Starting phenix.real_space_refine on Sat Aug 23 15:09:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wwp_37895/08_2025/8wwp_37895.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wwp_37895/08_2025/8wwp_37895.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wwp_37895/08_2025/8wwp_37895.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wwp_37895/08_2025/8wwp_37895.map" model { file = "/net/cci-nas-00/data/ceres_data/8wwp_37895/08_2025/8wwp_37895.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wwp_37895/08_2025/8wwp_37895.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 8243 2.51 5 N 2271 2.21 5 O 2563 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13125 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4375 Classifications: {'peptide': 583} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 28, 'TRANS': 552} Chain: "B" Number of atoms: 4368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 582, 4368 Classifications: {'peptide': 582} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 28, 'TRANS': 551} Chain: "C" Number of atoms: 4382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4382 Classifications: {'peptide': 584} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 28, 'TRANS': 553} Time building chain proxies: 3.19, per 1000 atoms: 0.24 Number of scatterers: 13125 At special positions: 0 Unit cell: (118.8, 118.8, 96.3, 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 48 16.00 O 2563 8.00 N 2271 7.00 C 8243 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.75 Conformation dependent library (CDL) restraints added in 603.4 milliseconds Enol-peptide restraints added in 1.2 microseconds 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3186 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 12 sheets defined 35.5% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 78 through 82 Processing helix chain 'A' and resid 97 through 109 Processing helix chain 'A' and resid 111 through 115 removed outlier: 3.700A pdb=" N PHE A 115 " --> pdb=" O ARG A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 154 removed outlier: 4.171A pdb=" N GLY A 154 " --> pdb=" O THR A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 183 removed outlier: 3.920A pdb=" N GLU A 183 " --> pdb=" O VAL A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 219 Processing helix chain 'A' and resid 225 through 236 removed outlier: 3.509A pdb=" N ALA A 236 " --> pdb=" O GLY A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 250 Processing helix chain 'A' and resid 273 through 282 removed outlier: 4.248A pdb=" N SER A 280 " --> pdb=" O TYR A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 313 Processing helix chain 'A' and resid 320 through 344 Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 414 through 418 removed outlier: 3.674A pdb=" N THR A 418 " --> pdb=" O PRO A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 443 removed outlier: 3.565A pdb=" N ILE A 432 " --> pdb=" O LYS A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 446 No H-bonds generated for 'chain 'A' and resid 444 through 446' Processing helix chain 'A' and resid 469 through 485 removed outlier: 3.607A pdb=" N GLY A 485 " --> pdb=" O LEU A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 532 Processing helix chain 'A' and resid 558 through 581 removed outlier: 3.540A pdb=" N LEU A 562 " --> pdb=" O PRO A 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 82 Processing helix chain 'B' and resid 97 through 109 Processing helix chain 'B' and resid 111 through 115 removed outlier: 3.701A pdb=" N PHE B 115 " --> pdb=" O ARG B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 154 removed outlier: 4.171A pdb=" N GLY B 154 " --> pdb=" O THR B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 183 removed outlier: 3.920A pdb=" N GLU B 183 " --> pdb=" O VAL B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 219 Processing helix chain 'B' and resid 225 through 236 removed outlier: 3.508A pdb=" N ALA B 236 " --> pdb=" O GLY B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 250 Processing helix chain 'B' and resid 273 through 282 removed outlier: 4.248A pdb=" N SER B 280 " --> pdb=" O TYR B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 313 Processing helix chain 'B' and resid 320 through 344 Processing helix chain 'B' and resid 389 through 393 Processing helix chain 'B' and resid 414 through 418 removed outlier: 3.674A pdb=" N THR B 418 " --> pdb=" O PRO B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 443 removed outlier: 3.565A pdb=" N ILE B 432 " --> pdb=" O LYS B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 446 No H-bonds generated for 'chain 'B' and resid 444 through 446' Processing helix chain 'B' and resid 469 through 485 removed outlier: 3.608A pdb=" N GLY B 485 " --> pdb=" O LEU B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 532 Processing helix chain 'B' and resid 558 through 581 removed outlier: 3.540A pdb=" N LEU B 562 " --> pdb=" O PRO B 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 82 Processing helix chain 'C' and resid 97 through 109 Processing helix chain 'C' and resid 111 through 115 removed outlier: 3.700A pdb=" N PHE C 115 " --> pdb=" O ARG C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 154 removed outlier: 4.171A pdb=" N GLY C 154 " --> pdb=" O THR C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 183 removed outlier: 3.920A pdb=" N GLU C 183 " --> pdb=" O VAL C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 219 Processing helix chain 'C' and resid 225 through 236 removed outlier: 3.508A pdb=" N ALA C 236 " --> pdb=" O GLY