Starting phenix.real_space_refine on Mon Jun 16 03:39:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f0a_28754/06_2025/8f0a_28754.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f0a_28754/06_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_28754/06_2025/8f0a_28754.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f0a_28754/06_2025/8f0a_28754.map" model { file = "/net/cci-nas-00/data/ceres_data/8f0a_28754/06_2025/8f0a_28754.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f0a_28754/06_2025/8f0a_28754.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: "E" 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, 'ASP:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 21 Restraints were copied for chains: D, F, C, B, c, b Time building chain proxies: 10.65, per 1000 atoms: 0.59 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: 4.46 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 2.07 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: 7.36 Time building geometry restraints manager: 5.50 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: 0.07 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } ncs_group { reference = chain 'a' selection = chain 'c' selection = chain 'b' } 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: 1.410 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: 0.320 Extract box with map and model: 0.690 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 43.130 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.320 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.24), 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 TRP 0.020 0.006 TRP a 48 HIS 0.005 0.002 HIS A 105 PHE 0.018 0.007 PHE B 198 TYR 0.058 0.009 TYR B 257 ARG 0.015 0.002 ARG A 187 Details of bonding type rmsd hydrogen bonds : bond 0.17567 ( 405) hydrogen bonds : angle 7.22748 ( 1062) covalent geometry : bond 0.03129 ( 8952) covalent geometry : angle 1.76788 (12084) *********************** 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 : 1.472 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: 0.7268 (t0) REVERT: A 193 GLU cc_start: 0.9343 (mm-30) cc_final: 0.8716 (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: 0.7371 (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: 0.8076 (p) REVERT: F 378 ASN cc_start: 0.8161 (m-40) cc_final: 0.7921 (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: 0.8960 (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: 2.9260 time to fit residues: 791.3366 Evaluate side-chains 211 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 209 time to evaluate : 1.359 ------------------------------------------------------------------------------- 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 98 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 91 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 106 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 = 0.3219 r_free = 0.3219 target = 0.081154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.051662 restraints weight = 55622.799| |-----------------------------------------------------------------------------| r_work (start): 0.2600 rms_B_bonded: 3.24 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: 0.7689 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8952 Z= 0.173 Angle : 0.692 6.262 12084 Z= 0.386 Chirality : 0.049 0.184 1449 Planarity : 0.004 0.045 1578 Dihedral : 7.311 86.253 1264 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 2.02 % Allowed : 11.36 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.24), residues: 1188 helix: 1.10 (0.36), residues: 228 sheet: 0.63 (0.26), residues: 384 loop : 0.75 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP