Starting phenix.real_space_refine on Wed Jul 30 23:46:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wwp_37895/07_2025/8wwp_37895.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wwp_37895/07_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_37895/07_2025/8wwp_37895.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wwp_37895/07_2025/8wwp_37895.map" model { file = "/net/cci-nas-00/data/ceres_data/8wwp_37895/07_2025/8wwp_37895.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wwp_37895/07_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-5711/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: 8.05, per 1000 atoms: 0.61 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: 3.84 Conformation dependent library (CDL) restraints added in 1.9 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: 1.59 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: 4.13 Time building geometry restraints manager: 4.03 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: 0.990 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: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 32.430 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 37.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13335 Z= 0.130 Angle : 0.507 5.959 18108 Z= 0.269 Chirality : 0.043 0.140 2124 Planarity : 0.003 0.023 2400 Dihedral : 17.165 88.484 4911 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 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 Details of bonding type rmsd hydrogen bonds : bond 0.14161 ( 651) hydrogen bonds : angle 5.78668 ( 1809) covalent geometry : bond 0.00301 (13335) covalent geometry : angle 0.50696 (18108) *********************** 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 : 1.474 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 129 average time/residue: 0.2039 time to fit residues: 42.1836 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 : 1.377 ------------------------------------------------------------------------------- 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 = 18197.014| |-----------------------------------------------------------------------------| r_work (start): 0.4540 rms_B_bonded: 3.38 r_work: 0.4411 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.4411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6715 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= 0.144 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 Details of bonding type rmsd hydrogen bonds : bond 0.03970 ( 651) hydrogen bonds : angle 4.92987 ( 1809) covalent geometry : bond 0.00345 (13335) covalent geometry : angle 0.53588 (18108) *********************** 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 : 1.579 Fit side-chains REVERT: A 218 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7544 (tm-30) REVERT: B 218 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7802 (tm-30) REVERT: B 580 MET cc_start: 0.6536 (OUTLIER) cc_final: 0.6323 (ptp) REVERT: C 218 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7767 (tm-30) REVERT: C 529 ASP cc_start: 0.5634 (OUTLIER) cc_final: 0.5363 (m-30) outliers start: 33 outliers final: 18 residues processed: 163 average time/residue: 0.1963 time to fit residues: 51.5052 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 : 1.566 ------------------------------------------------------------------------------- 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: 8.9990 chunk 19 optimal weight: 4.9990 chunk 63 optimal weight: 7.9990 chunk 92 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 49 optimal weight: 0.1980 chunk 66 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 overall best weight: 3.8388 ------------------------------------------------------------------------------- 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 = 0.4907 r_free = 0.4907 target = 0.215416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.175174 restraints weight = 18551.195| |-----------------------------------------------------------------------------| r_work (start): 0.4481 rms_B_bonded: 3.49 r_work: 0.4352 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.4352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6792 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13335 Z= 0.203 Angle : 0.613 6.725 18108 Z= 0.320 Chirality : 0.047 0.158 2124 Planarity : 0.004 0.031 2400 Dihedral : 4.368 18.873 1893 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 6.74 % Allowed : 27.97 % Favored : 65.29 % 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: 0.27 (0.21), residues: 1743 helix: 1.41 (0.23), residues: 555 sheet: 0.55 (0.24), residues: 423 loop : -0.94 (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 0.022 0.002 PHE B 68 TYR 0.021 0.002 TYR A 45 ARG 0.002 0.000 ARG C 596 Details of bonding type rmsd hydrogen bonds : bond 0.04836 ( 651) hydrogen bonds : angle 5.14831 ( 1809) covalent geometry : bond 0.00502 (13335) covalent geometry : angle 0.61289 (18108) *********************** 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 222 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 129 time to evaluate : 1.366 Fit side-chains REVERT: A 52 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7542 (pp) REVERT: A 341 LEU cc_start: 0.3074 (OUTLIER) cc_final: 0.2833 (mp) REVERT: B 341 LEU cc_start: 0.3392 (OUTLIER) cc_final: 0.3164 (mp) REVERT: C 52 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7365 (pp) REVERT: C 529 ASP cc_start: 0.5413 (OUTLIER) cc_final: 0.5112 (m-30) outliers start: 93 outliers final: 62 residues processed: 216 average time/residue: 0.1740 time to fit residues: 61.3874 Evaluate