Starting phenix.real_space_refine on Sat Jan 18 22:06:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wwp_37895/01_2025/8wwp_37895.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wwp_37895/01_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_37895/01_2025/8wwp_37895.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wwp_37895/01_2025/8wwp_37895.map" model { file = "/net/cci-nas-00/data/ceres_data/8wwp_37895/01_2025/8wwp_37895.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wwp_37895/01_2025/8wwp_37895.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 7.71, per 1000 atoms: 0.59 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: 3.10 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.44 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: 3.43 Time building geometry restraints manager: 3.60 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: 0.450 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: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 28.920 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.280 ------------------------------------------------------------------------------- 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= 0.201 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 : 9.97 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.002 0.001 TRP C 173 HIS 0.001 0.000 HIS C 369 PHE 0.011 0.001 PHE B 536 TYR 0.013 0.001 TYR B 45 ARG 0.002 0.000 ARG B 440 *********************** 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 : 1.433 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 129 average time/residue: 0.2083 time to fit residues: 42.5421 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 : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 20.0000 chunk 131 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 88 optimal weight: 20.0000 chunk 70 optimal weight: 1.9990 chunk 136 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 158 optimal weight: 8.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 = 0.4956 r_free = 0.4956 target = 0.220531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.180986 restraints weight = 18197.000| |-----------------------------------------------------------------------------| r_work (start): 0.4540 rms_B_bonded: 3.38 r_work: 0.4413 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.4413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6714 moved from start: 0.0710 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= 0.231 Angle : 0.536 6.568 18108 Z= 0.278 Chirality : 0.044 0.157 2124 Planarity : 0.003 0.023 2400 Dihedral : 3.874 19.748 1893 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.39 % Allowed : 29.57 % Favored : 68.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.21), residues: 1743 helix: 1.68 (0.23), residues: 554 sheet: 0.70 (0.25), residues: 423 loop : -0.87 (0.24), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 173 HIS 0.002 0.001 HIS B 410 PHE 0.013 0.001 PHE B 68 TYR 0.027 0.002 TYR C 45 ARG 0.002 0.000 ARG C 25 *********************** 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 169 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 136 time to evaluate : 1.644 Fit side-chains REVERT: A 218 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7541 (tm-30) REVERT: B 218 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7800 (tm-30) REVERT: B 580 MET cc_start: 0.6543 (OUTLIER) cc_final: 0.6328 (ptp) REVERT: C 218 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7766 (tm-30) REVERT: C 529 ASP cc_start: 0.5641 (OUTLIER) cc_final: 0.5369 (m-30) outliers start: 33 outliers final: 18 residues processed: 163 average time/residue: 0.2015 time to fit residues: 52.8572 Evaluate side-chains 154 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU 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 A residue 529 ASP Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 111 LEU 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 B residue 529 ASP Chi-restraints excluded: chain B residue 580 MET Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 132 LEU 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 529 ASP 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 164 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 63 optimal weight: 8.9990 chunk 92 optimal weight: 2.9990 chunk 60 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 80 optimal weight: 7.9990 chunk 55 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN ** A 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 GLN ** B 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 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 = 0.4899 r_free = 0.4899 target = 0.214496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.174379 restraints weight = 18581.927| |-----------------------------------------------------------------------------| r_work (start): 0.4470 rms_B_bonded: 3.51 r_work: 0.4344 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.4344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 13335 Z= 0.374 Angle : 0.641 6.889 18108 Z= 0.335 Chirality : 0.048 0.161 2124 Planarity : 0.004 0.033 2400 Dihedral : 4.508 19.109 1893 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 6.88 % Allowed : 28.19 % Favored : 64.