Starting phenix.real_space_refine on Sun Aug 24 07:45:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f0a_28754/08_2025/8f0a_28754.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f0a_28754/08_2025/8f0a_28754.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f0a_28754/08_2025/8f0a_28754.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f0a_28754/08_2025/8f0a_28754.map" model { file = "/net/cci-nas-00/data/ceres_data/8f0a_28754/08_2025/8f0a_28754.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f0a_28754/08_2025/8f0a_28754.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.053 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 42 5.16 5 C 5547 2.51 5 N 1566 2.21 5 O 1716 1.98 5 H 9189 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18060 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 4468 Classifications: {'peptide': 302} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 290} Chain breaks: 1 Chain: "D" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1154 Classifications: {'peptide': 75} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "a" Number of atoms: 398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 398 Classifications: {'peptide': 27} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 26} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Restraints were copied for chains: B, C, E, F, b, c Time building chain proxies: 4.16, per 1000 atoms: 0.23 Number of scatterers: 18060 At special positions: 0 Unit cell: (98.58, 112.36, 126.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 42 16.00 O 1716 8.00 N 1566 7.00 C 5547 6.00 H 9189 1.00 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: 1.82 Conformation dependent library (CDL) restraints added in 868.9 milliseconds Enol-peptide restraints added in 1.4 microseconds 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2178 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 21 sheets defined 23.3% alpha, 41.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 15 through 20 Processing helix chain 'A' and resid 21 through 24 Proline residue: A 24 - end of helix No H-bonds generated for 'chain 'A' and resid 21 through 24' Processing helix chain 'A' and resid 104 through 108 Processing helix chain 'A' and resid 154 through 158 Processing helix chain 'A' and resid 169 through 173 Processing helix chain 'A' and resid 244 through 258 removed outlier: 3.610A pdb=" N GLN A 253 " --> pdb=" O ASN A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 280 Processing helix chain 'A' and resid 297 through 303 Processing helix chain 'A' and resid 320 through 329 Processing helix chain 'B' and resid 15 through 20 Processing helix chain 'B' and resid 21 through 24 Proline residue: B 24 - end of helix No H-bonds generated for 'chain 'B' and resid 21 through 24' Processing helix chain 'B' and resid 104 through 108 Processing helix chain 'B' and resid 154 through 158 Processing helix chain 'B' and resid 169 through 173 Processing helix chain 'B' and resid 244 through 258 removed outlier: 3.612A pdb=" N GLN B 253 " --> pdb=" O ASN B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 280 Processing helix chain 'B' and resid 297 through 303 Processing helix chain 'B' and resid 320 through 329 Processing helix chain 'C' and resid 15 through 20 Processing helix chain 'C' and resid 21 through 24 Proline residue: C 24 - end of helix No H-bonds generated for 'chain 'C' and resid 21 through 24' Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'C' and resid 154 through 158 Processing helix chain 'C' and resid 169 through 173 Processing helix chain 'C' and resid 244 through 258 removed outlier: 3.612A pdb=" N GLN C 253 " --> pdb=" O ASN C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 280 Processing helix chain 'C' and resid 297 through 303 Processing helix chain 'C' and resid 320 through 329 Processing helix chain 'D' and resid 394 through 399 Processing helix chain 'D' and resid 417 through 426 Processing helix chain 'E' and resid 394 through 399 Processing helix chain 'E' and resid 417 through 426 Processing helix chain 'F' and resid 394 through 399 Processing helix chain 'F' and resid 417 through 426 Processing helix chain 'a' and resid 37 through 49 Processing helix chain 'b' and resid 37 through 49 Processing helix chain 'c' and resid 37 through 49 Processing sheet with id=AA1, first strand: chain 'a' and resid 34 through 36 removed outlier: 4.250A pdb=" N MET A 85 " --> pdb=" O PHE a 36 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N SER A 89 " --> pdb=" O ASN A 103 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ASN A 103 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N TYR A 99 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ILE A 136 " --> pdb=" O LYS A 130 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LYS A 130 " --> pdb=" O ILE A 136 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU A 138 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ILE A 113 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N MET A 127 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 11.689A pdb=" N THR A 111 " --> pdb=" O MET A 127 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N GLU A 32 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ILE A 113 " --> pdb=" O ASN A 30 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASN A 30 " --> pdb=" O ILE A 113 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N VAL A 115 " --> pdb=" O SER A 28 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N SER A 28 " --> pdb=" O VAL A 115 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 29 through 31 removed outlier: 5.792A pdb=" N ASN A 225 " --> pdb=" O ILE A 242 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ILE A 242 " --> pdb=" O ASN A 225 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLN A 200 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N LEU A 185 " --> pdb=" O GLN A 200 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU A 214 " --> pdb=" O ILE A 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 263 through 264 Processing sheet with id=AA4, first strand: chain 'A' and resid 316 through 317 removed outlier: 6.565A pdb=" N GLY A 340 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU A 313 " --> pdb=" O THR A 338 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N THR A 338 " --> pdb=" O LEU A 313 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 316 through 317 removed outlier: 6.661A pdb=" N MET A 268 " --> pdb=" O SER A 291 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'b' and resid 34 through 36 removed outlier: 4.253A pdb=" N MET B 85 " --> pdb=" O PHE b 36 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N SER B 89 " --> pdb=" O ASN B 103 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ASN B 103 " --> pdb=" O SER B 89 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N TYR B 99 " --> pdb=" O ILE B 93 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ILE B 136 " --> pdb=" O LYS B 130 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LYS B 130 " --> pdb=" O ILE B 136 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU B 138 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ILE B 113 " --> pdb=" O ALA B 125 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N MET B 127 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 