a 48 HIS 0.007 0.003 HIS c 33 PHE 0.012 0.002 PHE B 198 TYR 0.009 0.001 TYR b 34 ARG 0.007 0.001 ARG C 286 Details of bonding type rmsd hydrogen bonds : bond 0.05910 ( 405) hydrogen bonds : angle 6.06355 ( 1062) covalent geometry : bond 0.00367 ( 8952) covalent geometry : angle 0.69246 (12084) *********************** 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 254 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 235 time to evaluate : 1.617 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 32 GLU cc_start: 0.8911 (mt-10) cc_final: 0.8704 (tt0) REVERT: A 191 ASN cc_start: 0.8322 (t0) cc_final: 0.7825 (t0) REVERT: A 193 GLU cc_start: 0.9165 (mm-30) cc_final: 0.8873 (mp0) REVERT: A 207 ARG cc_start: 0.8252 (mmm-85) cc_final: 0.8004 (mtm-85) REVERT: A 275 GLU cc_start: 0.9408 (mp0) cc_final: 0.9199 (mp0) REVERT: B 191 ASN cc_start: 0.8122 (t0) cc_final: 0.7390 (t0) REVERT: B 193 GLU cc_start: 0.9220 (mm-30) cc_final: 0.8781 (tp30) REVERT: B 268 MET cc_start: 0.8663 (mmm) cc_final: 0.8150 (mmm) REVERT: C 12 MET cc_start: 0.6226 (mtp) cc_final: 0.5999 (mtp) REVERT: C 191 ASN cc_start: 0.8137 (t0) cc_final: 0.7450 (t0) REVERT: C 193 GLU cc_start: 0.9268 (mm-30) cc_final: 0.8756 (tp30) REVERT: D 375 GLU cc_start: 0.8834 (mp0) cc_final: 0.8616 (mp0) REVERT: D 389 ASN cc_start: 0.8477 (t0) cc_final: 0.8084 (t0) REVERT: D 415 VAL cc_start: 0.8955 (t) cc_final: 0.8390 (p) REVERT: D 437 GLN cc_start: 0.8272 (mt0) cc_final: 0.7832 (tp-100) REVERT: E 375 GLU cc_start: 0.8868 (mp0) cc_final: 0.8556 (mp0) REVERT: E 378 ASN cc_start: 0.8485 (m-40) cc_final: 0.8180 (t0) REVERT: E 389 ASN cc_start: 0.8993 (t0) cc_final: 0.8424 (t0) REVERT: E 405 ASP cc_start: 0.8060 (m-30) cc_final: 0.7684 (m-30) REVERT: E 415 VAL cc_start: 0.8748 (t) cc_final: 0.8330 (p) REVERT: E 437 GLN cc_start: 0.8463 (mt0) cc_final: 0.8135 (tp-100) REVERT: E 438 ARG cc_start: 0.7987 (mtm-85) cc_final: 0.7497 (mtt90) REVERT: F 375 GLU cc_start: 0.8843 (mp0) cc_final: 0.8494 (mp0) REVERT: F 378 ASN cc_start: 0.8378 (m-40) cc_final: 0.8109 (t0) REVERT: F 389 ASN cc_start: 0.8934 (t0) cc_final: 0.8433 (t0) REVERT: F 415 VAL cc_start: 0.8728 (t) cc_final: 0.8273 (p) REVERT: F 426 ASP cc_start: 0.9590 (m-30) cc_final: 0.9356 (p0) REVERT: F 437 GLN cc_start: 0.8318 (mt0) cc_final: 0.7996 (tm130) REVERT: b 31 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8712 (mt) REVERT: b 51 MET cc_start: 0.8797 (mmm) cc_final: 0.7977 (mmm) outliers start: 19 outliers final: 6 residues processed: 239 average time/residue: 2.7171 time to fit residues: 691.6190 Evaluate side-chains 225 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 218 time to evaluate : 1.405 ------------------------------------------------------------------------------- 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 436 ILE Chi-restraints excluded: chain E residue 436 ILE Chi-restraints excluded: chain E 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 100 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 116 optimal weight: 8.9990 chunk 88 optimal weight: 0.4980 chunk 4 optimal weight: 1.9990 chunk 2 optimal weight: 0.0980 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.3209 r_free = 0.3209 target = 0.080595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2594 r_free = 0.2594 target = 0.050348 restraints weight = 56078.468| |-----------------------------------------------------------------------------| r_work (start): 0.2581 rms_B_bonded: 3.23 r_work: 0.2434 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8952 Z= 0.168 Angle : 0.598 6.042 12084 Z= 0.326 Chirality : 0.046 0.162 1449 Planarity : 0.004 0.067 1578 Dihedral : 7.078 84.984 1260 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 1.49 % Allowed : 13.