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.21), residues: 1743 helix: 1.31 (0.23), residues: 555 sheet: 0.48 (0.24), residues: 423 loop : -0.95 (0.24), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP C 173 HIS 0.003 0.001 HIS B 410 PHE 0.025 0.002 PHE B 68 TYR 0.021 0.002 TYR A 45 ARG 0.003 0.000 ARG C 596 *********************** 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 225 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 130 time to evaluate : 1.646 Fit side-chains REVERT: A 52 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7584 (pp) REVERT: A 203 MET cc_start: 0.7114 (mtm) cc_final: 0.6878 (mtm) REVERT: A 341 LEU cc_start: 0.3095 (OUTLIER) cc_final: 0.2842 (mp) REVERT: B 203 MET cc_start: 0.7221 (mtm) cc_final: 0.6963 (mtm) REVERT: B 309 VAL cc_start: 0.6956 (OUTLIER) cc_final: 0.6617 (m) REVERT: B 341 LEU cc_start: 0.3384 (OUTLIER) cc_final: 0.3146 (mp) REVERT: C 52 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7380 (pp) REVERT: C 529 ASP cc_start: 0.5333 (OUTLIER) cc_final: 0.5029 (m-30) outliers start: 95 outliers final: 63 residues processed: 219 average time/residue: 0.1817 time to fit residues: 65.1813 Evaluate side-chains 194 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 125 time to evaluate : 1.465 ------------------------------------------------------------------------------- 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 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 132 LEU 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 228 VAL 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 381 ILE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 386 THR 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 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 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 309 VAL Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 353 THR 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 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 186 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 359 SER 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 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 17 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 129 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 38 optimal weight: 0.0570 chunk 127 optimal weight: 0.9980 chunk 51 optimal weight: 8.9990 chunk 78 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 chunk 116 optimal weight: 10.0000 overall best weight: 0.9500 ------------------------------------------------------------------------------- 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 124 GLN C 338 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4966 r_free = 0.4966 target = 0.221787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.182767 restraints weight = 18269.589| |-----------------------------------------------------------------------------| r_work (start): 0.4561 rms_B_bonded: 3.37 r_work: 0.4436 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.4436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6685 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13335 Z= 0.164 Angle : 0.511 6.712 18108 Z= 0.267 Chirality : 0.043 0.167 2124 Planarity : 0.003 0.026 2400 Dihedral : 4.020 21.292 1893 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.41 % Allowed : 32.32 % Favored : 64.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.21), residues: 1743 helix: 1.74 (0.23), residues: 555 sheet: 0.73 (0.24), residues: 427 loop : -0.97 (0.23), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 173 HIS 0.001 0.000 HIS B 409 PHE 0.009 0.001 PHE B 536 TYR 0.022 0.002 TYR C 45 ARG 0.004 0.000 ARG C 28 *********************** 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 189 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 142 time to evaluate : 1.438 Fit side-chains REVERT: A 341 LEU cc_start: 0.3037 (OUTLIER) cc_final: 0.2816 (mp) REVERT: C 529 ASP cc_start: 0.5755 (OUTLIER) cc_final: 0.5517 (m-30) outliers start: 47 outliers final: 25 residues processed: 186 average time/residue: 0.1997 time to fit residues: 59.0055 Evaluate side-chains 159 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 341 LEU 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 B residue 111 LEU Chi-restraints excluded: chain B residue 132 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 443 VAL 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 111 LEU 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 443 VAL 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 166 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 78 optimal weight: 9.9990 chunk 125 optimal weight: 0.8980 chunk 128 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 65 optimal weight: 0.0770 chunk 168 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 chunk 55 optimal weight: 10.0000 overall best weight: 1.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 124 GLN ** C 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4950 r_free = 0.4950 target = 0.220063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.180379 restraints weight = 18401.115| |-----------------------------------------------------------------------------| r_work (start): 0.4531 rms_B_bonded: 3.49 r_work: 0.4400 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.4400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6701 moved from start: 0.1307 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= 0.212 Angle : 0.543 8.184 18108 Z= 0.279 Chirality : 0.044 0.190 2124 Planarity : 0.003 0.026 2400 Dihedral : 4.040 20.274 1893 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 4.93 % Allowed : 31.