11.688A pdb=" N THR B 111 " --> pdb=" O MET B 127 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLU B 32 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ILE B 113 " --> pdb=" O ASN B 30 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ASN B 30 " --> pdb=" O ILE B 113 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N VAL B 115 " --> pdb=" O SER B 28 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N SER B 28 " --> pdb=" O VAL B 115 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'b' and resid 29 through 31 removed outlier: 5.793A pdb=" N ASN B 225 " --> pdb=" O ILE B 242 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ILE B 242 " --> pdb=" O ASN B 225 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLN B 200 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N LEU B 185 " --> pdb=" O GLN B 200 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU B 214 " --> pdb=" O ILE B 222 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 263 through 264 Processing sheet with id=AA9, first strand: chain 'B' and resid 316 through 317 removed outlier: 6.565A pdb=" N GLY B 340 " --> pdb=" O THR B 311 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LEU B 313 " --> pdb=" O THR B 338 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N THR B 338 " --> pdb=" O LEU B 313 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 316 through 317 removed outlier: 6.662A pdb=" N MET B 268 " --> pdb=" O SER B 291 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'c' and resid 34 through 36 removed outlier: 4.251A pdb=" N MET C 85 " --> pdb=" O PHE c 36 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N SER C 89 " --> pdb=" O ASN C 103 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ASN C 103 " --> pdb=" O SER C 89 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N TYR C 99 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ILE C 136 " --> pdb=" O LYS C 130 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LYS C 130 " --> pdb=" O ILE C 136 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU C 138 " --> pdb=" O VAL C 128 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE C 113 " --> pdb=" O ALA C 125 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N MET C 127 " --> pdb=" O THR C 111 " (cutoff:3.500A) removed outlier: 11.688A pdb=" N THR C 111 " --> pdb=" O MET C 127 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLU C 32 " --> pdb=" O THR C 111 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ILE C 113 " --> pdb=" O ASN C 30 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASN C 30 " --> pdb=" O ILE C 113 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N VAL C 115 " --> pdb=" O SER C 28 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N SER C 28 " --> pdb=" O VAL C 115 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'c' and resid 29 through 31 removed outlier: 5.792A pdb=" N ASN C 225 " --> pdb=" O ILE C 242 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ILE C 242 " --> pdb=" O ASN C 225 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLN C 200 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N LEU C 185 " --> pdb=" O GLN C 200 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU C 214 " --> pdb=" O ILE C 222 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 263 through 264 Processing sheet with id=AB5, first strand: chain 'C' and resid 316 through 317 removed outlier: 6.566A pdb=" N GLY C 340 " --> pdb=" O THR C 311 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LEU C 313 " --> pdb=" O THR C 338 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N THR C 338 " --> pdb=" O LEU C 313 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 316 through 317 removed outlier: 6.663A pdb=" N MET C 268 " --> pdb=" O SER C 291 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 375 through 378 removed outlier: 6.507A pdb=" N GLU D 375 " --> pdb=" O ASN D 388 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 375 through 378 removed outlier: 6.507A pdb=" N GLU D 375 " --> pdb=" O ASN D 388 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASN D 435 " --> pdb=" O ILE D 408 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ALA D 410 " --> pdb=" O ALA D 433 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ALA D 433 " --> pdb=" O ALA D 410 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 375 through 378 removed outlier: 6.506A pdb=" N GLU E 375 " --> pdb=" O ASN E 388 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 375 through 378 removed outlier: 6.506A pdb=" N GLU E 375 " --> pdb=" O ASN E 388 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ASN E 435 " --> pdb=" O ILE E 408 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ALA E 410 " --> pdb=" O ALA E 433 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ALA E 433 " --> pdb=" O ALA E 410 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 375 through 378 removed outlier: 6.505A pdb=" N GLU F 375 " --> pdb=" O ASN F 388 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 375 through 378 removed outlier: 6.505A pdb=" N GLU F 375 " --> pdb=" O ASN F 388 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASN F 435 " --> pdb=" O ILE F 408 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ALA F 410 " --> pdb=" O ALA F 433 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ALA F 433 " --> pdb=" O ALA F 410 " (cutoff:3.500A) 426 hydrogen bonds defined for protein. 1062 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: 4.92 Time building geometry restraints manager: 2.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.13: 9189 1.13 - 1.30: 1766 1.30 - 1.48: 3762 1.48 - 1.65: 3340 1.65 - 1.83: 84 Bond restraints: 18141 Sorted by residual: bond pdb=" CB HIS a 33 " pdb=" CG HIS a 33 " ideal model delta sigma weight residual 1.497 1.340 0.157 1.40e-02 5.10e+03 1.26e+02 bond pdb=" CB HIS b 33 " pdb=" CG HIS b 33 " ideal model delta sigma weight residual 1.497 1.340 0.157 1.40e-02 5.10e+03 1.25e+02 bond pdb=" CB HIS c 33 " pdb=" CG HIS c 33 " ideal model delta sigma weight residual 1.497 1.340 0.157 1.40e-02 5.10e+03 1.25e+02 bond pdb=" CB LEU b 32 " pdb=" CG LEU b 32 " ideal model delta sigma weight residual 1.530 1.327 0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" CB LEU c 32 " pdb=" CG LEU c 32 " ideal model delta sigma weight residual 1.530 1.328 0.202 2.00e-02 2.50e+03 1.02e+02 ... (remaining 18136 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 27507 2.41 - 4.83: 3614 4.83 - 7.24: 1568 7.24 - 9.66: 266 9.66 - 12.07: 9 Bond angle restraints: 32964 Sorted by residual: angle pdb=" C ASP A 131 " pdb=" N PRO A 132 " pdb=" CA PRO A 132 " ideal model delta sigma weight residual 119.56 127.70 -8.14 1.02e+00 9.61e-01 6.37e+01 angle pdb=" C ASP B 131 " pdb=" N PRO B 132 " pdb=" CA PRO B 132 " ideal model delta sigma weight residual 119.56 127.65 -8.09 1.02e+00 9.61e-01 6.29e+01 angle pdb=" N LEU b 32 " pdb=" CA LEU b 32 " pdb=" C LEU b 32 " ideal model delta sigma weight residual 110.68 121.67 -10.99 1.39e+00 5.18e-01 6.25e+01 angle pdb=" N LEU a 32 " pdb=" CA LEU a 32 " pdb=" C LEU a 32 " ideal model delta sigma weight residual 110.68 121.66 -10.98 1.39e+00 5.18e-01 6.24e+01 angle pdb=" C ASP C 131 " pdb=" N PRO C 132 " pdb=" CA PRO C 132 " ideal model delta sigma weight residual 119.56 127.61 -8.05 