C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 250 Processing helix chain 'C' and resid 273 through 282 removed outlier: 4.247A pdb=" N SER C 280 " --> pdb=" O TYR C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 313 Processing helix chain 'C' and resid 320 through 344 Processing helix chain 'C' and resid 389 through 393 Processing helix chain 'C' and resid 414 through 418 removed outlier: 3.675A pdb=" N THR C 418 " --> pdb=" O PRO C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 443 removed outlier: 3.565A pdb=" N ILE C 432 " --> pdb=" O LYS C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 446 No H-bonds generated for 'chain 'C' and resid 444 through 446' Processing helix chain 'C' and resid 469 through 485 removed outlier: 3.608A pdb=" N GLY C 485 " --> pdb=" O LEU C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 532 Processing helix chain 'C' and resid 558 through 581 removed outlier: 3.540A pdb=" N LEU C 562 " --> pdb=" O PRO C 558 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 18 removed outlier: 6.087A pdb=" N MET A 51 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N THR A 72 " --> pdb=" O ILE A 125 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N VAL A 127 " --> pdb=" O THR A 72 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ASP A 74 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N ILE A 129 " --> pdb=" O ASP A 74 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N GLU A 76 " --> pdb=" O ILE A 129 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N SER A 131 " --> pdb=" O GLU A 76 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 172 through 175 removed outlier: 4.121A pdb=" N PHE A 187 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ASP A 188 " --> pdb=" O ALA A 207 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ALA A 207 " --> pdb=" O ASP A 188 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL A 190 " --> pdb=" O VAL A 205 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N VAL A 205 " --> pdb=" O VAL A 190 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ALA A 192 " --> pdb=" O MET A 203 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N MET A 203 " --> pdb=" O THR A 552 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ALA A 539 " --> pdb=" O THR A 546 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N LEU A 548 " --> pdb=" O LYS A 537 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LYS A 537 " --> pdb=" O LEU A 548 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N LEU A 550 " --> pdb=" O ASP A 535 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N ASP A 535 " --> pdb=" O LEU A 550 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 358 through 362 removed outlier: 6.416A pdb=" N GLN A 380 " --> pdb=" O LEU A 463 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 394 through 395 removed outlier: 3.518A pdb=" N GLN A 394 " --> pdb=" O LYS A 405 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS A 405 " --> pdb=" O GLN A 394 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 16 through 18 removed outlier: 6.088A pdb=" N MET B 51 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N THR B 72 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N VAL B 127 " --> pdb=" O THR B 72 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ASP B 74 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N ILE B 129 " --> pdb=" O ASP B 74 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N GLU B 76 " --> pdb=" O ILE B 129 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N SER B 131 " --> pdb=" O GLU B 76 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 172 through 175 removed outlier: 4.121A pdb=" N PHE B 187 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ASP B 188 " --> pdb=" O ALA B 207 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ALA B 207 " --> pdb=" O ASP B 188 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL B 190 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N VAL B 205 " --> pdb=" O VAL B 190 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ALA B 192 " --> pdb=" O MET B 203 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N MET B 203 " --> pdb=" O THR B 552 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ALA B 539 " --> pdb=" O THR B 546 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N LEU B 548 " --> pdb=" O LYS B 537 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N LYS B 537 " --> pdb=" O LEU B 548 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N LEU B 550 " --> pdb=" O ASP B 535 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N ASP B 535 " --> pdb=" O LEU B 550 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 358 through 362 removed outlier: 6.417A pdb=" N GLN B 380 " --> pdb=" O LEU B 463 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 394 through 395 removed outlier: 3.518A pdb=" N GLN B 394 " --> pdb=" O LYS B 405 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS B 405 " --> pdb=" O GLN B 394 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 16 through 18 removed outlier: 6.087A pdb=" N MET C 51 " --> pdb=" O LEU C 130 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N THR C 72 " --> pdb=" O ILE C 125 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N VAL C 127 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ASP C 74 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N ILE C 129 " --> pdb=" O ASP C 74 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N GLU C 76 " --> pdb=" O ILE C 129 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N SER C 131 " --> pdb=" O GLU C 76 