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.21), residues: 1743 helix: 1.86 (0.23), residues: 545 sheet: 0.78 (0.25), residues: 423 loop : -0.94 (0.23), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 173 HIS 0.001 0.001 HIS B 410 PHE 0.013 0.001 PHE B 68 TYR 0.022 0.002 TYR A 45 ARG 0.001 0.000 ARG A 457 *********************** 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 196 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 128 time to evaluate : 1.466 Fit side-chains REVERT: A 52 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7417 (pp) REVERT: A 341 LEU cc_start: 0.2927 (OUTLIER) cc_final: 0.2695 (mp) REVERT: B 341 LEU cc_start: 0.3296 (OUTLIER) cc_final: 0.3084 (mp) REVERT: C 381 ILE cc_start: 0.7624 (OUTLIER) cc_final: 0.7341 (mp) REVERT: C 529 ASP cc_start: 0.5573 (OUTLIER) cc_final: 0.5280 (m-30) outliers start: 68 outliers final: 58 residues processed: 193 average time/residue: 0.1859 time to fit residues: 58.4287 Evaluate side-chains 187 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 124 time to evaluate : 1.472 ------------------------------------------------------------------------------- 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 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 275 TYR Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 379 THR 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 446 LEU 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 56 THR 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 139 ASP 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 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 478 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 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 132 LEU Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 275 TYR Chi-restraints excluded: chain C residue 341 LEU 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 443 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 59 optimal weight: 4.9990 chunk 105 optimal weight: 9.9990 chunk 134 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 166 optimal weight: 6.9990 chunk 156 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 144 optimal weight: 6.9990 chunk 93 optimal weight: 7.9990 chunk 153 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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** ** B 338 GLN ** 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 = 0.4911 r_free = 0.4911 target = 0.216019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.176517 restraints weight = 18565.124| |-----------------------------------------------------------------------------| r_work (start): 0.4490 rms_B_bonded: 3.39 r_work: 0.4363 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.4363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6786 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13335 Z= 0.306 Angle : 0.599 8.073 18108 Z= 0.310 Chirality : 0.046 0.154 2124 Planarity : 0.004 0.025 2400 Dihedral : 4.333 19.316 1893 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 6.30 % Allowed : 30.51 % Favored : 63.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.21), residues: 1743 helix: 1.64 (0.23), residues: 546 sheet: 0.63 (0.25), residues: 423 loop : -1.04 (0.23), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP C 173 HIS 0.002 0.001 HIS B 410 PHE 0.020 0.002 PHE B 68 TYR 0.025 0.002 TYR C 45 ARG 0.002 0.000 ARG C 573 *********************** 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 214 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 127 time to evaluate : 1.609 Fit side-chains REVERT: A 52 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7536 (pp) REVERT: A 341 LEU cc_start: 0.3122 (OUTLIER) cc_final: 0.2891 (mp) REVERT: A 582 GLU cc_start: 0.7480 (mm-30) cc_final: 0.7274 (mm-30) REVERT: B 341 LEU cc_start: 0.3340 (OUTLIER) cc_final: 0.3117 (mp) REVERT: C 218 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7773 (tm-30) REVERT: C 529 ASP cc_start: 0.5565 (OUTLIER) cc_final: 0.5270 (m-30) outliers start: 87 outliers final: 73 residues processed: 211 average time/residue: 0.1884 time to fit residues: 65.0523 Evaluate side-chains 199 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 121 time to evaluate : 1.558 ------------------------------------------------------------------------------- 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 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 275 TYR 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 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 443 VAL 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 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 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 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 473 SER 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 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 140 VAL Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 205 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 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 443 VAL Chi-restraints excluded: chain C residue 473 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 41 optimal weight: 5.9990 chunk 140 optimal weight: 2.9990 chunk 82 optimal weight: 20.0000 chunk 36 optimal weight: 4.9990 chunk 