1.02e+00 9.61e-01 6.22e+01 ... (remaining 32959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.51: 7933 16.51 - 33.03: 273 33.03 - 49.54: 116 49.54 - 66.05: 42 66.05 - 82.57: 9 Dihedral angle restraints: 8373 sinusoidal: 4749 harmonic: 3624 Sorted by residual: dihedral pdb=" CD2 HIS B 105 " pdb=" CG HIS B 105 " pdb=" ND1 HIS B 105 " pdb=" HD1 HIS B 105 " ideal model delta harmonic sigma weight residual 180.00 159.08 20.92 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CD2 HIS C 105 " pdb=" CG HIS C 105 " pdb=" ND1 HIS C 105 " pdb=" HD1 HIS C 105 " ideal model delta harmonic sigma weight residual 180.00 159.10 20.90 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CD2 HIS A 105 " pdb=" CG HIS A 105 " pdb=" ND1 HIS A 105 " pdb=" HD1 HIS A 105 " ideal model delta harmonic sigma weight residual 180.00 159.19 20.81 0 5.00e+00 4.00e-02 1.73e+01 ... (remaining 8370 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 858 0.110 - 0.219: 457 0.219 - 0.328: 111 0.328 - 0.438: 14 0.438 - 0.547: 9 Chirality restraints: 1449 Sorted by residual: chirality pdb=" CG LEU C 87 " pdb=" CB LEU C 87 " pdb=" CD1 LEU C 87 " pdb=" CD2 LEU C 87 " both_signs ideal model delta sigma weight residual False -2.59 -2.04 -0.55 2.00e-01 2.50e+01 7.49e+00 chirality pdb=" CG LEU A 87 " pdb=" CB LEU A 87 " pdb=" CD1 LEU A 87 " pdb=" CD2 LEU A 87 " both_signs ideal model delta sigma weight residual False -2.59 -2.04 -0.55 2.00e-01 2.50e+01 7.48e+00 chirality pdb=" CG LEU B 87 " pdb=" CB LEU B 87 " pdb=" CD1 LEU B 87 " pdb=" CD2 LEU B 87 " both_signs ideal model delta sigma weight residual False -2.59 -2.05 -0.54 2.00e-01 2.50e+01 7.30e+00 ... (remaining 1446 not shown) Planarity restraints: 2739 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS B 105 " 0.076 2.00e-02 2.50e+03 7.53e-02 1.28e+02 pdb=" CG HIS B 105 " 0.031 2.00e-02 2.50e+03 pdb=" ND1 HIS B 105 " 0.072 2.00e-02 2.50e+03 pdb=" CD2 HIS B 105 " -0.026 2.00e-02 2.50e+03 pdb=" CE1 HIS B 105 " 0.036 2.00e-02 2.50e+03 pdb=" NE2 HIS B 105 " -0.010 2.00e-02 2.50e+03 pdb=" HD1 HIS B 105 " -0.173 2.00e-02 2.50e+03 pdb=" HD2 HIS B 105 " -0.063 2.00e-02 2.50e+03 pdb=" HE1 HIS B 105 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 105 " -0.076 2.00e-02 2.50e+03 7.52e-02 1.27e+02 pdb=" CG HIS C 105 " -0.029 2.00e-02 2.50e+03 pdb=" ND1 HIS C 105 " -0.073 2.00e-02 2.50e+03 pdb=" CD2 HIS C 105 " 0.026 2.00e-02 2.50e+03 pdb=" CE1 HIS C 105 " -0.037 2.00e-02 2.50e+03 pdb=" NE2 HIS C 105 " 0.010 2.00e-02 2.50e+03 pdb=" HD1 HIS C 105 " 0.172 2.00e-02 2.50e+03 pdb=" HD2 HIS C 105 " 0.063 2.00e-02 2.50e+03 pdb=" HE1 HIS C 105 " -0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 105 " 0.076 2.00e-02 2.50e+03 7.50e-02 1.26e+02 pdb=" CG HIS A 105 " 0.029 2.00e-02 2.50e+03 pdb=" ND1 HIS A 105 " 0.072 2.00e-02 2.50e+03 pdb=" CD2 HIS A 105 " -0.025 2.00e-02 2.50e+03 pdb=" CE1 HIS A 105 " 0.036 2.00e-02 2.50e+03 pdb=" NE2 HIS A 105 " -0.010 2.00e-02 2.50e+03 pdb=" HD1 HIS A 105 " -0.172 2.00e-02 2.50e+03 pdb=" HD2 HIS A 105 " -0.063 2.00e-02 2.50e+03 pdb=" HE1 HIS A 105 " 0.057 2.00e-02 2.50e+03 ... (remaining 2736 not shown) Histogram of nonbonded interaction distances: 1.35 - 2.00: 418 2.00 - 2.65: 24724 2.65 - 3.30: 52799 3.30 - 3.95: 71192 3.95 - 4.60: 110521 Nonbonded interactions: 259654 Sorted by model distance: nonbonded pdb=" H SER B 134 " pdb=" H ASP B 135 " model vdw 1.353 2.100 nonbonded pdb=" H SER A 134 " pdb=" H ASP A 135 " model vdw 1.355 2.100 nonbonded pdb=" H SER C 134 " pdb=" H ASP C 135 " model vdw 1.355 2.100 nonbonded pdb=" HZ3 LYS B 114 " pdb=" OD1 ASP B 124 " model vdw 1.618 2.450 nonbonded pdb=" HZ3 LYS A 114 " pdb=" OD1 ASP A 124 " model vdw 1.618 2.450 ... (remaining 259649 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.390 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: 0.070 Extract box with map and model: 0.180 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 21.370 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6760 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 : 0.031 0.203 8952 Z= 1.557 Angle : 1.768 10.986 12084 Z= 1.183 Chirality : 0.132 0.547 1449 Planarity : 0.010 0.075 1578 Dihedral : 9.862 82.565 3327 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 0.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.24), residues: 1188 helix: -0.93 (0.30), residues: 231 sheet: 1.04 (0.28), residues: 366 loop : 0.92 (0.24), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG A 187 TYR 0.058 0.009 TYR B 257 PHE 0.018 0.007 PHE B 198 TRP 0.020 0.006 TRP a 48 HIS 0.005 0.002 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.03129 ( 8952) covalent geometry : angle 1.76788 (12084) hydrogen bonds : bond 0.17567 ( 405) hydrogen bonds : angle 7.22748 ( 1062) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Evaluate side-chains 255 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 ASN cc_start: 0.7805 (t0) cc_final: 0.7267 (t0) REVERT: A 193 GLU cc_start: 0.9343 (mm-30) cc_final: 0.8713 (tp30) REVERT: B 191 ASN cc_start: 0.7695 (t0) cc_final: 0.7102 (t0) REVERT: B 193 GLU cc_start: 0.9306 (mm-30) cc_final: 0.8711 (tp30) REVERT: C 191 ASN cc_start: 0.7626 (t0) cc_final: 0.6961 (t0) REVERT: C 193 GLU cc_start: 0.9342 (mm-30) cc_final: 0.8728 (tp30) REVERT: D 378 ASN cc_start: 0.8296 (m-40) cc_final: 0.8072 (t0) REVERT: D 389 ASN cc_start: 0.9496 (t0) cc_final: 0.8521 (t0) REVERT: D 437 GLN cc_start: 0.7803 (mt0) cc_final: 0.7367 (tp-100) REVERT: E 378 ASN cc_start: 0.8307 (m-40) cc_final: 0.7973 (t0) REVERT: E 389 ASN cc_start: 0.9507 (t0) cc_final: 0.8702 (t0) REVERT: E 415 VAL cc_start: 0.8418 (t) cc_final: 0.8075 (p) REVERT: F 378 ASN cc_start: 0.8161 (m-40) cc_final: 0.7924 (t0) REVERT: F 389 ASN cc_start: 0.9440 (t0) cc_final: 0.8742 (t0) REVERT: F 415 VAL cc_start: 0.8678 (t) cc_final: 0.8345 (p) REVERT: F 424 VAL cc_start: 0.9198 (t) cc_final: 0.8961 (m) REVERT: F 437 GLN cc_start: 0.8004 (mt0) cc_final: 0.7599 (tp-100) outliers start: 0 outliers final: 2 residues processed: 255 average time/residue: 1.3734 time to fit residues: 370.3124 Evaluate side-chains 213 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 211 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 407 ILE Chi-restraints excluded: chain F residue 440 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 5.9990 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.081404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.051977 restraints weight = 56042.825| |-----------------------------------------------------------------------------| r_work (start): 0.2605 rms_B_bonded: 3.23 r_work: 0.2452 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8952 Z= 0.157 Angle : 0.697 6.327 12084 Z= 0.383 Chirality : 0.049 0.188 1449 Planarity : 0.004 0.043 1578 Dihedral : 7.397 86.294 1264 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 1.59 % Allowed : 11.68 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.24), residues: 1188 helix: 1.09 (0.37), residues: 228 sheet: 0.59 (0.26), residues: 384 loop : 0.72 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 286 TYR 0.010 0.001 TYR b 34 PHE 0.012 0.002 PHE B 198 TRP 0.002 0.001 TRP a 48 HIS 0.006 0.003 HIS c 33 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 8952) covalent geometry : angle 0.69730 (12084) hydrogen bonds : bond 0.05782 ( 405) hydrogen bonds : angle 6.09539 ( 