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 172 through 175 removed outlier: 4.121A pdb=" N PHE C 187 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ASP C 188 " --> pdb=" O ALA C 207 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ALA C 207 " --> pdb=" O ASP C 188 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL C 190 " --> pdb=" O VAL C 205 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N VAL C 205 " --> pdb=" O VAL C 190 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ALA C 192 " --> pdb=" O MET C 203 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N MET C 203 " --> pdb=" O THR C 552 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ALA C 539 " --> pdb=" O THR C 546 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N LEU C 548 " --> pdb=" O LYS C 537 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LYS C 537 " --> pdb=" O LEU C 548 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N LEU C 550 " --> pdb=" O ASP C 535 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N ASP C 535 " --> pdb=" O LEU C 550 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 358 through 362 removed outlier: 6.417A pdb=" N GLN C 380 " --> pdb=" O LEU C 463 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 394 through 395 removed outlier: 3.517A pdb=" N GLN C 394 " --> pdb=" O LYS C 405 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS C 405 " --> pdb=" O GLN C 394 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 651 hydrogen bonds defined for protein. 1809 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.92 Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4521 1.34 - 1.46: 1770 1.46 - 1.57: 6957 1.57 - 1.69: 0 1.69 - 1.81: 87 Bond restraints: 13335 Sorted by residual: bond pdb=" C ARG C 109 " pdb=" N PRO C 110 " ideal model delta sigma weight residual 1.331 1.343 -0.012 7.90e-03 1.60e+04 2.20e+00 bond pdb=" C ARG A 109 " pdb=" N PRO A 110 " ideal model delta sigma weight residual 1.331 1.342 -0.011 7.90e-03 1.60e+04 1.84e+00 bond pdb=" C ARG B 109 " pdb=" N PRO B 110 " ideal model delta sigma weight residual 1.331 1.342 -0.010 7.90e-03 1.60e+04 1.64e+00 bond pdb=" CB GLU B 226 " pdb=" CG GLU B 226 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.18e+00 bond pdb=" C ARG B 112 " pdb=" N PRO B 113 " ideal model delta sigma weight residual 1.339 1.376 -0.037 3.40e-02 8.65e+02 1.17e+00 ... (remaining 13330 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.19: 17561 1.19 - 2.38: 412 2.38 - 3.58: 102 3.58 - 4.77: 27 4.77 - 5.96: 6 Bond angle restraints: 18108 Sorted by residual: angle pdb=" C ASP B 299 " pdb=" N GLN B 300 " pdb=" CA GLN B 300 " ideal model delta sigma weight residual 121.54 126.01 -4.47 1.91e+00 2.74e-01 5.47e+00 angle pdb=" C ASP C 299 " pdb=" N GLN C 300 " pdb=" CA GLN C 300 " ideal model delta sigma weight residual 121.54 125.99 -4.45 1.91e+00 2.74e-01 5.43e+00 angle pdb=" C ASP A 299 " pdb=" N GLN A 300 " pdb=" CA GLN A 300 " ideal model delta sigma weight residual 121.54 125.99 -4.45 1.91e+00 2.74e-01 5.42e+00 angle pdb=" C MET C 51 " pdb=" N LEU C 52 " pdb=" CA LEU C 52 " ideal model delta sigma weight residual 122.21 118.76 3.45 1.62e+00 3.81e-01 4.52e+00 angle pdb=" C MET B 51 " pdb=" N LEU B 52 " pdb=" CA LEU B 52 " ideal model delta sigma weight residual 122.21 118.80 3.41 1.62e+00 3.81e-01 4.43e+00 ... (remaining 18103 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 6894 17.70 - 35.39: 923 35.39 - 53.09: 211 53.09 - 70.79: 48 70.79 - 88.48: 21 Dihedral angle restraints: 8097 sinusoidal: 3132 harmonic: 4965 Sorted by residual: dihedral pdb=" CA ASP A 299 " pdb=" C ASP A 299 " pdb=" N GLN A 300 " pdb=" CA GLN A 300 " ideal model delta harmonic sigma weight residual 180.00 157.98 22.02 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA ASP C 299 " pdb=" C ASP C 299 " pdb=" N GLN C 300 " pdb=" CA GLN C 300 " ideal model delta harmonic sigma weight residual 180.00 158.00 22.00 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA ASP B 299 " pdb=" C ASP B 299 " pdb=" N GLN B 300 " pdb=" CA GLN B 300 " ideal model delta harmonic sigma weight residual 180.00 158.00 22.00 0 5.00e+00 4.00e-02 1.94e+01 ... (remaining 8094 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1212 0.028 - 0.056: 561 0.056 - 0.084: 186 0.084 - 0.112: 122 0.112 - 0.140: 43 Chirality restraints: 2124 Sorted by residual: chirality pdb=" CA ILE C 17 " pdb=" N ILE C 17 " pdb=" C ILE C 17 " pdb=" CB ILE C 17 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.89e-01 chirality pdb=" CA ILE B 17 " pdb=" N ILE B 17 " pdb=" C ILE B 17 " pdb=" CB ILE B 17 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.80e-01 chirality pdb=" CA ILE A 17 " pdb=" N ILE A 17 " pdb=" C ILE A 17 " pdb=" CB ILE A 17 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.78e-01 ... (remaining 2121 not shown) Planarity restraints: 2400 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 16 " -0.009 2.00e-02 2.50e+03 1.73e-02 3.00e+00 pdb=" C THR C 16 " 0.030 2.00e-02 2.50e+03 pdb=" O THR C 16 " -0.011 2.00e-02 2.50e+03 pdb=" N ILE C 17 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 16 " -0.008 2.00e-02 2.50e+03 1.71e-02 2.93e+00 pdb=" C THR A 16 " 0.030 2.00e-02 2.50e+03 pdb=" O THR A 16 " -0.011 2.00e-02 2.50e+03 pdb=" N ILE A 17 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 16 " 0.008 2.00e-02 2.50e+03 1.70e-02 2.89e+00 pdb=" C THR B 16 " -0.029 2.00e-02 2.50e+03 pdb=" O THR B 16 " 0.011 2.00e-02 2.50e+03 pdb=" N ILE B 17 " 0.010 2.00e-02 2.50e+03 ... (remaining 2397 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3059 2.79 - 3.32: 11935 3.32 - 3.84: 20710 3.84 - 4.37: 22298 4.37 - 4.90: 40790 Nonbonded interactions: 98792 Sorted by model distance: nonbonded pdb=" N GLU B 226 " pdb=" OE1 GLU B 226 " model vdw 2.262 3.120 nonbonded pdb=" N GLU A 226 " pdb=" OE1 GLU A 226 " model vdw 2.263 3.120 nonbonded pdb=" N GLU C 226 " pdb=" OE1 GLU C 226 " model vdw 2.263 3.120 nonbonded pdb=" O TYR A 275 " pdb=" OG SER A 279 " model vdw 2.302 3.040 nonbonded pdb=" O TYR B 275 " pdb=" OG SER B 279 " model vdw 2.302 3.040 ... (remaining 98787 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 15 through 596) selection = chain 'B' selection = (chain 'C' and resid 15 through 596) } 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: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.770 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 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 0.037 13335 Z= 0.130 Angle : 0.507 5.959 18108 Z= 0.269 Chirality : 0.043 0.140 2124 Planarity : 0.003 0.023 2400 Dihedral : 17.165 88.484 4911 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.30 % Favored : 95.52 % Rotamer: Outliers : 0.07 % Allowed : 30.58 % Favored : 69.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.18 % 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 aren not related in a simple way. whole: 0.23 (0.21), residues: 1743 helix: 1.54 (0.23), residues: 552 sheet: 0.41 (0.24), residues: 426 loop : -1.03 (0.24), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 440 TYR 0.013 0.001 TYR B 45 PHE 0.011 0.001 PHE B 536 TRP 0.002 0.001 TRP C 173 HIS 0.001 0.000 HIS C 369 Details of bonding type rmsd covalent geometry : bond 0.00301 (13335) covalent geometry : angle 0.50696 (18108) hydrogen bonds : bond 0.14161 ( 651) hydrogen bonds : angle 5.78668 ( 1809) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 129 time to evaluate : 0.454 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 129 average time/residue: 0.0755 time to fit residues: 15.8729 Evaluate side-chains 125 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.0030 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.0000 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.0470 chunk 149 optimal weight: 9.9990 overall best weight: 0.9494 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN ** A 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 GLN ** B 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 338 GLN ** C 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4997 r_free = 0.4997 target = 0.224846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.184871 restraints weight = 18318.865| |-----------------------------------------------------------------------------| r_work (start): 0.4579 rms_B_bonded: 3.51 r_work: 0.4450 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.4450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6633 moved from start: 0.0650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13335 Z= 0.101 Angle : 0.492 6.660 18108 Z= 0.255 Chirality : 0.043 0.144 2124 Planarity : 0.003 0.024 2400 Dihedral : 3.647 19.425 1893 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.96 % Allowed : 28.99 % Favored : 69.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.18 % 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 aren not related in a simple way. whole: 0.57 (0.21), residues: 1743 helix: 1.82 (0.23), residues: 552 sheet: 0.71 (0.25), residues: 429 loop : -0.92 (0.24), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 320 TYR 0.026 0.001 TYR C 45 PHE 0.010 0.001 PHE B 536 TRP 0.001 0.001 TRP B 173 HIS 0.001 0.000 HIS A 369 Details of bonding type rmsd covalent geometry : bond 0.00232 (13335) covalent geometry : angle 0.49173 (18108) hydrogen bonds : bond 0.03279 ( 651) hydrogen bonds : angle 4.72871 ( 1809) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 137 time to evaluate : 0.497 Fit side-chains REVERT: A 218 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7556 (tm-30) REVERT: B 218 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7797 (tm-30) REVERT: B 454 TYR cc_start: 0.7809 (m-80) cc_final: 0.7566 (m-10) REVERT: C 218 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7786 (tm-30) outliers start: 27 outliers final: 12 residues processed: 162 average time/residue: 0.0791 time to fit residues: 20.8314 Evaluate side-chains 150 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 135 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 580 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 103 optimal weight: 20.0000 chunk 36 optimal weight: 8.9990 chunk 21 optimal weight: 6.9990 chunk 166 optimal weight: 10.0000 chunk 30 optimal weight: 20.0000 chunk 156 optimal weight: 0.9990 chunk 110 optimal weight: 10.0000 chunk 148 optimal weight: 7.9990 chunk 60 optimal weight: 9.9990 chunk 79 optimal weight: 7.9990 chunk 144 optimal weight: 0.4980 overall best weight: 4.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 369 HIS ** 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 = 0.4901 r_free = 0.4901 target = 0.214681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.174492 restraints weight = 18683.976| |-----------------------------------------------------------------------------| r_work (start): 0.4464 rms_B_bonded: 3.53 r_work: 0.4330 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.4330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6813 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 13335 Z= 0.250 Angle : 0.653 6.438 18108 Z= 0.339 Chirality : 0.048 0.196 2124 Planarity : 0.004 0.032 2400 Dihedral : 4.378 18.980 1893 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 5.87 % Allowed : 28.04 % Favored : 66.