445 (mmm) cc_final: 0.8210 (mmm) REVERT: D 442 TYR cc_start: 0.8092 (m-80) cc_final: 0.7684 (m-80) REVERT: D 480 TRP cc_start: 0.6296 (t-100) cc_final: 0.6071 (m-90) REVERT: D 497 MET cc_start: 0.7830 (mtp) cc_final: 0.7151 (mmm) outliers start: 49 outliers final: 37 residues processed: 204 average time/residue: 0.0737 time to fit residues: 24.9055 Evaluate side-chains 207 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 167 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 421 CYS Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 421 CYS Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 454 GLU Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 421 CYS Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 421 CYS Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 494 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [91, 68, 65, 159, 49, 154, 28, 97, 103, 55, 106] chunk 91 optimal weight: 4.9990 chunk 68 optimal weight: 8.9990 chunk 65 optimal weight: 0.9990 chunk 159 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 154 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 461 ASN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.192055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.163886 restraints weight = 14051.896| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 1.36 r_work: 0.3437 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13300 Z= 0.140 Angle : 0.584 9.749 18028 Z= 0.286 Chirality : 0.039 0.224 2120 Planarity : 0.004 0.078 2176 Dihedral : 20.359 175.553 1804 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.04 % Allowed : 20.23 % Favored : 76.73 % 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: 1.80 (0.22), residues: 1560 helix: 2.74 (0.17), residues: 956 sheet: -0.36 (0.41), residues: 180 loop : -1.91 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 317 TYR 0.018 0.001 TYR B 442 PHE 0.011 0.001 PHE C 296 TRP 0.016 0.001 TRP A 480 HIS 0.002 0.001 HIS B 443 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (13292) covalent geometry : angle 0.58267 / 0.29 (18012) SS BOND : bond 0.00623 / 0.33 ( 8) SS BOND : angle 1.23776 / 0.67 ( 16) hydrogen bonds : bond 0.03471 / 2.28 ( 876) hydrogen bonds : angle 3.79655 / 2.71 ( 2604) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 171 time to evaluate : 0.413 Fit side-chains revert: symmetry clash REVERT: A 127 THR cc_start: 0.8507 (OUTLIER) cc_final: 0.8057 (m) REVERT: A 296 PHE cc_start: 0.6685 (m-80) cc_final: 0.6296 (m-80) REVERT: A 442 TYR cc_start: 0.8328 (m-80) cc_final: 0.7809 (m-80) REVERT: C 127 THR cc_start: 0.8513 (OUTLIER) cc_final: 0.8063 (m) REVERT: C 296 PHE cc_start: 0.6726 (m-80) cc_final: 0.6287 (m-80) REVERT: C 309 THR cc_start: 0.7419 (m) cc_final: 0.7181 (p) REVERT: C 426 MET cc_start: 0.7529 (mmt) cc_final: 0.7124 (mmt) REVERT: C 497 MET cc_start: 0.8129 (OUTLIER) cc_final: 0.6706 (tpt) REVERT: B 127 THR cc_start: 0.8505 (OUTLIER) cc_final: 0.8054 (m) REVERT: B 296 PHE cc_start: 0.6685 (m-80) cc_final: 0.6306 (m-80) REVERT: B 359 ILE cc_start: 0.8602 (mt) cc_final: 0.8307 (mt) REVERT: B 480 TRP cc_start: 0.6547 (m100) cc_final: 0.5566 (m100) REVERT: D 127 THR cc_start: 0.8515 (OUTLIER) cc_final: 0.8059 (m) REVERT: D 296 PHE cc_start: 0.6811 (m-80) cc_final: 0.6395 (m-80) REVERT: D 299 MET cc_start: 0.7289 (OUTLIER) cc_final: 0.7035 (ttp) REVERT: D 365 MET cc_start: 0.8439 (mmm) cc_final: 0.8196 (mmm) REVERT: D 442 TYR cc_start: 0.8123 (m-80) cc_final: 0.7697 (m-80) REVERT: D 474 GLN cc_start: 0.6308 (pp30) cc_final: 0.6032 (mp10) REVERT: D 480 TRP cc_start: 0.6414 (t-100) cc_final: 0.6121 (m-90) REVERT: D 497 MET cc_start: 0.7791 (mtp) cc_final: 0.7067 (mmm) outliers start: 44 outliers final: 36 residues processed: 193 average time/residue: 0.0771 time to fit residues: 25.1618 Evaluate side-chains 211 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 169 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 421 CYS Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 421 CYS Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 454 GLU Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain C residue 497 MET Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 421 CYS Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 421 CYS Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 494 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [94, 4, 31, 42, 35, 144, 56, 76, 119, 29, 110] chunk 94 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 31 optimal weight: 5.9990 chunk 42 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 144 optimal weight: 0.8980 chunk 56 optimal weight: 0.0980 chunk 76 optimal weight: 0.0980 chunk 119 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 chunk 110 optimal weight: 4.