105 optimal weight: 0.3980 chunk 23 optimal weight: 8.9990 chunk 130 optimal weight: 0.3980 chunk 77 optimal weight: 9.9990 chunk 135 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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 = 0.4946 r_free = 0.4946 target = 0.219680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.180493 restraints weight = 18450.621| |-----------------------------------------------------------------------------| r_work (start): 0.4536 rms_B_bonded: 3.37 r_work: 0.4407 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.4407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6732 moved from start: 0.1435 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= 0.197 Angle : 0.541 7.361 18108 Z= 0.279 Chirality : 0.044 0.142 2124 Planarity : 0.003 0.026 2400 Dihedral : 4.119 21.116 1893 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 6.01 % Allowed : 30.51 % Favored : 63.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.21), residues: 1743 helix: 1.81 (0.23), residues: 549 sheet: 0.77 (0.25), residues: 423 loop : -0.98 (0.23), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 173 HIS 0.001 0.000 HIS B 409 PHE 0.012 0.001 PHE B 68 TYR 0.025 0.002 TYR C 454 ARG 0.001 0.000 ARG C 596 *********************** 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 214 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 131 time to evaluate : 1.466 Fit side-chains REVERT: A 52 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7417 (pp) REVERT: A 216 LEU cc_start: 0.6427 (OUTLIER) cc_final: 0.6142 (mp) REVERT: A 341 LEU cc_start: 0.2957 (OUTLIER) cc_final: 0.2719 (mp) REVERT: B 292 ILE cc_start: 0.3258 (OUTLIER) cc_final: 0.2822 (mm) REVERT: B 341 LEU cc_start: 0.3245 (OUTLIER) cc_final: 0.3031 (mp) REVERT: B 387 LEU cc_start: 0.6569 (OUTLIER) cc_final: 0.6292 (mp) REVERT: C 218 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7778 (tm-30) REVERT: C 292 ILE cc_start: 0.3625 (OUTLIER) cc_final: 0.3376 (mm) REVERT: C 381 ILE cc_start: 0.7680 (OUTLIER) cc_final: 0.7400 (mp) outliers start: 83 outliers final: 63 residues processed: 209 average time/residue: 0.2020 time to fit residues: 67.4528 Evaluate side-chains 197 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 125 time to evaluate : 1.412 ------------------------------------------------------------------------------- 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 127 VAL Chi-restraints excluded: chain A residue 132 LEU 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 216 LEU Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 364 VAL 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 473 SER 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 48 ASP 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 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 216 LEU Chi-restraints excluded: chain B residue 228 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 386 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 510 VAL Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 529 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 140 VAL Chi-restraints excluded: chain C residue 143 ILE 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 292 ILE 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 371 SER 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 443 VAL Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 473 SER 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 580 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 106 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 171 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 chunk 140 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 63 optimal weight: 8.9990 chunk 54 optimal weight: 7.9990 chunk 148 optimal weight: 6.9990 chunk 129 optimal weight: 9.9990 chunk 103 optimal weight: 5.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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 338 GLN ** 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 = 0.4840 r_free = 0.4840 target = 0.219608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.175934 restraints weight = 19856.890| |-----------------------------------------------------------------------------| r_work (start): 0.4402 rms_B_bonded: 3.33 r_work: 0.4274 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.4274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 13335 Z= 0.542 Angle : 0.775 11.793 18108 Z= 0.401 Chirality : 0.052 0.187 2124 Planarity : 0.005 0.040 2400 Dihedral : 4.989 20.920 1893 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 7.61 % Allowed : 28.91 % Favored : 63.