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.18 % 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 aren not related in a simple way. whole: 0.23 (0.21), residues: 1743 helix: 1.36 (0.23), residues: 555 sheet: 0.54 (0.24), residues: 423 loop : -0.97 (0.24), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 312 TYR 0.022 0.002 TYR A 45 PHE 0.024 0.002 PHE B 68 TRP 0.006 0.002 TRP A 173 HIS 0.004 0.001 HIS B 410 Details of bonding type rmsd covalent geometry : bond 0.00618 (13335) covalent geometry : angle 0.65265 (18108) hydrogen bonds : bond 0.05226 ( 651) hydrogen bonds : angle 5.26167 ( 1809) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 123 time to evaluate : 0.567 Fit side-chains REVERT: A 341 LEU cc_start: 0.3162 (OUTLIER) cc_final: 0.2934 (mp) REVERT: B 341 LEU cc_start: 0.3351 (OUTLIER) cc_final: 0.3142 (mp) REVERT: C 52 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7421 (pp) REVERT: C 529 ASP cc_start: 0.5431 (OUTLIER) cc_final: 0.5110 (m-30) outliers start: 81 outliers final: 56 residues processed: 197 average time/residue: 0.0843 time to fit residues: 27.1533 Evaluate side-chains 178 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 118 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 529 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 157 optimal weight: 5.9990 chunk 166 optimal weight: 10.0000 chunk 43 optimal weight: 0.0970 chunk 50 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 135 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 142 optimal weight: 8.9990 chunk 81 optimal weight: 6.9990 chunk 169 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 overall best weight: 4.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 369 HIS ** 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 = 0.4896 r_free = 0.4896 target = 0.214398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.174315 restraints weight = 18640.103| |-----------------------------------------------------------------------------| r_work (start): 0.4469 rms_B_bonded: 3.50 r_work: 0.4338 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.4338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6772 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13335 Z= 0.214 Angle : 0.625 6.553 18108 Z= 0.328 Chirality : 0.047 0.163 2124 Planarity : 0.004 0.029 2400 Dihedral : 4.545 21.513 1893 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 6.96 % Allowed : 28.48 % Favored : 64.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.18 % 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 aren not related in a simple way. whole: 0.03 (0.21), residues: 1743 helix: 1.20 (0.23), residues: 558 sheet: 0.48 (0.24), residues: 423 loop : -1.14 (0.23), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 312 TYR 0.029 0.002 TYR C 45 PHE 0.024 0.002 PHE B 68 TRP 0.005 0.002 TRP C 173 HIS 0.003 0.001 HIS B 410 Details of bonding type rmsd covalent geometry : bond 0.00529 (13335) covalent geometry : angle 0.62450 (18108) hydrogen bonds : bond 0.04867 ( 651) hydrogen bonds : angle 5.20304 ( 1809) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 131 time to evaluate : 0.487 Fit side-chains REVERT: A 52 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7586 (pp) REVERT: A 203 MET cc_start: 0.7089 (mtm) cc_final: 0.6869 (mtm) REVERT: A 218 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7713 (tm-30) REVERT: A 341 LEU cc_start: 0.3029 (OUTLIER) cc_final: 0.2797 (mp) REVERT: C 52 LEU cc_start: 0.7664 (OUTLIER) cc_final: 0.7327 (pp) REVERT: C 218 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7786 (tm-30) REVERT: C 529 ASP cc_start: 0.5381 (OUTLIER) cc_final: 0.5082 (m-30) outliers start: 96 outliers final: 65 residues processed: 222 average time/residue: 0.0811 time to fit residues: 28.8949 Evaluate side-chains 197 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 126 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 275 TYR Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 529 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 153 optimal weight: 0.7980 chunk 27 optimal weight: 0.0050 chunk 70 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 24 optimal weight: 9.9990 chunk 85 optimal weight: 0.5980 chunk 22 optimal weight: 4.9990 chunk 128 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 chunk 125 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN B 338 GLN C 338 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4982 r_free = 0.4982 target = 0.223297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.184078 restraints weight = 18441.507| |-----------------------------------------------------------------------------| r_work (start): 0.4572 rms_B_bonded: 3.50 r_work: 0.4443 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.4443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6682 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13335 Z= 0.101 Angle : 0.513 7.377 18108 Z= 0.268 Chirality : 0.043 0.192 2124 Planarity : 0.003 0.027 2400 Dihedral : 3.983 20.301 1893 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.61 % Allowed : 33.33 % Favored : 64.