side-chains 190 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 123 time to evaluate : 1.500 ------------------------------------------------------------------------------- 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 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 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 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 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: 8.9990 chunk 70 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 129 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 chunk 38 optimal weight: 0.3980 chunk 127 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 78 optimal weight: 0.2980 chunk 59 optimal weight: 2.9990 chunk 116 optimal weight: 10.0000 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN B 338 GLN C 338 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4985 r_free = 0.4985 target = 0.223769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.184943 restraints weight = 18196.137| |-----------------------------------------------------------------------------| r_work (start): 0.4581 rms_B_bonded: 3.38 r_work: 0.4455 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.4455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6666 moved from start: 0.1149 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= 0.100 Angle : 0.500 6.743 18108 Z= 0.261 Chirality : 0.043 0.162 2124 Planarity : 0.003 0.026 2400 Dihedral : 3.885 21.536 1893 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.90 % Allowed : 32.25 % Favored : 64.86 % 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: 0.64 (0.21), residues: 1743 helix: 1.98 (0.23), residues: 541 sheet: 0.79 (0.24), residues: 429 loop : -0.94 (0.23), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 173 HIS 0.002 0.000 HIS B 409 PHE 0.008 0.001 PHE B 157 TYR 0.022 0.002 TYR C 45 ARG 0.003 0.000 ARG C 28 Details of bonding type rmsd hydrogen bonds : bond 0.03010 ( 651) hydrogen bonds : angle 4.51303 ( 1809) covalent geometry : bond 0.00225 (13335) covalent geometry : angle 0.50028 (18108) *********************** 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 181 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 141 time to evaluate : 1.554 Fit side-chains REVERT: C 582 GLU cc_start: 0.7225 (mm-30) cc_final: 0.7023 (mm-30) outliers start: 40 outliers final: 23 residues processed: 178 average time/residue: 0.1987 time to fit residues: 56.3181 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 : 1.425 ------------------------------------------------------------------------------- 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 364 VAL Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain B residue 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 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 359 SER 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 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: 1.9990 chunk 78 optimal weight: 0.0020 chunk 125 optimal weight: 0.3980 chunk 128 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 65 optimal weight: 0.9980 chunk 168 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 55 optimal weight: 9.9990 overall best weight: 1.0792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 124 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4976 r_free = 0.4976 target = 0.222933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.183721 restraints weight = 18358.707| |-----------------------------------------------------------------------------| r_work (start): 0.4570 rms_B_bonded: 3.41 r_work: 0.4443 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.4443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6680 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13335 Z= 0.103 Angle : 0.515 7.691 18108 Z= 0.262 Chirality : 0.043 0.186 2124 Planarity : 0.003 0.027 2400 Dihedral : 3.784 20.137 1893 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.41 % Allowed : 31.30 % Favored : 65.29 % 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: 0.72 (0.21), residues: 1743 helix: 2.06 (0.23), residues: 540 sheet: 0.86 (0.25), residues: 429 loop : -0.92 (0.23), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 173 HIS 0.001 0.000 HIS B 409 PHE 0.010 0.001 PHE B 536 TYR 0.021 0.002 TYR C 45 ARG 0.001 0.000 ARG B 457 Details of bonding type rmsd hydrogen bonds : bond 0.03100 ( 651) hydrogen bonds : angle 4.42740 ( 1809) covalent geometry : bond 0.00243 (13335) covalent geometry : angle 0.51535 (18108) *********************** 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 181 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 134 time to evaluate : 1.495 Fit side-chains REVERT: A 341 LEU cc_start: 0.2947 (OUTLIER) cc_final: 0.2714 (mp) REVERT: C 582 GLU cc_start: 0.7229 (mm-30) cc_final: 0.7012 (mm-30) outliers start: 47 outliers final: 38 residues processed: 178 average time/residue: 0.1809 time to fit residues: 52.4905 Evaluate side-chains 165 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 126 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 205 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 385 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 514 VAL 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 200 VAL Chi-restraints excluded: chain C residue 275 TYR Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 385 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 59 optimal weight: 6.9990 chunk 105 optimal weight: 0.9990 chunk 134 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 166 optimal weight: 10.0000 chunk 156 optimal weight: 