1062) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Evaluate side-chains 253 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 238 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLU cc_start: 0.8914 (mt-10) cc_final: 0.8702 (tt0) REVERT: A 191 ASN cc_start: 0.8311 (t0) cc_final: 0.7791 (t0) REVERT: A 193 GLU cc_start: 0.9167 (mm-30) cc_final: 0.8881 (mp0) REVERT: A 207 ARG cc_start: 0.8252 (mmm-85) cc_final: 0.7947 (mtm-85) REVERT: A 275 GLU cc_start: 0.9399 (mp0) cc_final: 0.9186 (mp0) REVERT: B 191 ASN cc_start: 0.8117 (t0) cc_final: 0.7796 (t0) REVERT: B 193 GLU cc_start: 0.9226 (mm-30) cc_final: 0.8798 (tp30) REVERT: B 268 MET cc_start: 0.8665 (mmm) cc_final: 0.8158 (mmm) REVERT: C 12 MET cc_start: 0.6386 (mtp) cc_final: 0.6147 (mtp) REVERT: C 191 ASN cc_start: 0.8139 (t0) cc_final: 0.7790 (t0) REVERT: C 193 GLU cc_start: 0.9266 (mm-30) cc_final: 0.8768 (tp30) REVERT: D 375 GLU cc_start: 0.8824 (mp0) cc_final: 0.8597 (mp0) REVERT: D 389 ASN cc_start: 0.8481 (t0) cc_final: 0.8039 (t0) REVERT: D 415 VAL cc_start: 0.8957 (t) cc_final: 0.8393 (p) REVERT: D 437 GLN cc_start: 0.8258 (mt0) cc_final: 0.7561 (tm130) REVERT: E 375 GLU cc_start: 0.8872 (mp0) cc_final: 0.8576 (mp0) REVERT: E 378 ASN cc_start: 0.8492 (m-40) cc_final: 0.8181 (t0) REVERT: E 389 ASN cc_start: 0.9003 (t0) cc_final: 0.8444 (t0) REVERT: E 405 ASP cc_start: 0.8051 (m-30) cc_final: 0.7279 (m-30) REVERT: E 415 VAL cc_start: 0.8776 (t) cc_final: 0.8350 (p) REVERT: E 437 GLN cc_start: 0.8458 (mt0) cc_final: 0.8130 (tp-100) REVERT: E 438 ARG cc_start: 0.7977 (mtm-85) cc_final: 0.7278 (mtt90) REVERT: F 375 GLU cc_start: 0.8847 (mp0) cc_final: 0.8511 (mp0) REVERT: F 378 ASN cc_start: 0.8386 (m-40) cc_final: 0.8117 (t0) REVERT: F 389 ASN cc_start: 0.8928 (t0) cc_final: 0.8438 (t0) REVERT: F 415 VAL cc_start: 0.8729 (t) cc_final: 0.8284 (p) REVERT: F 426 ASP cc_start: 0.9588 (m-30) cc_final: 0.9355 (p0) REVERT: F 437 GLN cc_start: 0.8311 (mt0) cc_final: 0.7995 (tm130) REVERT: b 31 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8719 (mt) REVERT: b 51 MET cc_start: 0.8762 (mmm) cc_final: 0.7965 (mmm) REVERT: b 52 LYS cc_start: 0.7942 (mppt) cc_final: 0.7700 (mppt) REVERT: c 50 THR cc_start: 0.7283 (p) cc_final: 0.6883 (p) REVERT: c 51 MET cc_start: 0.8627 (mmp) cc_final: 0.8370 (mmm) REVERT: c 52 LYS cc_start: 0.7802 (mtmm) cc_final: 0.7348 (mppt) outliers start: 15 outliers final: 9 residues processed: 240 average time/residue: 1.3170 time to fit residues: 335.3308 Evaluate side-chains 229 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 219 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain D residue 382 ASP Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain E residue 382 ASP Chi-restraints excluded: chain E residue 436 ILE Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain F residue 446 LEU Chi-restraints excluded: chain b residue 31 LEU Chi-restraints excluded: chain c residue 38 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 72 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 58 optimal weight: 0.4980 chunk 46 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 67 optimal weight: 0.0970 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 412 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.081319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2606 r_free = 0.2606 target = 0.050838 restraints weight = 56549.151| |-----------------------------------------------------------------------------| r_work (start): 0.2593 rms_B_bonded: 3.33 r_work: 0.2442 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8952 Z= 0.133 Angle : 0.596 6.532 12084 Z= 0.323 Chirality : 0.047 0.162 1449 Planarity : 0.004 0.060 1578 Dihedral : 7.142 85.148 1260 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 1.70 % Allowed : 13.27 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.24), residues: 1188 helix: 1.59 (0.38), residues: 228 sheet: 0.56 (0.27), residues: 339 loop : 0.51 (0.23), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 286 TYR 0.005 0.001 TYR b 34 PHE 0.009 0.001 PHE B 123 TRP 0.004 0.001 TRP a 48 HIS 0.005 0.002 HIS c 33 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 8952) covalent geometry : angle 0.59643 (12084) hydrogen bonds : bond 0.04443 ( 405) hydrogen bonds : angle 5.58561 ( 1062) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Evaluate side-chains 246 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 230 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 MET cc_start: 0.9210 (mtm) cc_final: 0.8904 (mtm) REVERT: A 133 ARG cc_start: 0.8668 (mmm-85) cc_final: 0.7677 (mmm-85) REVERT: A 191 ASN cc_start: 0.8263 (t0) cc_final: 0.7962 (t0) REVERT: A 193 GLU cc_start: 0.9165 (mm-30) cc_final: 0.8582 (tm-30) REVERT: A 207 ARG cc_start: 0.8315 (mmm-85) cc_final: 0.8056 (mtm-85) REVERT: A 271 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8242 (mt-10) REVERT: B 191 ASN cc_start: 0.8144 (t0) cc_final: 0.7839 (t0) REVERT: B 193 GLU cc_start: 0.9209 (mm-30) cc_final: 0.8798 (tp30) REVERT: B 268 MET cc_start: 0.8699 (mmm) cc_final: 0.8181 (mmm) REVERT: B 286 ARG cc_start: 0.8291 (mtt-85) cc_final: 0.7829 (mtt-85) REVERT: C 85 MET cc_start: 0.8698 (mtp) cc_final: 0.8446 (mtm) REVERT: C 193 GLU cc_start: 0.9275 (mm-30) cc_final: 0.8812 (tp30) REVERT: C 268 MET cc_start: 0.8702 (mmm) cc_final: 0.8314 (mmm) REVERT: C 331 MET cc_start: 0.9510 (mtm) cc_final: 0.9304 (mtp) REVERT: D 387 VAL cc_start: 0.9215 (t) cc_final: 0.8982 (p) REVERT: D 389 ASN cc_start: 0.8534 (t0) cc_final: 0.8136 (t0) REVERT: D 437 GLN cc_start: 0.8426 (mt0) cc_final: 0.8077 (tm130) REVERT: E 378 ASN cc_start: 0.8453 (m-40) cc_final: 0.8132 (t0) REVERT: E 387 VAL cc_start: 0.9242 (OUTLIER) cc_final: 0.8989 (p) REVERT: E 389 ASN cc_start: 0.9020 (t0) cc_final: 0.8568 (t0) REVERT: E 401 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8912 (tt) REVERT: E 415 VAL cc_start: 0.8713 (t) cc_final: 0.8331 (p) REVERT: E 436 ILE cc_start: 0.8051 (OUTLIER) cc_final: 0.7808 (pp) REVERT: E 437 GLN cc_start: 0.8423 (mt0) cc_final: 0.7903 (tm130) REVERT: E 438 ARG cc_start: 0.7969 (mtm-85) cc_final: 0.7639 (mtt180) REVERT: F 378 ASN cc_start: 0.8433 (m-40) cc_final: 0.8147 (t0) REVERT: F 389 ASN cc_start: 0.8943 (t0) cc_final: 0.8589 (t0) REVERT: F 405 ASP cc_start: 0.8195 (m-30) cc_final: 0.7177 (m-30) REVERT: F 415 VAL cc_start: 0.8832 (t) cc_final: 0.8335 (p) REVERT: F 437 GLN cc_start: 0.8351 (mt0) cc_final: 0.8044 (tm130) REVERT: b 51 MET cc_start: 0.8742 (mmm) cc_final: 0.7924 (mmm) REVERT: c 51 MET cc_start: 0.8703 (mmp) cc_final: 0.8423 (mmm) outliers start: 16 outliers final: 7 residues processed: 231 average time/residue: 1.3213 time to fit residues: 323.2695 Evaluate side-chains 227 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 217 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain D residue 382 ASP Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain E residue 382 ASP Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain E residue 391 LYS Chi-restraints excluded: chain E residue 401 LEU Chi-restraints excluded: chain E residue 436 ILE Chi-restraints excluded: chain F residue 391 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 96 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 99 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.080232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2591 