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.18 % 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 aren not related in a simple way. whole: 0.57 (0.21), residues: 1743 helix: 1.93 (0.23), residues: 545 sheet: 0.76 (0.25), residues: 429 loop : -1.01 (0.23), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 329 TYR 0.027 0.002 TYR B 45 PHE 0.010 0.001 PHE B 536 TRP 0.002 0.001 TRP C 173 HIS 0.002 0.000 HIS B 409 Details of bonding type rmsd covalent geometry : bond 0.00231 (13335) covalent geometry : angle 0.51251 (18108) hydrogen bonds : bond 0.03067 ( 651) hydrogen bonds : angle 4.54286 ( 1809) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 136 time to evaluate : 0.494 Fit side-chains REVERT: A 216 LEU cc_start: 0.6298 (OUTLIER) cc_final: 0.6002 (mp) REVERT: B 387 LEU cc_start: 0.6503 (OUTLIER) cc_final: 0.6221 (mp) outliers start: 36 outliers final: 25 residues processed: 169 average time/residue: 0.0903 time to fit residues: 23.9852 Evaluate side-chains 152 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 275 TYR Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 580 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 85 optimal weight: 0.1980 chunk 158 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 chunk 107 optimal weight: 0.0370 chunk 46 optimal weight: 3.9990 chunk 149 optimal weight: 20.0000 chunk 138 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 166 optimal weight: 8.9990 chunk 117 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 overall best weight: 1.8464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 124 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4955 r_free = 0.4955 target = 0.220565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.181107 restraints weight = 18378.576| |-----------------------------------------------------------------------------| r_work (start): 0.4540 rms_B_bonded: 3.50 r_work: 0.4410 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.4410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13335 Z= 0.125 Angle : 0.531 6.587 18108 Z= 0.276 Chirality : 0.044 0.198 2124 Planarity : 0.003 0.024 2400 Dihedral : 3.992 19.436 1893 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 4.20 % Allowed : 31.81 % Favored : 63.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.18 % 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 aren not related in a simple way. whole: 0.61 (0.21), residues: 1743 helix: 1.88 (0.23), residues: 547 sheet: 0.84 (0.25), residues: 423 loop : -0.95 (0.23), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 329 TYR 0.024 0.002 TYR C 45 PHE 0.012 0.001 PHE B 68 TRP 0.002 0.001 TRP C 173 HIS 0.001 0.000 HIS B 409 Details of bonding type rmsd covalent geometry : bond 0.00304 (13335) covalent geometry : angle 0.53134 (18108) hydrogen bonds : bond 0.03455 ( 651) hydrogen bonds : angle 4.59314 ( 1809) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 128 time to evaluate : 0.381 Fit side-chains REVERT: A 52 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7386 (pp) REVERT: A 216 LEU cc_start: 0.6261 (OUTLIER) cc_final: 0.5964 (mp) REVERT: C 292 ILE cc_start: 0.3616 (OUTLIER) cc_final: 0.3370 (mm) outliers start: 58 outliers final: 46 residues processed: 180 average time/residue: 0.0756 time to fit residues: 21.8394 Evaluate side-chains 173 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 124 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain B residue 48 ASP Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 275 TYR Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 580 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 155 optimal weight: 0.0070 chunk 107 optimal weight: 0.5980 chunk 111 optimal weight: 6.9990 chunk 113 optimal weight: 6.9990 chunk 154 optimal weight: 9.9990 chunk 56 optimal weight: 10.0000 chunk 148 optimal weight: 5.9990 chunk 50 optimal weight: 10.0000 chunk 94 optimal weight: 3.9990 chunk 10 optimal weight: 0.4980 chunk 136 optimal weight: 10.0000 overall best weight: 2.2202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 369 HIS ** 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 = 0.4944 r_free = 0.4944 target = 0.219404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.179643 restraints weight = 18418.664| |-----------------------------------------------------------------------------| r_work (start): 0.4527 rms_B_bonded: 3.49 r_work: 0.4397 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.4397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6739 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13335 Z= 0.137 Angle : 0.546 6.603 18108 Z= 0.284 Chirality : 0.044 0.144 2124 Planarity : 0.003 0.023 2400 Dihedral : 4.078 21.860 1893 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 5.29 % Allowed : 31.01 % Favored : 63.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.18 % 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 aren not related in a simple way. whole: 0.56 (0.21), residues: 1743 helix: 1.83 (0.23), residues: 547 sheet: 0.82 (0.25), residues: 423 loop : -0.98 (0.23), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 329 TYR 0.024 0.002 TYR C 454 PHE 0.014 0.001 PHE B 68 TRP 0.003 0.001 TRP C 173 HIS 0.001 0.001 HIS C 410 Details of bonding type rmsd covalent geometry : bond 0.00336 (13335) covalent geometry : angle 0.54586 (18108) hydrogen bonds : bond 0.03698 ( 651) hydrogen bonds : angle 4.66899 ( 1809) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 127 time to evaluate : 0.611 Fit side-chains REVERT: A 52 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7449 (pp) REVERT: A 216 LEU cc_start: 0.6307 (OUTLIER) cc_final: 0.6013 (mp) REVERT: A 292 ILE cc_start: 0.3517 (OUTLIER) cc_final: 0.2891 (tp) REVERT: B 292 ILE cc_start: 0.3259 (OUTLIER) cc_final: 0.2806 (mm) REVERT: B 341 LEU cc_start: 0.3231 (OUTLIER) cc_final: 0.2988 (mp) REVERT: B 387 LEU cc_start: 0.6640 (OUTLIER) cc_final: 0.6352 (mp) REVERT: C 133 ASP cc_start: 0.7382 (OUTLIER) cc_final: 0.7168 (t0) REVERT: C 275 TYR cc_start: 0.5333 (OUTLIER) cc_final: 0.4980 (m-10) REVERT: C 292 ILE cc_start: 0.3643 (OUTLIER) cc_final: 0.3396 (mm) REVERT: C 529 ASP