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.21), residues: 1743 helix: 0.97 (0.23), residues: 558 sheet: 0.39 (0.24), residues: 422 loop : -1.35 (0.23), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.003 TRP C 173 HIS 0.004 0.001 HIS B 410 PHE 0.034 0.003 PHE A 68 TYR 0.025 0.003 TYR C 45 ARG 0.004 0.001 ARG B 573 *********************** 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 231 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 126 time to evaluate : 1.514 Fit side-chains REVERT: A 203 MET cc_start: 0.7249 (mtm) cc_final: 0.6981 (mtm) REVERT: A 216 LEU cc_start: 0.6645 (OUTLIER) cc_final: 0.6397 (mp) REVERT: A 256 LYS cc_start: 0.5406 (OUTLIER) cc_final: 0.5099 (pttp) REVERT: A 341 LEU cc_start: 0.3336 (OUTLIER) cc_final: 0.3074 (mp) REVERT: B 341 LEU cc_start: 0.3436 (OUTLIER) cc_final: 0.3205 (mp) REVERT: B 387 LEU cc_start: 0.6758 (OUTLIER) cc_final: 0.6429 (mt) REVERT: C 218 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7734 (tm-30) REVERT: C 275 TYR cc_start: 0.5705 (OUTLIER) cc_final: 0.5232 (m-10) REVERT: C 292 ILE cc_start: 0.3813 (OUTLIER) cc_final: 0.3579 (mm) outliers start: 105 outliers final: 86 residues processed: 224 average time/residue: 0.2049 time to fit residues: 72.5827 Evaluate side-chains 217 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 123 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ASP 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 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 216 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 256 LYS Chi-restraints excluded: chain A residue 275 TYR 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 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 396 ILE Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 443 VAL 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 A residue 524 ILE 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 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 140 VAL Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 205 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 341 LEU Chi-restraints excluded: chain B residue 359 SER 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 387 LEU Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 397 ASP 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 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 140 VAL Chi-restraints excluded: chain C residue 143 ILE 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 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 292 ILE 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 371 SER 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 396 ILE Chi-restraints excluded: chain C residue 443 VAL 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 161 optimal weight: 5.9990 chunk 118 optimal weight: 8.9990 chunk 63 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 113 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 = 0.4888 r_free = 0.4888 target = 0.214671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.173600 restraints weight = 18520.824| |-----------------------------------------------------------------------------| r_work (start): 0.4445 rms_B_bonded: 3.63 r_work: 0.4314 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.4314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6796 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13335 Z= 0.273 Angle : 0.608 8.739 18108 Z= 0.315 Chirality : 0.046 0.148 2124 Planarity : 0.004 0.029 2400 Dihedral : 4.574 20.922 1893 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 6.38 % Allowed : 30.00 % Favored : 63.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.21), residues: 1743 helix: 1.32 (0.23), residues: 559 sheet: 0.51 (0.25), residues: 423 loop : -1.23 (0.23), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 173 HIS 0.002 0.001 HIS B 410 PHE 0.025 0.002 PHE A 416 TYR 0.034 0.003 TYR C 454 ARG 0.006 0.000 ARG B 329 *********************** 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 214 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 126 time to evaluate : 1.470 Fit side-chains REVERT: A 52 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7490 (pp) REVERT: A 216 LEU cc_start: 0.6442 (OUTLIER) cc_final: 0.6195 (mp) REVERT: A 341 LEU cc_start: 0.3141 (OUTLIER) cc_final: 0.2892 (mp) REVERT: B 292 ILE cc_start: 0.3835 (OUTLIER) cc_final: 0.3388 (mm) REVERT: B 341 LEU cc_start: 0.3363 (OUTLIER) cc_final: 0.3114 (mp) REVERT: B 387 LEU cc_start: 0.6598 (OUTLIER) cc_final: 0.6250 (mt) REVERT: C 218 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7718 (tm-30) REVERT: C 275 TYR cc_start: 0.5602 (OUTLIER) cc_final: 0.5167 (m-10) REVERT: C 292 ILE cc_start: 0.3836 (OUTLIER) cc_final: 0.3630 (mm) REVERT: C 381 ILE cc_start: 0.7743 (OUTLIER) cc_final: 0.7482 (mt) outliers start: 88 outliers final: 74 residues processed: 208 average time/residue: 0.2291 time to fit residues: 76.4801 Evaluate side-chains 207 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 123 time to evaluate : 1.496 ------------------------------------------------------------------------------- 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 71 LEU 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 140 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 216 LEU 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 364 VAL Chi-restraints excluded: chain A residue 379 THR 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 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 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 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 140 VAL Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 205 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 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 371 SER 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 387 LEU 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 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 140 VAL Chi-restraints excluded: chain C residue 143 ILE 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 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 292 ILE 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 