0.1980 chunk 2 optimal weight: 9.9990 chunk 144 optimal weight: 0.5980 chunk 93 optimal weight: 0.0040 chunk 153 optimal weight: 0.3980 chunk 36 optimal weight: 6.9990 overall best weight: 0.4392 ------------------------------------------------------------------------------- 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 = 0.5009 r_free = 0.5009 target = 0.226530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.187608 restraints weight = 18483.926| |-----------------------------------------------------------------------------| r_work (start): 0.4610 rms_B_bonded: 3.43 r_work: 0.4482 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.4482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6649 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13335 Z= 0.092 Angle : 0.492 6.746 18108 Z= 0.251 Chirality : 0.042 0.128 2124 Planarity : 0.003 0.025 2400 Dihedral : 3.582 19.228 1893 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.26 % Allowed : 30.94 % Favored : 65.80 % 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: 0.84 (0.21), residues: 1743 helix: 2.10 (0.23), residues: 546 sheet: 0.96 (0.25), residues: 429 loop : -0.85 (0.24), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 173 HIS 0.001 0.000 HIS B 409 PHE 0.009 0.001 PHE B 536 TYR 0.019 0.001 TYR C 45 ARG 0.001 0.000 ARG A 165 Details of bonding type rmsd hydrogen bonds : bond 0.02659 ( 651) hydrogen bonds : angle 4.22599 ( 1809) covalent geometry : bond 0.00209 (13335) covalent geometry : angle 0.49187 (18108) *********************** 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 180 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 135 time to evaluate : 1.539 Fit side-chains REVERT: C 133 ASP cc_start: 0.7060 (OUTLIER) cc_final: 0.6831 (t0) REVERT: C 582 GLU cc_start: 0.7209 (mm-30) cc_final: 0.6987 (mm-30) outliers start: 45 outliers final: 33 residues processed: 176 average time/residue: 0.1859 time to fit residues: 53.0412 Evaluate side-chains 160 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 126 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR 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 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 580 MET 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 174 VAL 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 127 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 275 TYR Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 580 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 41 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 82 optimal weight: 0.4980 chunk 36 optimal weight: 7.9990 chunk 105 optimal weight: 8.9990 chunk 23 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 77 optimal weight: 9.9990 chunk 135 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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 = 0.4960 r_free = 0.4960 target = 0.221018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.181269 restraints weight = 18439.223| |-----------------------------------------------------------------------------| r_work (start): 0.4537 rms_B_bonded: 3.51 r_work: 0.4406 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.4406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6707 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13335 Z= 0.144 Angle : 0.547 6.810 18108 Z= 0.280 Chirality : 0.044 0.192 2124 Planarity : 0.003 0.024 2400 Dihedral : 3.854 20.777 1893 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 4.28 % Allowed : 30.43 % Favored : 65.29 % 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: 0.75 (0.21), residues: 1743 helix: 1.92 (0.23), residues: 547 sheet: 0.97 (0.25), residues: 423 loop : -0.84 (0.23), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 173 HIS 0.001 0.001 HIS C 410 PHE 0.013 0.001 PHE B 68 TYR 0.032 0.002 TYR C 45 ARG 0.001 0.000 ARG C 28 Details of bonding type rmsd hydrogen bonds : bond 0.03665 ( 651) hydrogen bonds : angle 4.52376 ( 1809) covalent geometry : bond 0.00352 (13335) covalent geometry : angle 0.54660 (18108) *********************** 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 182 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 123 time to evaluate : 1.449 Fit side-chains REVERT: A 341 LEU cc_start: 0.2834 (OUTLIER) cc_final: 0.2615 (mp) REVERT: C 582 GLU cc_start: 0.7263 (mm-30) cc_final: 0.7035 (mm-30) outliers start: 59 outliers final: 49 residues processed: 179 average time/residue: 0.1921 time to fit residues: 54.6742 Evaluate side-chains 172 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 122 time to evaluate : 1.377 ------------------------------------------------------------------------------- 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 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 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 510 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 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 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 140 VAL Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 275 TYR Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 473 SER Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 524 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 106 optimal weight: 8.9990 chunk 32 optimal weight: 10.0000 chunk 171 optimal weight: 9.9990 chunk 114 optimal weight: 9.9990 chunk 140 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 63 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 chunk 148 optimal weight: 3.9990 chunk 129 optimal weight: 7.9990 chunk 103 optimal weight: 9.