r_free = 0.2591 target = 0.050134 restraints weight = 56937.519| |-----------------------------------------------------------------------------| r_work (start): 0.2579 rms_B_bonded: 3.29 r_work: 0.2429 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8952 Z= 0.188 Angle : 0.583 7.020 12084 Z= 0.314 Chirality : 0.046 0.153 1449 Planarity : 0.004 0.074 1578 Dihedral : 7.065 84.462 1260 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 1.59 % Allowed : 15.07 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.24), residues: 1188 helix: 1.81 (0.38), residues: 228 sheet: 0.25 (0.27), residues: 354 loop : 0.53 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 286 TYR 0.006 0.001 TYR b 34 PHE 0.009 0.001 PHE C 123 TRP 0.003 0.001 TRP c 48 HIS 0.005 0.002 HIS c 33 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 8952) covalent geometry : angle 0.58325 (12084) hydrogen bonds : bond 0.04010 ( 405) hydrogen bonds : angle 5.33895 ( 1062) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Evaluate side-chains 231 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 216 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 MET cc_start: 0.9273 (mtm) cc_final: 0.8983 (mtm) REVERT: A 133 ARG cc_start: 0.8768 (mmm-85) cc_final: 0.7689 (mmm-85) REVERT: A 191 ASN cc_start: 0.8313 (t0) cc_final: 0.7965 (t0) REVERT: A 193 GLU cc_start: 0.9179 (mm-30) cc_final: 0.8564 (tm-30) REVERT: A 207 ARG cc_start: 0.8393 (mmm-85) cc_final: 0.8106 (mtm-85) REVERT: A 254 MET cc_start: 0.8902 (mtt) cc_final: 0.8691 (mtt) REVERT: A 271 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8227 (mt-10) REVERT: B 133 ARG cc_start: 0.8728 (mmm-85) cc_final: 0.8182 (mmm-85) REVERT: B 191 ASN cc_start: 0.8194 (t0) cc_final: 0.7856 (t0) REVERT: B 193 GLU cc_start: 0.9208 (mm-30) cc_final: 0.8720 (tp30) REVERT: B 268 MET cc_start: 0.8697 (mmm) cc_final: 0.8183 (mmm) REVERT: B 271 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8105 (mm-30) REVERT: C 12 MET cc_start: 0.6536 (mtp) cc_final: 0.6326 (mtt) REVERT: C 85 MET cc_start: 0.8772 (mtp) cc_final: 0.8519 (mtm) REVERT: C 193 GLU cc_start: 0.9280 (mm-30) cc_final: 0.8789 (tp30) REVERT: C 268 MET cc_start: 0.8739 (mmm) cc_final: 0.8030 (mmm) REVERT: D 389 ASN cc_start: 0.8477 (t0) cc_final: 0.8004 (t0) REVERT: D 415 VAL cc_start: 0.8985 (t) cc_final: 0.8523 (p) REVERT: D 426 ASP cc_start: 0.9589 (m-30) cc_final: 0.9330 (p0) REVERT: D 437 GLN cc_start: 0.8442 (mt0) cc_final: 0.8064 (tm130) REVERT: E 378 ASN cc_start: 0.8461 (m-40) cc_final: 0.8148 (t0) REVERT: E 389 ASN cc_start: 0.9105 (t0) cc_final: 0.8720 (t0) REVERT: E 413 GLN cc_start: 0.8917 (mm-40) cc_final: 0.8478 (mm-40) REVERT: E 436 ILE cc_start: 0.8045 (OUTLIER) cc_final: 0.7763 (pp) REVERT: E 437 GLN cc_start: 0.8354 (mt0) cc_final: 0.7820 (tm130) REVERT: E 438 ARG cc_start: 0.8104 (mtm-85) cc_final: 0.7634 (mtt180) REVERT: F 378 ASN cc_start: 0.8466 (m-40) cc_final: 0.8205 (t0) REVERT: F 389 ASN cc_start: 0.8898 (t0) cc_final: 0.8478 (t0) REVERT: F 415 VAL cc_start: 0.8925 (t) cc_final: 0.8583 (p) REVERT: F 437 GLN cc_start: 0.8415 (mt0) cc_final: 0.8024 (tm130) REVERT: a 52 LYS cc_start: 0.8645 (mtpt) cc_final: 0.8364 (mppt) REVERT: b 51 MET cc_start: 0.8774 (mmm) cc_final: 0.8029 (mmm) REVERT: c 51 MET cc_start: 0.8737 (mmp) cc_final: 0.8466 (mmm) outliers start: 15 outliers final: 9 residues processed: 217 average time/residue: 1.3287 time to fit residues: 305.4556 Evaluate side-chains 221 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 211 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain D residue 382 ASP Chi-restraints excluded: chain D residue 430 SER Chi-restraints excluded: chain E residue 382 ASP Chi-restraints excluded: chain E residue 391 LYS Chi-restraints excluded: chain E residue 401 LEU Chi-restraints excluded: chain E residue 436 ILE Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain F residue 391 LYS Chi-restraints excluded: chain F residue 430 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 80 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.079516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2583 r_free = 0.2583 target = 0.049565 restraints weight = 57094.231| |-----------------------------------------------------------------------------| r_work (start): 0.2569 rms_B_bonded: 3.26 r_work: 0.2419 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8952 Z= 0.235 Angle : 0.590 6.780 12084 Z= 0.317 Chirality : 0.046 0.150 1449 Planarity : 0.004 0.057 1578 Dihedral : 6.979 84.208 1260 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 1.91 % Allowed : 14.76 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.24), residues: 1188 helix: 1.86 (0.37), residues: 228 sheet: 0.14 (0.26), residues: 354 loop : 0.48 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 422 TYR 0.007 0.001 TYR b 34 PHE 0.010 0.001 PHE C 123 TRP 0.002 0.001 TRP c 48 HIS 0.004 0.002 HIS a 33 Details of bonding type rmsd covalent geometry : bond 0.00523 ( 8952) covalent geometry : angle 0.59009 (12084) hydrogen bonds : bond 0.03902 ( 405) hydrogen bonds : angle 5.29410 ( 1062) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Evaluate side-chains 233 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 215 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 MET cc_start: 0.9273 (mtm) cc_final: 0.8986 (mtm) REVERT: A 133 ARG cc_start: 0.8802 (mmm-85) cc_final: 0.8241 (mmm-85) REVERT: A 191 ASN cc_start: 0.8378 (t0) cc_final: 0.8030 (t0) REVERT: A 193 GLU cc_start: 0.9188 (mm-30) cc_final: 0.8815 (tp30) REVERT: A 207 ARG cc_start: 0.8411 (mmm-85) cc_final: 0.8174 (mtm-85) REVERT: A 254 MET cc_start: 0.8949 (mtt) cc_final: 0.8720 (mtt) REVERT: A 271 GLU cc_start: 0.8786 (mt-10) cc_final: 0.8145 (mm-30) REVERT: B 32 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8554 (mt-10) REVERT: B 133 ARG cc_start: 0.8761 (mmm-85) cc_final: 0.8108 (mmm-85) REVERT: B 191 ASN cc_start: 0.8224 (t0) cc_final: 0.7938 (t0) REVERT: B 193 GLU cc_start: 0.9221 (mm-30) cc_final: 0.8608 (tp30) REVERT: B 271 GLU cc_start: 0.8889 (OUTLIER) cc_final: 0.8173 (mm-30) REVERT: C 12 MET cc_start: 0.6443 (mtp) cc_final: 0.6241 (mtt) REVERT: C 85 MET cc_start: 0.8800 (mtp) cc_final: 0.8559 (mtm) REVERT: C 193 GLU cc_start: 0.9285 (mm-30) cc_final: 0.8779 (tp30) REVERT: C 268 MET cc_start: 0.8740 (mmm) cc_final: 0.7961 (mmm) REVERT: D 387 VAL cc_start: 0.9161 (t) cc_final: 0.8885 (p) REVERT: D 415 VAL cc_start: 0.8916 (t) cc_final: 0.8515 (p) REVERT: D 426 ASP cc_start: 0.9601 (m-30) cc_final: 0.9333 (p0) REVERT: D 437 GLN cc_start: 0.8408 (mt0) cc_final: 0.7963 (tm130) REVERT: E 378 ASN cc_start: 0.8480 (m-40) cc_final: 0.8179 (t0) REVERT: E 389 ASN cc_start: 0.9033 (t0) cc_final: 0.8707 (t0) REVERT: E 413 GLN cc_start: 0.8924 (mm-40) cc_final: 0.8474 (mm-40) REVERT: E 436 ILE cc_start: 0.8084 (OUTLIER) cc_final: 0.7796 (pp) REVERT: E 437 GLN cc_start: 0.8409 (mt0) cc_final: 0.7832 (tm130) REVERT: E 438 ARG cc_start: 0.8154 (mtm-85) cc_final: 0.7731 (mtt180) REVERT: F 375 GLU cc_start: 0.8836 (mp0) cc_final: 0.8621 (mp0) REVERT: F 376 MET cc_start: 0.6030 (pmt) cc_final: 0.5798 (pmt) REVERT: F 378 ASN cc_start: 0.8522 (m-40) cc_final: 0.8235 (t0) REVERT: F 389 ASN cc_start: 0.8846 (t0) cc_final: 0.8514 (t0) REVERT: F 415 VAL cc_start: 0.8931 (t) cc_final: 0.8597 (p) REVERT: F 437 GLN cc_start: 0.8423 (mt0) cc_final: 0.8018 (tm130) REVERT: b 51 MET cc_start: 0.8980 (mmm) cc_final: 0.8106 (mmm) REVERT: c 51 MET cc_start: 0.8785 (mmp) cc_final: 0.8529 (mmm) outliers start: 18 outliers final: 11 residues processed: 215 average time/residue: 1.3172 time to fit residues: 300.7036 Evaluate side-chains 221 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 208 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain D residue 382 ASP Chi-restraints excluded: chain D residue 430 SER Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain E residue 401 LEU Chi-restraints excluded: chain E residue 430 SER Chi-restraints excluded: chain E residue 436 ILE Chi-restraints excluded: chain F residue 391 LYS Chi-restraints excluded: chain F residue 430 SER Chi-restraints excluded: chain F residue 446 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 44 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 116 optimal weight: 9.9990 chunk 91 optimal weight: 0.3980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.080235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.051092 restraints weight = 56272.827| |-----------------------------------------------------------------------------| r_work (start): 0.2607 rms_B_bonded: 3.18 r_work: 0.2450 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.4259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8952 Z= 0.128 Angle : 0.559 7.733 12084 Z= 0.296 Chirality : 0.046 0.151 1449 Planarity : 0.004 0.055 1578 Dihedral : 6.925 83.456 1260 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 1.27 % Allowed : 16.24 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.24), residues: 1188 helix: 1.84 (0.37), residues: 231 sheet: 0.15 (0.25), residues: 384 loop : 0.54 (0.25), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 286 TYR 0.004 0.001 TYR b 34 PHE 0.007 0.001 PHE c 36 TRP 0.002 0.000 TRP b 48 HIS 0.004 0.002 HIS b 33 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 8952) covalent geometry : angle 0.55917 (12084) hydrogen bonds : bond 0.03482 ( 405) hydrogen bonds : angle 5.13970 ( 1062) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Evaluate side-chains 226 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 214 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 MET cc_start: 0.9260 (mtm) cc_final: 0.8994 (mtm) REVERT: A 133 ARG cc_start: 0.8776 (mmm-85) cc_final: 0.8183 (mmm-85) REVERT: A 191 ASN cc_start: 0.8290 (t0) cc_final: 0.8013 (t0) REVERT: A 193 GLU cc_start: 0.9178 (mm-30) cc_final: 0.8809 (tp30) REVERT: A 207 ARG cc_start: 0.8347 (mmm-85) cc_final: 0.8116 (mtm-85) REVERT: A 271 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8155 (mm-30) REVERT: B 85 MET cc_start: 0.8517 (mtp) cc_final: 0.8239 (mtm) REVERT: B 133 ARG cc_start: 0.8745 (mmm-85) cc_final: 0.8093 (mmm-85) REVERT: B 191 ASN cc_start: 0.8166 (t0) cc_final: 0.7888 (t0) REVERT: B 193 GLU cc_start: 0.9208 (mm-30) cc_final: 0.8613 (tp30) REVERT: B 271 GLU cc_start: 0.8890 (mt-10) cc_final: 0.8139 (mm-30) REVERT: C 85 MET cc_start: 0.8758 (mtp) cc_final: 0.8521 (mtm) REVERT: C 193 GLU cc_start: 0.9277 (mm-30) cc_final: 0.8774 (tp30) REVERT: C 268 MET cc_start: 0.8784 (mmm) cc_final: 0.8045 (mmm) REVERT: D 376 MET cc_start: 0.7057 (pmt) cc_final: 0.6521 (pmm) REVERT: D 387 VAL cc_start: 0.9120 (t) cc_final: 0.8785 (p) REVERT: D 389 ASN cc_start: 0.8769 (t0) cc_final: 0.8550 (t0) REVERT: D 426 ASP cc_start: 0.9592 (m-30) cc_final: 0.9317 (p0) REVERT: D 437 GLN cc_start: 0.8386 (mt0) cc_final: 0.7930 (tm130) REVERT: E 376 MET cc_start: 0.6517 (pmt) cc_final: 0.5767 (pmm) REVERT: E 378 ASN cc_start: 0.8441 (m-40) cc_final: 0.8174 (t0) REVERT: E 389 ASN cc_start: 0.8986 (t0) cc_final: 0.8662 (t0) REVERT: E 413 GLN cc_start: 0.8959 (mm-40) cc_final: 0.8482 (mm-40) REVERT: E 436 ILE cc_start: 0.7981 (OUTLIER) cc_final: 0.7678 (pp) REVERT: E 437 GLN cc_start: 0.8459 (mt0) cc_final: 0.7860 (tm130) REVERT: E 438 ARG cc_start: 0.8336 (mtm-85) cc_final: 0.7809 (mtt180) REVERT: F 378 ASN cc_start: 0.8541 (m-40) cc_final: 0.8256 (t0) REVERT: F 389 ASN cc_start: 0.8901 (t0) cc_final: 0.8654 (t0) REVERT: F 402 LYS cc_start: 0.9334 (mtpt) cc_final: 0.9130 (mtmt) REVERT: F 415 VAL cc_start: 0.8931 (t) cc_final: 0.8593 (p) REVERT: F 437 GLN cc_start: 0.8411 (mt0) cc_final: 0.7984 (tm130) REVERT: b 51 MET cc_start: 0.8954 (mmm) cc_final: 0.8128 (mmm) REVERT: b 53 LYS cc_start: 0.9282 (ttpp) cc_final: 0.8946 (tppp) REVERT: c 51 MET cc_start: 0.8914 (mmp) cc_final: 0.8610 (mmm) REVERT: c 52 LYS cc_start: 0.8178 (mppt) cc_final: 0.7669 (mptt) outliers start: 12 outliers final: 6 residues processed: 214 average time/residue: 1.3710 time to fit residues: 311.0027 Evaluate side-chains 218 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 210 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain D residue 382 ASP Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain E residue 401 LEU Chi-restraints excluded: chain E residue 430 SER Chi-restraints excluded: chain E residue 436 ILE Chi-restraints excluded: chain F residue 391 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 35 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 412 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.079991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.050888 restraints weight = 57033.597| |-----------------------------------------------------------------------------| r_work (start): 0.2601 rms_B_bonded: 3.23 r_work: 0.2443 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.4389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8952 Z= 0.170 Angle : 0.575 8.385 12084 Z= 0.302 Chirality : 0.045 0.147 1449 Planarity : 0.004 0.060 1578 Dihedral : 6.883 82.553 1260 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 1.70 % Allowed : 16.88 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.24), residues: 1188 helix: 1.84 (0.37), residues: 231 sheet: 0.16 (0.25), residues: 384 loop : 0.54 (0.25), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 286 TYR 0.005 0.001 TYR b 34 PHE 0.008 0.001 PHE C 123 TRP 0.003 0.001 TRP c 48 HIS 0.004 0.002 HIS b 33 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 8952) covalent geometry : angle 0.57461 (12084) hydrogen bonds : bond 0.03476 ( 405) hydrogen bonds : angle 5.08696 ( 1062) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Evaluate side-chains 226 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 210 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 MET cc_start: 0.9282 (mtm) cc_final: 0.9017 (mmm) REVERT: A 133 ARG cc_start: 0.8789 (mmm-85) cc_final: 0.8205 (mmm-85) REVERT: A 191 ASN cc_start: 0.8326 (t0) cc_final: 0.8043 (t0) REVERT: A 193 GLU cc_start: 0.9187 (mm-30) cc_final: 0.8812 (tp30) REVERT: A 207 ARG cc_start: 0.8416 (mmm-85) cc_final: 0.8206 (mtm-85) REVERT: A 271 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8220 (mm-30) REVERT: B 133 ARG cc_start: 0.8740 (mmm-85) cc_final: 0.8098 (mmm-85) REVERT: B 191 ASN cc_start: 0.8198 (t0) cc_final: 0.7915 (t0) REVERT: B 193 GLU cc_start: 0.9221 (mm-30) cc_final: 0.8630 (tp30) REVERT: B 271 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8204 (mm-30) REVERT: B 286 ARG cc_start: 0.8474 (mtt-85) cc_final: 0.8024 (mtt-85) REVERT: C 85 MET cc_start: 0.8756 (mtp) cc_final: 0.8523 (mtm) REVERT: C 193 GLU cc_start: 0.9295 (mm-30) cc_final: 0.8781 (tp30) REVERT: C 268 