371 SER 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 62 optimal weight: 10.0000 chunk 100 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 chunk 9 optimal weight: 0.0060 chunk 31 optimal weight: 20.0000 chunk 95 optimal weight: 8.9990 chunk 99 optimal weight: 3.9990 chunk 133 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 106 optimal weight: 0.1980 chunk 142 optimal weight: 9.9990 overall best weight: 2.0402 ------------------------------------------------------------------------------- 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 = 0.4909 r_free = 0.4909 target = 0.226690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.183947 restraints weight = 19627.428| |-----------------------------------------------------------------------------| r_work (start): 0.4492 rms_B_bonded: 3.32 r_work: 0.4366 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.4366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6786 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13335 Z= 0.224 Angle : 0.575 9.300 18108 Z= 0.297 Chirality : 0.044 0.150 2124 Planarity : 0.004 0.026 2400 Dihedral : 4.345 21.468 1893 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 6.23 % Allowed : 30.29 % Favored : 63.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.21), residues: 1743 helix: 1.65 (0.23), residues: 549 sheet: 0.63 (0.25), residues: 423 loop : -1.13 (0.23), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 173 HIS 0.001 0.000 HIS B 409 PHE 0.014 0.001 PHE B 68 TYR 0.036 0.002 TYR C 454 ARG 0.006 0.000 ARG B 329 ********************** 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 214 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 128 time to evaluate : 1.520 Fit side-chains REVERT: A 52 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7523 (pp) REVERT: A 216 LEU cc_start: 0.6469 (OUTLIER) cc_final: 0.6194 (mp) REVERT: A 341 LEU cc_start: 0.3100 (OUTLIER) cc_final: 0.2845 (mp) REVERT: B 292 ILE cc_start: 0.3361 (OUTLIER) cc_final: 0.2902 (mm) REVERT: B 341 LEU cc_start: 0.3327 (OUTLIER) cc_final: 0.3096 (mp) REVERT: B 387 LEU cc_start: 0.6562 (OUTLIER) cc_final: 0.6270 (mp) REVERT: C 218 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7733 (tm-30) REVERT: C 226 GLU cc_start: 0.6934 (mp0) cc_final: 0.6705 (mp0) REVERT: C 275 TYR cc_start: 0.5571 (OUTLIER) cc_final: 0.5167 (m-10) REVERT: C 292 ILE cc_start: 0.3862 (OUTLIER) cc_final: 0.3644 (mm) REVERT: C 381 ILE cc_start: 0.7730 (OUTLIER) cc_final: 0.7444 (mp) outliers start: 86 outliers final: 74 residues processed: 208 average time/residue: 0.2062 time to fit residues: 69.0552 Evaluate side-chains 211 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 127 time to evaluate : 1.497 ------------------------------------------------------------------------------- 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 71 LEU 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 205 VAL Chi-restraints excluded: chain A residue 216 LEU 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 364 VAL Chi-restraints excluded: chain A residue 379 THR 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 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 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 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 140 VAL Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 205 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 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 371 SER 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 387 LEU 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 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 143 ILE 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 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 292 ILE 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 371 SER 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 107 optimal weight: 5.9990 chunk 159 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 chunk 85 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 167 optimal weight: 10.0000 chunk 115 optimal weight: 7.9990 chunk 132 optimal weight: 5.9990 chunk 135 optimal weight: 5.9990 chunk 133 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- 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 = 0.4917 r_free = 0.4917 target = 0.216724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.177526 restraints weight = 18530.625| |-----------------------------------------------------------------------------| r_work (start): 0.4502 rms_B_bonded: 3.36 r_work: 0.4373 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.4373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6782 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13335 Z= 0.264 Angle : 0.598 9.985 18108 Z= 0.309 Chirality : 0.045 0.153 2124 Planarity : 0.004 0.029 2400 Dihedral : 4.389 20.786 1893 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 6.30 % Allowed : 30.29 % Favored : 63.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.21), residues: 1743 helix: 1.55 (0.23), residues: 552 sheet: 0.62 (0.25), residues: 423 loop : -1.13 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 173 HIS 0.002 0.001 HIS B 410 PHE 0.017 0.001 PHE B 68 TYR 0.040 0.002 TYR C 454 ARG 0.008 0.000 ARG B 329 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6591.21 seconds wall clock time: 117 minutes 28.22 seconds (7048.22 seconds total)