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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 = 0.4854 r_free = 0.4854 target = 0.210185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.169972 restraints weight = 18717.487| |-----------------------------------------------------------------------------| r_work (start): 0.4416 rms_B_bonded: 3.49 r_work: 0.4286 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.4286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6877 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.073 13335 Z= 0.345 Angle : 0.816 12.077 18108 Z= 0.423 Chirality : 0.053 0.215 2124 Planarity : 0.005 0.042 2400 Dihedral : 5.114 21.081 1893 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 5.65 % Allowed : 29.42 % 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: -0.27 (0.20), residues: 1743 helix: 0.85 (0.23), residues: 559 sheet: 0.42 (0.24), residues: 422 loop : -1.30 (0.23), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.003 TRP C 173 HIS 0.005 0.001 HIS B 410 PHE 0.037 0.003 PHE B 68 TYR 0.037 0.003 TYR B 45 ARG 0.005 0.001 ARG B 165 Details of bonding type rmsd hydrogen bonds : bond 0.06589 ( 651) hydrogen bonds : angle 5.68165 ( 1809) covalent geometry : bond 0.00857 (13335) covalent geometry : angle 0.81564 (18108) *********************** 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 201 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 123 time to evaluate : 1.397 Fit side-chains REVERT: A 203 MET cc_start: 0.7231 (mtm) cc_final: 0.6943 (mtm) REVERT: A 341 LEU cc_start: 0.3391 (OUTLIER) cc_final: 0.3161 (mp) REVERT: A 582 GLU cc_start: 0.7560 (mm-30) cc_final: 0.7325 (mm-30) REVERT: B 387 LEU cc_start: 0.6726 (OUTLIER) cc_final: 0.6406 (mt) REVERT: C 275 TYR cc_start: 0.5694 (OUTLIER) cc_final: 0.5268 (m-10) REVERT: C 292 ILE cc_start: 0.4069 (OUTLIER) cc_final: 0.3863 (mm) REVERT: C 534 MET cc_start: 0.8305 (tpp) cc_final: 0.7942 (tmm) REVERT: C 582 GLU cc_start: 0.7289 (mm-30) cc_final: 0.7089 (mm-30) outliers start: 78 outliers final: 64 residues processed: 198 average time/residue: 0.2089 time to fit residues: 64.1609 Evaluate side-chains 184 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 116 time to evaluate : 1.434 ------------------------------------------------------------------------------- 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 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 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 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 186 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 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 443 VAL Chi-restraints excluded: chain B residue 446 LEU 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 216 LEU 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 379 THR 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 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: 4.9990 chunk 118 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 58 optimal weight: 10.0000 chunk 5 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 57 optimal weight: 7.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 = 0.4935 r_free = 0.4935 target = 0.218603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.179047 restraints weight = 18468.810| |-----------------------------------------------------------------------------| r_work (start): 0.4517 rms_B_bonded: 3.46 r_work: 0.4388 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.4388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13335 Z= 0.135 Angle : 0.570 7.474 18108 Z= 0.295 Chirality : 0.045 0.141 2124 Planarity : 0.003 0.025 2400 Dihedral : 4.349 21.053 1893 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 4.86 % Allowed : 30.22 % 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: 0.22 (0.21), residues: 1743 helix: 1.37 (0.23), residues: 563 sheet: 0.63 (0.24), residues: 423 loop : -1.08 (0.23), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 173 HIS 0.001 0.001 HIS B 369 PHE 0.013 0.001 PHE B 68 TYR 0.031 0.002 TYR C 454 ARG 0.004 0.000 ARG B 329 Details of bonding type rmsd hydrogen bonds : bond 0.03771 ( 651) hydrogen bonds : angle 4.82809 ( 1809) covalent geometry : bond 0.00329 (13335) covalent geometry : angle 0.57014 (18108) *********************** 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 196 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 129 time to evaluate : 1.470 Fit side-chains REVERT: A 216 LEU cc_start: 0.6475 (OUTLIER) cc_final: 0.6203 (mp) REVERT: A 226 GLU cc_start: 0.6989 (mp0) cc_final: 0.6782 (mp0) REVERT: A 341 LEU cc_start: 0.3076 (OUTLIER) cc_final: 0.2840 (mp) REVERT: A 582 GLU cc_start: 0.7475 (mm-30) cc_final: 0.7269 (mm-30) REVERT: B 292 ILE cc_start: 0.3450 (OUTLIER) cc_final: 0.3022 (mm) REVERT: B 341 LEU cc_start: 0.3568 (OUTLIER) cc_final: 0.3344 (mp) REVERT: B 387 LEU cc_start: 0.6602 (OUTLIER) cc_final: 0.6258 (mt) REVERT: C 133 ASP cc_start: 0.7769 (OUTLIER) cc_final: 0.7363 (t0) REVERT: C 381 ILE cc_start: 0.7701 (OUTLIER) cc_final: 0.7423 (mp) REVERT: C 387 LEU cc_start: 0.6586 (OUTLIER) cc_final: 0.6350 (mp) REVERT: C 582 GLU cc_start: 0.7203 (mm-30) cc_final: 0.6994 (mm-30) outliers start: 67 outliers final: 55 residues processed: 193 average time/residue: 0.1928 time to fit residues: 59.1809 Evaluate side-chains 189 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 126 time to evaluate : 1.537 ------------------------------------------------------------------------------- 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 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 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 