cc_start: 0.5659 (OUTLIER) cc_final: 0.5346 (m-30) outliers start: 73 outliers final: 57 residues processed: 194 average time/residue: 0.0828 time to fit residues: 25.8983 Evaluate side-chains 190 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 123 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain B residue 48 ASP Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain C residue 48 ASP Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 275 TYR Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 473 SER Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 529 ASP Chi-restraints excluded: chain C residue 580 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 96 optimal weight: 0.0670 chunk 6 optimal weight: 3.9990 chunk 24 optimal weight: 20.0000 chunk 147 optimal weight: 20.0000 chunk 128 optimal weight: 0.9980 chunk 36 optimal weight: 6.9990 chunk 151 optimal weight: 6.9990 chunk 109 optimal weight: 0.0770 chunk 157 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 93 optimal weight: 0.1980 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5002 r_free = 0.5002 target = 0.225667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.187282 restraints weight = 18305.545| |-----------------------------------------------------------------------------| r_work (start): 0.4609 rms_B_bonded: 3.32 r_work: 0.4489 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.4489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6670 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13335 Z= 0.097 Angle : 0.502 6.416 18108 Z= 0.261 Chirality : 0.042 0.130 2124 Planarity : 0.003 0.024 2400 Dihedral : 3.751 21.088 1893 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 4.20 % Allowed : 31.38 % Favored : 64.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.18 % 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 aren not related in a simple way. whole: 0.77 (0.21), residues: 1743 helix: 2.06 (0.23), residues: 544 sheet: 0.90 (0.25), residues: 429 loop : -0.88 (0.24), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 329 TYR 0.021 0.001 TYR A 45 PHE 0.009 0.001 PHE B 536 TRP 0.001 0.000 TRP C 173 HIS 0.001 0.000 HIS B 409 Details of bonding type rmsd covalent geometry : bond 0.00224 (13335) covalent geometry : angle 0.50181 (18108) hydrogen bonds : bond 0.02752 ( 651) hydrogen bonds : angle 4.32115 ( 1809) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 138 time to evaluate : 0.509 Fit side-chains REVERT: A 216 LEU cc_start: 0.6139 (OUTLIER) cc_final: 0.5864 (mp) REVERT: A 292 ILE cc_start: 0.3305 (OUTLIER) cc_final: 0.2664 (tp) REVERT: B 292 ILE cc_start: 0.3075 (OUTLIER) cc_final: 0.2716 (mm) REVERT: B 341 LEU cc_start: 0.3244 (OUTLIER) cc_final: 0.3001 (mp) REVERT: B 387 LEU cc_start: 0.6607 (OUTLIER) cc_final: 0.6386 (mp) REVERT: C 133 ASP cc_start: 0.7245 (OUTLIER) cc_final: 0.7033 (t0) REVERT: C 218 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7802 (tm-30) REVERT: C 292 ILE cc_start: 0.3357 (OUTLIER) cc_final: 0.3066 (mm) outliers start: 58 outliers final: 37 residues processed: 191 average time/residue: 0.0797 time to fit residues: 24.0788 Evaluate side-chains 173 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 128 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain C residue 48 ASP Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 275 TYR Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 473 SER Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 514 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 96 optimal weight: 0.9980 chunk 158 optimal weight: 0.9990 chunk 136 optimal weight: 9.9990 chunk 57 optimal weight: 8.9990 chunk 19 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 163 optimal weight: 4.9990 chunk 77 optimal weight: 9.9990 chunk 124 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 369 HIS ** 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 = 0.4941 r_free = 0.4941 target = 0.219288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.179564 restraints weight = 18532.609| |-----------------------------------------------------------------------------| r_work (start): 0.4522 rms_B_bonded: 3.51 r_work: 0.4392 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.4392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6732 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13335 Z= 0.151 Angle : 0.569 7.916 18108 Z= 0.293 Chirality : 0.044 0.199 2124 Planarity : 0.003 0.024 2400 Dihedral : 4.045 20.283 1893 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 4.28 % Allowed : 31.01 % Favored : 64.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.18 % 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 aren not related in a simple way. whole: 0.64 (0.21), residues: 1743 helix: 1.90 (0.23), residues: 543 sheet: 0.88 (0.25), residues: 423 loop : -0.93 (0.23), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 329 TYR 0.026 0.002 TYR A 45 PHE 0.015 0.001 PHE B 68 TRP 0.004 0.001 TRP A 173 HIS 0.002 0.001 HIS C 410 Details of bonding type rmsd covalent geometry : bond 0.00373 (13335) covalent geometry : angle 0.56937 (18108) hydrogen bonds : bond 0.03901 ( 651) hydrogen bonds : angle 4.62657 ( 1809) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 122 time to evaluate : 0.426 Fit side-chains REVERT: A 216 LEU cc_start: 0.6208 (OUTLIER) cc_final: 0.5903 (mp) REVERT: A 292 ILE cc_start: 0.3512 (OUTLIER) cc_final: 0.2911 (tp) REVERT: A 341 LEU cc_start: 0.2934 (OUTLIER) cc_final: 0.2729 (mp) REVERT: A 582 GLU cc_start: 0.7442 (mm-30) cc_final: 0.7170 (mm-30) REVERT: B 292 ILE cc_start: 0.3361 (OUTLIER) cc_final: 0.2936 (mm) REVERT: B 341 LEU