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 474 GLN ** 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 = 0.4118 r_free = 0.4118 target = 0.195063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.167521 restraints weight = 14199.953| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 1.38 r_work: 0.3503 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13300 Z= 0.116 Angle : 0.562 9.862 18028 Z= 0.273 Chirality : 0.038 0.208 2120 Planarity : 0.004 0.080 2176 Dihedral : 20.333 175.563 1804 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.18 % Allowed : 20.17 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.22), residues: 1560 helix: 2.84 (0.17), residues: 956 sheet: -0.09 (0.43), residues: 160 loop : -1.92 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 317 TYR 0.015 0.001 TYR B 442 PHE 0.012 0.001 PHE B 469 TRP 0.020 0.001 TRP A 480 HIS 0.003 0.001 HIS A 511 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 (13292) covalent geometry : angle 0.56108 / 0.27 (18012) SS BOND : bond 0.00661 / 0.35 ( 8) SS BOND : angle 0.99346 / 0.53 ( 16) hydrogen bonds : bond 0.03231 / 2.12 ( 876) hydrogen bonds : angle 3.69215 / 2.64 ( 2604) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 173 time to evaluate : 0.340 Fit side-chains REVERT: A 127 THR cc_start: 0.8465 (OUTLIER) cc_final: 0.7957 (m) REVERT: A 296 PHE cc_start: 0.6498 (m-80) cc_final: 0.6118 (m-80) REVERT: A 442 TYR cc_start: 0.8290 (m-80) cc_final: 0.7789 (m-80) REVERT: A 480 TRP cc_start: 0.6324 (m100) cc_final: 0.5480 (m100) REVERT: C 127 THR cc_start: 0.8469 (OUTLIER) cc_final: 0.7964 (m) REVERT: C 296 PHE cc_start: 0.6704 (m-80) cc_final: 0.6268 (m-80) REVERT: C 309 THR cc_start: 0.7408 (m) cc_final: 0.7171 (p) REVERT: C 426 MET cc_start: 0.7464 (mmt) cc_final: 0.7080 (mmt) REVERT: C 497 MET cc_start: 0.8075 (OUTLIER) cc_final: 0.6667 (tpt) REVERT: B 127 THR cc_start: 0.8460 (OUTLIER) cc_final: 0.7955 (m) REVERT: B 296 PHE cc_start: 0.6568 (m-80) cc_final: 0.6203 (m-80) REVERT: B 480 TRP cc_start: 0.6405 (m100) cc_final: 0.5524 (m100) REVERT: D 127 THR cc_start: 0.8476 (OUTLIER) cc_final: 0.7965 (m) REVERT: D 296 PHE cc_start: 0.6783 (m-80) cc_final: 0.6302 (m-80) REVERT: D 365 MET cc_start: 0.8468 (mmm) cc_final: 0.8238 (mmm) REVERT: D 442 TYR cc_start: 0.8104 (m-80) cc_final: 0.7688 (m-80) REVERT: D 497 MET cc_start: 0.7777 (mtp) cc_final: 0.7061 (mmm) outliers start: 46 outliers final: 40 residues processed: 197 average time/residue: 0.0772 time to fit residues: 25.5773 Evaluate side-chains 216 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 171 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 421 CYS Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 421 CYS Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 454 GLU Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain C residue 497 MET Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 421 CYS Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 421 CYS Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 494 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [101, 79, 47, 106, 91, 50, 131, 142, 31, 32, 110] chunk 101 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 106 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 131 optimal weight: 0.8980 chunk 142 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 110 optimal weight: 6.