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.24), residues: 1188 helix: 1.68 (0.38), residues: 228 sheet: 0.36 (0.25), residues: 384 loop : 0.65 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP a 48 HIS 0.006 0.002 HIS c 33 PHE 0.009 0.001 PHE B 123 TYR 0.006 0.001 TYR b 34 ARG 0.008 0.001 ARG C 286 Details of bonding type rmsd hydrogen bonds : bond 0.04477 ( 405) hydrogen bonds : angle 5.56481 ( 1062) covalent geometry : bond 0.00365 ( 8952) covalent geometry : angle 0.59773 (12084) *********************** 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 238 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 224 time to evaluate : 1.611 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: 0.9217 (mtm) cc_final: 0.8927 (mtm) REVERT: A 133 ARG cc_start: 0.8697 (mmm-85) cc_final: 0.7716 (mmm-85) REVERT: A 191 ASN cc_start: 0.8311 (t0) cc_final: 0.8036 (t0) REVERT: A 193 GLU cc_start: 0.9170 (mm-30) cc_final: 0.8585 (tm-30) REVERT: A 207 ARG cc_start: 0.8380 (mmm-85) cc_final: 0.8065 (mtm-85) REVERT: A 271 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8195 (mt-10) REVERT: B 133 ARG cc_start: 0.8733 (mmm-85) cc_final: 0.8170 (mmm-85) REVERT: B 191 ASN cc_start: 0.8189 (t0) cc_final: 0.7923 (t0) REVERT: B 193 GLU cc_start: 0.9212 (mm-30) cc_final: 0.8719 (tp30) REVERT: B 268 MET cc_start: 0.8689 (mmm) cc_final: 0.8172 (mmm) REVERT: B 271 GLU cc_start: 0.8840 (mt-10) cc_final: 0.8176 (mm-30) REVERT: C 12 MET cc_start: 0.6043 (mtp) cc_final: 0.5816 (mtp) REVERT: C 85 MET cc_start: 0.8732 (mtp) cc_final: 0.8488 (mtm) REVERT: C 191 ASN cc_start: 0.8226 (t0) cc_final: 0.7751 (t0) REVERT: C 193 GLU cc_start: 0.9272 (mm-30) cc_final: 0.8786 (tp30) REVERT: C 268 MET cc_start: 0.8739 (mmm) cc_final: 0.8331 (mmm) REVERT: D 389 ASN cc_start: 0.8554 (t0) cc_final: 0.8110 (t0) REVERT: D 437 GLN cc_start: 0.8337 (mt0) cc_final: 0.7895 (tm130) REVERT: E 378 ASN cc_start: 0.8460 (m-40) cc_final: 0.8147 (t0) REVERT: E 389 ASN cc_start: 0.9013 (t0) cc_final: 0.8565 (t0) REVERT: E 415 VAL cc_start: 0.8743 (t) cc_final: 0.8362 (p) REVERT: E 436 ILE cc_start: 0.8068 (OUTLIER) cc_final: 0.7830 (pp) REVERT: E 437 GLN cc_start: 0.8340 (mt0) cc_final: 0.7860 (tm130) REVERT: E 438 ARG cc_start: 0.7978 (mtm-85) cc_final: 0.7644 (mtt180) REVERT: E 447 MET cc_start: 0.8250 (tmm) cc_final: 0.8046 (tmm) REVERT: F 378 ASN cc_start: 0.8438 (m-40) cc_final: 0.8152 (t0) REVERT: F 389 ASN cc_start: 0.8947 (t0) cc_final: 0.8596 (t0) REVERT: F 415 VAL cc_start: 0.8839 (t) cc_final: 0.8417 (p) REVERT: F 437 GLN cc_start: 0.8344 (mt0) cc_final: 0.8042 (tm130) REVERT: a 52 LYS cc_start: 0.8577 (mtpt) cc_final: 0.8277 (mppt) REVERT: b 51 MET cc_start: 0.8864 (mmm) cc_final: 0.8028 (mmm) REVERT: c 51 MET cc_start: 0.8846 (mmp) cc_final: 0.8612 (mmm) REVERT: c 52 LYS cc_start: 0.7744 (mppt) cc_final: 0.7464 (mppt) outliers start: 14 outliers final: 6 residues processed: 224 average time/residue: 2.7848 time to fit residues: 663.7014 Evaluate side-chains 221 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 214 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 446 LEU 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 Chi-restraints excluded: chain F residue 446 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 101 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 87 optimal weight: 0.0040 chunk 73 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.9598 ------------------------------------------------------------------------------- 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 = 0.3217 r_free = 0.3217 target = 0.080756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.050647 restraints weight = 56253.496| |-----------------------------------------------------------------------------| r_work (start): 0.2594 rms_B_bonded: 3.26 r_work: 0.2445 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.3856 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 : 0.568 6.386 12084 Z= 0.304 Chirality : 0.046 0.155 1449 Planarity : 0.004 0.071 1578 Dihedral : 6.974 84.212 1260 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 1.49 % Allowed : 14.65 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.24), residues: 1188 helix: 1.83 (0.38), residues: 228 sheet: 0.41 (0.26), residues: 369 loop : 0.52 (0.24), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP c 48 HIS 0.005 0.002 HIS c 33 PHE 0.008 0.001 PHE C 123 TYR 0.004 0.001 TYR b 34 ARG 0.009 0.001 ARG C 286 Details of bonding type rmsd hydrogen bonds : bond 0.03861 ( 405) hydrogen bonds : angle 5.30494 ( 1062) covalent geometry : bond 0.00296 ( 8952) covalent geometry : angle 0.56843 (12084) *********************** 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 232 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 218 time to evaluate : 1.417 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: A 23 MET cc_start: 0.9258 (mtm) cc_final: 0.8959 (mtm) REVERT: A 133 ARG cc_start: 0.8769 (mmm-85) cc_final: 0.7693 (mmm-85) REVERT: A 191 ASN cc_start: 0.8262 (t0) cc_final: 0.7980 (t0) REVERT: A 193 GLU cc_start: 0.9173 (mm-30) cc_final: 0.8566 (tm-30) REVERT: A 207 ARG cc_start: 0.8377 (mmm-85) cc_final: 0.8091 (mtm-85) REVERT: A 271 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8244 (mm-30) REVERT: B 32 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8453 (mt-10) REVERT: B 191 ASN cc_start: 0.8145 (t0) cc_final: 0.7871 (t0) REVERT: B 193 GLU cc_start: 0.9194 (mm-30) cc_final: 0.8705 (tp30) REVERT: B 268 MET cc_start: 0.8711 (mmm) cc_final: 0.8194 (mmm) REVERT: B 286 ARG cc_start: 0.8345 (mtt-85) cc_final: 0.7901 (mtt-85) REVERT: C 12 MET cc_start: 0.6130 (mtp) cc_final: 0.5867 (mtt) REVERT: C 85 MET cc_start: 0.8670 (mtp) cc_final: 0.8407 (mtm) REVERT: C 191 ASN cc_start: 0.8354 (t0) cc_final: 0.7322 (t0) REVERT: C 193 GLU cc_start: 0.9277 (mm-30) cc_final: 0.8810 (tp30) REVERT: C 268 MET cc_start: 0.8768 (mmm) cc_final: 0.8097 (mmm) REVERT: D 389 ASN cc_start: 0.8540 (t0) cc_final: 0.8193 (t0) REVERT: D 426 ASP cc_start: 0.9579 (m-30) cc_final: 0.9332 (p0) REVERT: D 437 GLN cc_start: 0.8379 (mt0) cc_final: 0.8021 (tm130) REVERT: E 378 ASN cc_start: 0.8518 (m-40) cc_final: 0.8224 (t0) REVERT: E 413 GLN cc_start: 0.8905 (mm-40) cc_final: 0.8463 (mm-40) REVERT: E 436 ILE cc_start: 0.8041 (OUTLIER) cc_final: 0.7699 (pp) REVERT: E 437 GLN cc_start: 0.8398 (mt0) cc_final: 0.7836 (tm130) REVERT: E 438 ARG cc_start: 0.8170 (mtm-85) cc_final: 0.7500 (mtt180) REVERT: E 447 MET cc_start: 0.8330 (tmm) cc_final: 0.8087 (tmm) REVERT: F 378 ASN cc_start: 0.8454 (m-40) cc_final: 0.8198 (t0) REVERT: F 389 ASN cc_start: 0.8914 (t0) cc_final: 0.8504 (t0) REVERT: F 415 VAL cc_start: 0.8897 (t) cc_final: 0.8546 (p) REVERT: F 437 GLN cc_start: 0.8379 (mt0) cc_final: 0.8043 (tm130) REVERT: b 51 MET cc_start: 0.8866 (mmm) cc_final: 0.8090 (mmm) REVERT: b 53 LYS cc_start: 0.9199 (ttpp) cc_final: 0.8840 (tppp) REVERT: c 50 THR cc_start: 0.7618 (p) cc_final: 0.7238 (p) REVERT: c 51 MET cc_start: 0.8834 (mmp) cc_final: 0.8614 (mmm) REVERT: c 52 LYS cc_start: 0.7791 (mppt) cc_final: 0.7500 (mppt) outliers start: 14 outliers final: 8 residues processed: 220 average time/residue: 2.8482 time to fit residues: 665.8966 Evaluate side-chains 216 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 207 time to evaluate : 1.