MET cc_start: 0.8777 (mmm) cc_final: 0.8245 (mmm) REVERT: D 376 MET cc_start: 0.7075 (pmt) cc_final: 0.6483 (pmm) REVERT: D 426 ASP cc_start: 0.9600 (m-30) cc_final: 0.9316 (p0) REVERT: D 437 GLN cc_start: 0.8357 (mt0) cc_final: 0.7885 (tm130) REVERT: E 376 MET cc_start: 0.6501 (pmt) cc_final: 0.5754 (pmm) REVERT: E 378 ASN cc_start: 0.8464 (m-40) cc_final: 0.8194 (t0) REVERT: E 389 ASN cc_start: 0.9010 (t0) cc_final: 0.8744 (t0) REVERT: E 413 GLN cc_start: 0.8963 (mm-40) cc_final: 0.8515 (mm110) REVERT: E 437 GLN cc_start: 0.8447 (mt0) cc_final: 0.7829 (tm130) REVERT: F 376 MET cc_start: 0.5991 (pmt) cc_final: 0.5377 (pmm) REVERT: F 378 ASN cc_start: 0.8548 (m-40) cc_final: 0.8283 (t0) REVERT: F 389 ASN cc_start: 0.8835 (t0) cc_final: 0.8494 (t0) REVERT: F 415 VAL cc_start: 0.8953 (t) cc_final: 0.8621 (p) REVERT: F 437 GLN cc_start: 0.8418 (mt0) cc_final: 0.8016 (tm130) REVERT: a 52 LYS cc_start: 0.8020 (mppt) cc_final: 0.7611 (mppt) REVERT: b 51 MET cc_start: 0.8972 (mmm) cc_final: 0.8127 (mmm) REVERT: b 53 LYS cc_start: 0.9305 (ttpp) cc_final: 0.8962 (tppp) REVERT: c 51 MET cc_start: 0.8872 (mmp) cc_final: 0.8554 (mmm) outliers start: 16 outliers final: 11 residues processed: 210 average time/residue: 1.5592 time to fit residues: 346.0711 Evaluate side-chains 221 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 208 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain D residue 382 ASP Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain E residue 401 LEU Chi-restraints excluded: chain E residue 430 SER Chi-restraints excluded: chain E residue 434 LEU Chi-restraints excluded: chain E residue 436 ILE Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain F residue 391 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 57 optimal weight: 0.6980 chunk 115 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 114 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.080873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.051835 restraints weight = 56561.648| |-----------------------------------------------------------------------------| r_work (start): 0.2627 rms_B_bonded: 3.23 r_work: 0.2470 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.4519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8952 Z= 0.114 Angle : 0.573 9.745 12084 Z= 0.298 Chirality : 0.046 0.147 1449 Planarity : 0.004 0.061 1578 Dihedral : 6.814 80.951 1260 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.06 % Allowed : 17.73 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.25), residues: 1188 helix: 2.01 (0.38), residues: 231 sheet: 0.37 (0.26), residues: 381 loop : 0.60 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 286 TYR 0.003 0.000 TYR F 444 PHE 0.026 0.001 PHE a 36 TRP 0.003 0.000 TRP c 48 HIS 0.004 0.002 HIS b 33 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 8952) covalent geometry : angle 0.57276 (12084) hydrogen bonds : bond 0.03194 ( 405) hydrogen bonds : angle 4.95113 ( 1062) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Evaluate side-chains 221 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 211 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 MET cc_start: 0.9257 (mtm) cc_final: 0.8925 (mmm) REVERT: A 133 ARG cc_start: 0.8787 (mmm-85) cc_final: 0.8265 (mmm-85) REVERT: A 191 ASN cc_start: 0.8259 (t0) cc_final: 0.7991 (t0) REVERT: A 193 GLU cc_start: 0.9193 (mm-30) cc_final: 0.8807 (tp30) REVERT: A 207 ARG cc_start: 0.8354 (mmm-85) cc_final: 0.8144 (mtm-85) REVERT: A 271 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8229 (mm-30) REVERT: B 133 ARG cc_start: 0.8746 (mmm-85) cc_final: 0.8102 (mmm-85) REVERT: B 191 ASN cc_start: 0.8100 (t0) cc_final: 0.7822 (t0) REVERT: B 193 GLU cc_start: 0.9212 (mm-30) cc_final: 0.8643 (tp30) REVERT: B 271 GLU cc_start: 0.8924 (mt-10) cc_final: 0.8204 (mm-30) REVERT: C 85 MET cc_start: 0.8632 (mtp) cc_final: 0.8407 (mtm) REVERT: C 193 GLU cc_start: 0.9280 (mm-30) cc_final: 0.8704 (tp30) REVERT: C 268 MET cc_start: 0.8768 (mmm) cc_final: 0.8243 (mmm) REVERT: D 376 MET cc_start: 0.7150 (pmt) cc_final: 0.6521 (pmm) REVERT: D 401 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.9008 (tp) REVERT: D 426 ASP cc_start: 0.9600 (m-30) cc_final: 0.9347 (p0) REVERT: D 437 GLN cc_start: 0.8350 (mt0) cc_final: 0.7884 (tm130) REVERT: E 376 MET cc_start: 0.6386 (pmt) cc_final: 0.5622 (pmm) REVERT: E 378 ASN cc_start: 0.8535 (m-40) cc_final: 0.8264 (t0) REVERT: E 389 ASN cc_start: 0.9027 (t0) cc_final: 0.8732 (t0) REVERT: E 402 LYS cc_start: 0.9324 (mtmm) cc_final: 0.9004 (ptpp) REVERT: E 413 GLN cc_start: 0.8947 (mm-40) cc_final: 0.8575 (mm-40) REVERT: E 437 GLN cc_start: 0.8455 (mt0) cc_final: 0.7915 (tm130) REVERT: F 378 ASN cc_start: 0.8648 (m-40) cc_final: 0.8393 (t0) REVERT: F 415 VAL cc_start: 0.8926 (t) cc_final: 0.8609 (p) REVERT: F 437 GLN cc_start: 0.8522 (mt0) cc_final: 0.8121 (tm130) REVERT: b 51 MET cc_start: 0.8976 (mmm) cc_final: 0.8199 (mmm) REVERT: b 53 LYS cc_start: 0.9258 (ttpp) cc_final: 0.8935 (tppp) REVERT: c 51 MET cc_start: 0.8854 (mmp) cc_final: 0.8546 (mmm) outliers start: 10 outliers final: 2 residues processed: 211 average time/residue: 1.4972 time to fit residues: 334.9087 Evaluate side-chains 210 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 206 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain D residue 382 ASP Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain F residue 391 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 100 optimal weight: 3.9990 chunk 102 optimal weight: 0.5980 chunk 75 optimal weight: 3.9990 chunk 43 optimal weight: 0.0980 chunk 72 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.081756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.053335 restraints weight = 58161.664| |-----------------------------------------------------------------------------| r_work (start): 0.2635 rms_B_bonded: 3.27 r_work: 0.2496 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.4625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8952 Z= 0.135 Angle : 0.581 10.833 12084 Z= 0.302 Chirality : 0.045 0.145 1449 Planarity : 0.004 0.063 1578 Dihedral : 6.738 79.240 1260 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.06 % Allowed : 18.37 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.24), residues: 1188 helix: 2.01 (0.37), residues: 231 sheet: 0.37 (0.26), residues: 381 loop : 0.63 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 286 TYR 0.003 0.001 TYR b 34 PHE 0.013 0.001 PHE a 36 TRP 0.003 0.001 TRP c 48 HIS 0.004 0.002 HIS b 33 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 8952) covalent geometry : angle 0.58068 (12084) hydrogen bonds : bond 0.03232 ( 405) hydrogen bonds : angle 4.88863 ( 1062) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Evaluate side-chains 217 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 207 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 MET cc_start: 0.9291 (mtm) cc_final: 0.8994 (mmm) REVERT: A 133 ARG cc_start: 0.8876 (mmm-85) cc_final: 0.8345 (mmm-85) REVERT: A 191 ASN cc_start: 0.8428 (t0) cc_final: 0.8174 (t0) REVERT: A 193 GLU cc_start: 0.9196 (mm-30) cc_final: 0.8851 (tp30) REVERT: A 207 ARG cc_start: 0.8528 (mmm-85) cc_final: 0.8307 (mtm-85) REVERT: B 133 ARG cc_start: 0.8837 (mmm-85) cc_final: 0.8175 (mmm-85) REVERT: B 191 ASN cc_start: 0.8248 (t0) cc_final: 0.7849 (t0) REVERT: B 193 GLU