cc_start: 0.3310 (OUTLIER) cc_final: 0.3084 (mp) REVERT: C 133 ASP cc_start: 0.7357 (OUTLIER) cc_final: 0.7103 (t0) REVERT: C 275 TYR cc_start: 0.5474 (OUTLIER) cc_final: 0.5121 (m-10) REVERT: C 292 ILE cc_start: 0.3578 (OUTLIER) cc_final: 0.3368 (mm) outliers start: 59 outliers final: 49 residues processed: 178 average time/residue: 0.0803 time to fit residues: 22.9259 Evaluate side-chains 177 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 120 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain C residue 48 ASP Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 275 TYR Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 473 SER Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 514 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 167 optimal weight: 6.9990 chunk 70 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 133 optimal weight: 10.0000 chunk 60 optimal weight: 9.9990 chunk 6 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 147 optimal weight: 20.0000 chunk 28 optimal weight: 20.0000 chunk 128 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 369 HIS ** 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 = 0.4920 r_free = 0.4920 target = 0.216934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.177022 restraints weight = 18646.479| |-----------------------------------------------------------------------------| r_work (start): 0.4497 rms_B_bonded: 3.50 r_work: 0.4370 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.4370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6775 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13335 Z= 0.183 Angle : 0.610 9.394 18108 Z= 0.315 Chirality : 0.046 0.154 2124 Planarity : 0.004 0.028 2400 Dihedral : 4.322 20.423 1893 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 4.42 % Allowed : 30.87 % Favored : 64.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.18 % 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 aren not related in a simple way. whole: 0.35 (0.21), residues: 1743 helix: 1.54 (0.23), residues: 556 sheet: 0.74 (0.25), residues: 423 loop : -1.06 (0.23), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 329 TYR 0.030 0.002 TYR A 45 PHE 0.019 0.002 PHE B 68 TRP 0.004 0.002 TRP C 173 HIS 0.002 0.001 HIS C 410 Details of bonding type rmsd covalent geometry : bond 0.00454 (13335) covalent geometry : angle 0.60972 (18108) hydrogen bonds : bond 0.04331 ( 651) hydrogen bonds : angle 4.83355 ( 1809) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 121 time to evaluate : 0.492 Fit side-chains REVERT: A 216 LEU cc_start: 0.6374 (OUTLIER) cc_final: 0.6076 (mp) REVERT: A 292 ILE cc_start: 0.3601 (OUTLIER) cc_final: 0.2991 (tp) REVERT: A 341 LEU cc_start: 0.3074 (OUTLIER) cc_final: 0.2864 (mp) REVERT: A 582 GLU cc_start: 0.7488 (mm-30) cc_final: 0.7272 (mm-30) REVERT: B 218 GLU cc_start: 0.7813 (tm-30) cc_final: 0.7516 (tm-30) REVERT: B 292 ILE cc_start: 0.3402 (OUTLIER) cc_final: 0.2942 (mm) REVERT: B 341 LEU cc_start: 0.3339 (OUTLIER) cc_final: 0.3102 (mp) REVERT: B 387 LEU cc_start: 0.6612 (OUTLIER) cc_final: 0.6306 (mp) REVERT: C 133 ASP cc_start: 0.7599 (OUTLIER) cc_final: 0.7369 (t0) REVERT: C 275 TYR cc_start: 0.5682 (OUTLIER) cc_final: 0.5263 (m-10) REVERT: C 292 ILE cc_start: 0.3886 (OUTLIER) cc_final: 0.3668 (mm) outliers start: 61 outliers final: 50 residues processed: 178 average time/residue: 0.0739 time to fit residues: 21.5652 Evaluate side-chains 178 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 119 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain C residue 48 ASP Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 275 TYR Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 473 SER Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 514 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 13 optimal weight: 1.9990 chunk 160 optimal weight: 3.9990 chunk 26 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 86 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 143 optimal weight: 8.9990 chunk 128 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 155 optimal weight: 0.7980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 369 HIS ** 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 = 0.4941 r_free = 0.4941 target = 0.219404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.179858 restraints weight = 18525.256| |-----------------------------------------------------------------------------| r_work (start): 0.4528 rms_B_bonded: 3.48 r_work: 0.4400 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.4400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6735 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13335 Z= 0.136 Angle : 0.564 9.187 18108 Z= 0.291 Chirality : 0.044 0.209 2124 Planarity : 0.003 0.027 2400 Dihedral : 4.164 19.865 1893 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 4.20 % Allowed : 31.30 % Favored : 64.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.18 % 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 aren not related in a simple way. whole: 0.44 (0.21), residues: 1743 helix: 1.64 (0.23), residues: 559 sheet: 0.78 (0.25), residues: 423 loop : -1.03 (0.23), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 329 TYR 0.032 0.002 TYR C 454 PHE 0.014 0.001 PHE B 68 TRP 0.003 0.001 TRP C 173 HIS 0.001 0.001 HIS B 409 Details of bonding type rmsd covalent geometry : bond 0.00334 (13335) covalent geometry : angle 0.56443 (18108) hydrogen bonds : bond 0.03704 ( 651) hydrogen bonds : angle 4.64814 ( 1809) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2963.33 seconds wall clock time: 51 minutes 19.77 seconds (3079.77 seconds total)