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 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 127 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 341 LEU 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 469 THR Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 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 127 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 133 ASP 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 228 VAL Chi-restraints excluded: chain C residue 275 TYR Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 387 LEU 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: 9.9990 chunk 100 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 9 optimal weight: 0.0050 chunk 31 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 133 optimal weight: 10.0000 chunk 61 optimal weight: 0.8980 chunk 106 optimal weight: 5.9990 chunk 142 optimal weight: 7.9990 overall best weight: 1.3598 ------------------------------------------------------------------------------- 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 = 0.4954 r_free = 0.4954 target = 0.220539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.180923 restraints weight = 18447.346| |-----------------------------------------------------------------------------| r_work (start): 0.4540 rms_B_bonded: 3.47 r_work: 0.4411 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.4411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6734 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13335 Z= 0.116 Angle : 0.543 7.074 18108 Z= 0.281 Chirality : 0.043 0.135 2124 Planarity : 0.003 0.027 2400 Dihedral : 4.100 20.998 1893 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 4.20 % Allowed : 30.94 % Favored : 64.86 % 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: 0.52 (0.21), residues: 1743 helix: 1.72 (0.23), residues: 553 sheet: 0.83 (0.25), residues: 423 loop : -0.99 (0.23), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 173 HIS 0.001 0.000 HIS B 409 PHE 0.023 0.001 PHE A 416 TYR 0.034 0.002 TYR C 454 ARG 0.007 0.000 ARG B 329 Details of bonding type rmsd hydrogen bonds : bond 0.03381 ( 651) hydrogen bonds : angle 4.58047 ( 1809) covalent geometry : bond 0.00278 (13335) covalent geometry : angle 0.54273 (18108) ********************** 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 186 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 128 time to evaluate : 1.454 Fit side-chains REVERT: A 341 LEU cc_start: 0.3066 (OUTLIER) cc_final: 0.2837 (mp) REVERT: A 582 GLU cc_start: 0.7458 (mm-30) cc_final: 0.7252 (mm-30) REVERT: B 292 ILE cc_start: 0.3357 (OUTLIER) cc_final: 0.2941 (mm) REVERT: B 341 LEU cc_start: 0.3466 (OUTLIER) cc_final: 0.3255 (mp) REVERT: B 387 LEU cc_start: 0.6577 (OUTLIER) cc_final: 0.6303 (mp) REVERT: C 275 TYR cc_start: 0.5572 (OUTLIER) cc_final: 0.5170 (m-10) REVERT: C 582 GLU cc_start: 0.7198 (mm-30) cc_final: 0.6988 (mm-30) outliers start: 58 outliers final: 48 residues processed: 184 average time/residue: 0.1958 time to fit residues: 57.6570 Evaluate side-chains 180 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 127 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 140 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 205 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 385 THR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 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 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 364 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 473 SER 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 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 228 VAL Chi-restraints excluded: chain C residue 275 TYR Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 514 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 107 optimal weight: 3.9990 chunk 159 optimal weight: 0.9990 chunk 50 optimal weight: 10.0000 chunk 85 optimal weight: 0.0770 chunk 0 optimal weight: 10.0000 chunk 167 optimal weight: 5.9990 chunk 115 optimal weight: 10.0000 chunk 132 optimal weight: 4.9990 chunk 135 optimal weight: 9.9990 chunk 133 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.8146 ------------------------------------------------------------------------------- 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 = 0.4952 r_free = 0.4952 target = 0.220253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.180606 restraints weight = 18549.037| |-----------------------------------------------------------------------------| r_work (start): 0.4534 rms_B_bonded: 3.49 r_work: 0.4405 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.4405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6711 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13335 Z= 0.126 Angle : 0.551 7.623 18108 Z= 0.284 Chirality : 0.044 0.142 2124 Planarity : 0.003 0.026 2400 Dihedral : 4.081 20.645 1893 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 4.49 % Allowed : 30.72 % Favored : 64.78 % 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: 0.55 (0.21), residues: 1743 helix: 1.76 (0.23), residues: 550 sheet: 0.85 (0.25), residues: 423 loop : -0.97 (0.23), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 173 HIS 0.001 0.000 HIS B 409 PHE 0.011 0.001 PHE B 68 TYR 0.039 0.002 TYR C 454 ARG 0.007 0.000 ARG B 329 Details of bonding type rmsd hydrogen bonds : bond 0.03536 ( 651) hydrogen bonds : angle 4.57434 ( 1809) covalent geometry : bond 0.00308 (13335) covalent geometry : angle 0.55129 (18108) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6876.41 seconds wall clock time: 118 minutes 15.19 seconds (7095.19 seconds total)