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 474 GLN ** 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 = 0.4085 r_free = 0.4085 target = 0.191865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.165020 restraints weight = 14345.024| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 1.32 r_work: 0.3456 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13300 Z= 0.137 Angle : 0.584 9.987 18028 Z= 0.285 Chirality : 0.039 0.202 2120 Planarity : 0.004 0.083 2176 Dihedral : 20.344 175.548 1804 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.04 % Allowed : 20.37 % Favored : 76.59 % 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: 1.89 (0.22), residues: 1560 helix: 2.80 (0.17), residues: 956 sheet: -0.33 (0.40), residues: 180 loop : -1.83 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 317 TYR 0.017 0.001 TYR B 442 PHE 0.018 0.001 PHE B 469 TRP 0.020 0.001 TRP A 480 HIS 0.003 0.001 HIS C 443 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (13292) covalent geometry : angle 0.58282 / 0.29 (18012) SS BOND : bond 0.00569 / 0.31 ( 8) SS BOND : angle 1.14428 / 0.62 ( 16) hydrogen bonds : bond 0.03426 / 2.24 ( 876) hydrogen bonds : angle 3.75692 / 2.68 ( 2604) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 172 time to evaluate : 0.397 Fit side-chains REVERT: A 127 THR cc_start: 0.8499 (OUTLIER) cc_final: 0.8052 (m) REVERT: A 296 PHE cc_start: 0.6596 (m-80) cc_final: 0.6221 (m-80) REVERT: A 442 TYR cc_start: 0.8286 (m-80) cc_final: 0.7840 (m-80) REVERT: A 480 TRP cc_start: 0.6319 (m100) cc_final: 0.5398 (m100) REVERT: C 127 THR cc_start: 0.8493 (OUTLIER) cc_final: 0.8047 (m) REVERT: C 296 PHE cc_start: 0.6736 (m-80) cc_final: 0.6293 (m-80) REVERT: C 309 THR cc_start: 0.7418 (m) cc_final: 0.7182 (p) REVERT: C 426 MET cc_start: 0.7545 (mmt) cc_final: 0.7169 (mmt) REVERT: C 497 MET cc_start: 0.8095 (OUTLIER) cc_final: 0.6621 (tpt) REVERT: B 127 THR cc_start: 0.8498 (OUTLIER) cc_final: 0.8048 (m) REVERT: B 296 PHE cc_start: 0.6608 (m-80) cc_final: 0.6241 (m-80) REVERT: B 359 ILE cc_start: 0.8601 (mt) cc_final: 0.8313 (mt) REVERT: B 480 TRP cc_start: 0.6417 (m100) cc_final: 0.5514 (m100) REVERT: D 127 THR cc_start: 0.8506 (OUTLIER) cc_final: 0.8051 (m) REVERT: D 296 PHE cc_start: 0.6806 (m-80) cc_final: 0.6328 (m-80) REVERT: D 365 MET cc_start: 0.8423 (mmm) cc_final: 0.8196 (mmm) REVERT: D 442 TYR cc_start: 0.8098 (m-80) cc_final: 0.7696 (m-80) REVERT: D 480 TRP cc_start: 0.6139 (t-100) cc_final: 0.5504 (m-90) REVERT: D 497 MET cc_start: 0.7686 (mtp) cc_final: 0.7047 (mmm) outliers start: 44 outliers final: 39 residues processed: 197 average time/residue: 0.0700 time to fit residues: 23.1114 Evaluate side-chains 215 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 171 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 421 CYS Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 421 CYS Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 454 GLU Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain C residue 497 MET Chi-restraints excluded: chain C residue 510 TYR Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 421 CYS Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 421 CYS Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 494 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [60, 107, 28, 8, 111, 147, 94, 49, 67, 152, 20] chunk 60 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 28 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 chunk 111 optimal weight: 0.9980 chunk 147 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 152 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 474 GLN ** 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 = 0.4087 r_free = 0.4087 target = 0.191984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.164354 restraints weight = 14208.885| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 1.36 r_work: 0.3462 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13300 Z= 0.139 Angle : 0.586 9.855 18028 Z= 0.287 Chirality : 0.039 0.201 2120 Planarity : 0.004 0.083 2176 Dihedral : 20.357 175.714 1804 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.31 % Allowed : 20.30 % Favored : 76.38 % 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: 1.89 (0.22), residues: 1560 helix: 2.79 (0.17), residues: 956 sheet: -0.33 (0.40), residues: 180 loop : -1.79 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 317 TYR 0.018 0.001 TYR B 442 PHE 0.016 0.001 PHE B 469 TRP 0.015 0.001 TRP B 480 HIS 0.003 0.001 HIS D 443 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (13292) covalent geometry : angle 0.58495 / 0.29 (18012) SS BOND : bond 0.00626 / 0.34 ( 8) SS BOND : angle 1.19758 / 0.65 ( 16) hydrogen bonds : bond 0.03469 / 2.27 ( 876) hydrogen bonds : angle 3.79503 / 2.71 ( 2604) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2932.39 seconds wall clock time: 50 minutes 58.92 seconds (3058.92 seconds total)