cc_start: 0.9200 (mm-30) cc_final: 0.8669 (tp30) REVERT: B 271 GLU cc_start: 0.8964 (OUTLIER) cc_final: 0.8334 (mm-30) REVERT: B 286 ARG cc_start: 0.8525 (mtt-85) cc_final: 0.8113 (mtt-85) REVERT: C 85 MET cc_start: 0.8772 (mtp) cc_final: 0.8561 (mtm) REVERT: C 193 GLU cc_start: 0.9267 (mm-30) cc_final: 0.8744 (tp30) REVERT: C 268 MET cc_start: 0.8903 (mmm) cc_final: 0.8390 (mmm) REVERT: D 376 MET cc_start: 0.7217 (pmt) cc_final: 0.6590 (pmm) REVERT: D 401 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.9051 (tp) REVERT: D 426 ASP cc_start: 0.9571 (m-30) cc_final: 0.9319 (p0) REVERT: D 437 GLN cc_start: 0.8408 (mt0) cc_final: 0.7940 (tm130) REVERT: E 376 MET cc_start: 0.6362 (pmt) cc_final: 0.5559 (pmm) REVERT: E 378 ASN cc_start: 0.8599 (m-40) cc_final: 0.8291 (t0) REVERT: E 389 ASN cc_start: 0.9014 (t0) cc_final: 0.8805 (t0) REVERT: E 402 LYS cc_start: 0.9318 (mtmm) cc_final: 0.8988 (ptpp) REVERT: E 436 ILE cc_start: 0.8030 (OUTLIER) cc_final: 0.7742 (pp) REVERT: E 437 GLN cc_start: 0.8534 (mt0) cc_final: 0.7950 (tm130) REVERT: F 376 MET cc_start: 0.7547 (pmm) cc_final: 0.7063 (pmm) REVERT: F 378 ASN cc_start: 0.8801 (m-40) cc_final: 0.8513 (t0) REVERT: F 415 VAL cc_start: 0.9017 (t) cc_final: 0.8696 (p) REVERT: F 437 GLN cc_start: 0.8596 (mt0) cc_final: 0.8158 (tp-100) REVERT: a 52 LYS cc_start: 0.8124 (mppt) cc_final: 0.7835 (mptt) REVERT: b 51 MET cc_start: 0.9007 (mmm) cc_final: 0.8239 (mmm) REVERT: b 53 LYS cc_start: 0.9401 (ttpp) cc_final: 0.9066 (tppp) REVERT: c 51 MET cc_start: 0.8957 (mmp) cc_final: 0.8627 (mmm) outliers start: 10 outliers final: 4 residues processed: 208 average time/residue: 1.3492 time to fit residues: 297.3866 Evaluate side-chains 211 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 204 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain D residue 382 ASP Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain E residue 434 LEU Chi-restraints excluded: chain E residue 436 ILE Chi-restraints excluded: chain F residue 391 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 0 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 90 optimal weight: 8.9990 chunk 86 optimal weight: 0.0980 chunk 106 optimal weight: 3.9990 chunk 29 optimal weight: 0.4980 chunk 62 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.081716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.053330 restraints weight = 57838.044| |-----------------------------------------------------------------------------| r_work (start): 0.2607 rms_B_bonded: 3.25 r_work: 0.2470 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.4678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8952 Z= 0.134 Angle : 0.606 12.037 12084 Z= 0.311 Chirality : 0.045 0.145 1449 Planarity : 0.004 0.063 1578 Dihedral : 6.726 81.802 1260 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.06 % Allowed : 19.00 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.24), residues: 1188 helix: 2.01 (0.37), residues: 231 sheet: 0.43 (0.26), residues: 381 loop : 0.65 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 286 TYR 0.003 0.001 TYR b 34 PHE 0.014 0.001 PHE b 36 TRP 0.003 0.000 TRP c 48 HIS 0.004 0.002 HIS b 33 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 8952) covalent geometry : angle 0.60645 (12084) hydrogen bonds : bond 0.03183 ( 405) hydrogen bonds : angle 4.84416 ( 1062) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Evaluate side-chains 214 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 204 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 MET cc_start: 0.9267 (mtm) cc_final: 0.8969 (mmm) REVERT: A 133 ARG cc_start: 0.8851 (mmm-85) cc_final: 0.8337 (mmm-85) REVERT: A 191 ASN cc_start: 0.8369 (t0) cc_final: 0.8087 (t0) REVERT: A 193 GLU cc_start: 0.9210 (mm-30) cc_final: 0.8839 (tp30) REVERT: A 207 ARG cc_start: 0.8463 (mmm-85) cc_final: 0.8250 (mtm-85) REVERT: B 133 ARG cc_start: 0.8819 (mmm-85) cc_final: 0.8160 (mmm-85) REVERT: B 191 ASN cc_start: 0.8226 (t0) cc_final: 0.7846 (t0) REVERT: B 193 GLU cc_start: 0.9215 (mm-30) cc_final: 0.8667 (tp30) REVERT: B 271 GLU cc_start: 0.8946 (OUTLIER) cc_final: 0.8335 (mm-30) REVERT: C 85 MET cc_start: 0.8716 (mtp) cc_final: 0.8508 (mtm) REVERT: C 193 GLU cc_start: 0.9271 (mm-30) cc_final: 0.8733 (tp30) REVERT: C 268 MET cc_start: 0.8863 (mmm) cc_final: 0.7948 (mmm) REVERT: D 376 MET cc_start: 0.7175 (pmt) cc_final: 0.6543 (pmm) REVERT: D 401 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.9062 (tp) REVERT: D 426 ASP cc_start: 0.9574 (m-30) cc_final: 0.9321 (p0) REVERT: D 437 GLN cc_start: 0.8392 (mt0) cc_final: 0.7980 (tm130) REVERT: E 376 MET cc_start: 0.6394 (pmt) cc_final: 0.5606 (pmm) REVERT: E 378 ASN cc_start: 0.8666 (m-40) cc_final: 0.8336 (t0) REVERT: E 389 ASN cc_start: 0.9119 (t0) cc_final: 0.8905 (t0) REVERT: E 402 LYS cc_start: 0.9302 (mtmm) cc_final: 0.8939 (ptpp) REVERT: E 436 ILE cc_start: 0.7913 (OUTLIER) cc_final: 0.7624 (pp) REVERT: E 437 GLN cc_start: 0.8520 (mt0) cc_final: 0.7933 (tm130) REVERT: F 376 MET cc_start: 0.7621 (pmm) cc_final: 0.7142 (pmm) REVERT: F 378 ASN cc_start: 0.8813 (m-40) cc_final: 0.8517 (t0) REVERT: F 415 VAL cc_start: 0.9023 (t) cc_final: 0.8725 (p) REVERT: F 437 GLN cc_start: 0.8570 (mt0) cc_final: 0.8139 (tp-100) REVERT: a 52 LYS cc_start: 0.8068 (mppt) cc_final: 0.7771 (mptt) REVERT: b 51 MET cc_start: 0.8990 (mmm) cc_final: 0.8262 (mmm) REVERT: b 53 LYS cc_start: 0.9378 (ttpp) cc_final: 0.9063 (tppp) REVERT: c 51 MET cc_start: 0.8938 (mmp) cc_final: 0.8605 (mmm) outliers start: 10 outliers final: 4 residues processed: 204 average time/residue: 1.2227 time to fit residues: 264.7076 Evaluate side-chains 210 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 203 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain E residue 430 SER Chi-restraints excluded: chain E residue 434 LEU Chi-restraints excluded: chain E residue 436 ILE Chi-restraints excluded: chain F residue 391 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 1 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 109 optimal weight: 0.2980 chunk 102 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 17 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.081735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.052273 restraints weight = 56046.712| |-----------------------------------------------------------------------------| r_work (start): 0.2636 rms_B_bonded: 3.28 r_work: 0.2486 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.4769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8952 Z= 0.109 Angle : 0.591 12.260 12084 Z= 0.302 Chirality : 0.045 0.157 1449 Planarity : 0.004 0.063 1578 Dihedral : 6.627 82.909 1260 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.64 % Allowed : 19.53 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.25), residues: 1188 helix: 2.05 (0.37), residues: 231 sheet: 0.52 (0.26), residues: 381 loop : 0.71 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 286 TYR 0.003 0.000 TYR F 444 PHE 0.021 0.001 PHE a 36 TRP 0.003 0.000 TRP c 48 HIS 0.005 0.002 HIS b 33 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 8952) covalent geometry : angle 0.59062 (12084) hydrogen bonds : bond 0.03020 ( 405) hydrogen bonds : angle 4.74307 ( 1062) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7449.40 seconds wall clock time: 126 minutes 29.39 seconds (7589.39 seconds total)