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain D residue 430 SER Chi-restraints excluded: chain E residue 391 LYS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 38 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 88 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 27 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 = 0.3213 r_free = 0.3213 target = 0.080613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.051249 restraints weight = 56697.565| |-----------------------------------------------------------------------------| r_work (start): 0.2601 rms_B_bonded: 3.22 r_work: 0.2449 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8952 Z= 0.122 Angle : 0.550 6.839 12084 Z= 0.293 Chirality : 0.046 0.150 1449 Planarity : 0.004 0.054 1578 Dihedral : 6.842 83.355 1260 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 1.06 % Allowed : 15.92 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.24), residues: 1188 helix: 1.86 (0.38), residues: 228 sheet: 0.32 (0.26), residues: 354 loop : 0.64 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP c 48 HIS 0.004 0.002 HIS c 33 PHE 0.020 0.001 PHE a 36 TYR 0.005 0.001 TYR F 444 ARG 0.007 0.001 ARG A 286 Details of bonding type rmsd hydrogen bonds : bond 0.03539 ( 405) hydrogen bonds : angle 5.17015 ( 1062) covalent geometry : bond 0.00274 ( 8952) covalent geometry : angle 0.55014 (12084) *********************** 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 222 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 212 time to evaluate : 1.421 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: 0.9257 (mtm) cc_final: 0.8981 (mtm) REVERT: A 133 ARG cc_start: 0.8774 (mmm-85) cc_final: 0.8252 (mmm-85) REVERT: A 191 ASN cc_start: 0.8238 (t0) cc_final: 0.7957 (t0) REVERT: A 193 GLU cc_start: 0.9182 (mm-30) cc_final: 0.8808 (tp30) REVERT: A 207 ARG cc_start: 0.8394 (mmm-85) cc_final: 0.8131 (mtm-85) REVERT: A 254 MET cc_start: 0.8883 (mtt) cc_final: 0.8641 (mtt) REVERT: A 271 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8214 (mm-30) REVERT: B 85 MET cc_start: 0.8456 (mtp) cc_final: 0.8187 (mtm) REVERT: B 133 ARG cc_start: 0.8735 (mmm-85) cc_final: 0.7977 (mmm-85) REVERT: B 191 ASN cc_start: 0.8175 (t0) cc_final: 0.7810 (t0) REVERT: B 193 GLU cc_start: 0.9194 (mm-30) cc_final: 0.8633 (tp30) REVERT: B 268 MET cc_start: 0.8774 (mmm) cc_final: 0.8262 (mmm) REVERT: C 85 MET cc_start: 0.8708 (mtp) cc_final: 0.8469 (mtm) REVERT: C 191 ASN cc_start: 0.8136 (t0) cc_final: 0.7394 (t0) REVERT: C 193 GLU cc_start: 0.9273 (mm-30) cc_final: 0.8829 (tp30) REVERT: C 268 MET cc_start: 0.8788 (mmm) cc_final: 0.7961 (mmm) REVERT: C 331 MET cc_start: 0.9360 (OUTLIER) cc_final: 0.9075 (mtp) REVERT: D 415 VAL cc_start: 0.8980 (t) cc_final: 0.8570 (p) REVERT: D 426 ASP cc_start: 0.9590 (m-30) cc_final: 0.9310 (p0) REVERT: D 437 GLN cc_start: 0.8392 (mt0) cc_final: 0.8036 (tm130) REVERT: E 378 ASN cc_start: 0.8462 (m-40) cc_final: 0.8185 (t0) REVERT: E 413 GLN cc_start: 0.8902 (mm-40) cc_final: 0.8456 (mm-40) REVERT: E 437 GLN cc_start: 0.8435 (mt0) cc_final: 0.7892 (tm130) REVERT: E 438 ARG cc_start: 0.8064 (mtm-85) cc_final: 0.7668 (mtt180) REVERT: E 447 MET cc_start: 0.8467 (tmm) cc_final: 0.8160 (tmm) REVERT: F 376 MET cc_start: 0.5981 (pmt) cc_final: 0.5383 (pmm) REVERT: F 378 ASN cc_start: 0.8495 (m-40) cc_final: 0.8214 (t0) REVERT: F 389 ASN cc_start: 0.8867 (t0) cc_final: 0.8555 (t0) REVERT: F 415 VAL cc_start: 0.8914 (t) cc_final: 0.8575 (p) REVERT: F 437 GLN cc_start: 0.8422 (mt0) cc_final: 0.8123 (tm130) REVERT: b 51 MET cc_start: 0.9000 (mmm) cc_final: 0.8168 (mmm) REVERT: b 52 LYS cc_start: 0.8214 (mppt) cc_final: 0.8001 (mppt) REVERT: b 53 LYS cc_start: 0.9222 (ttpp) cc_final: 0.8870 (tppp) REVERT: c 50 THR cc_start: 0.7673 (p) cc_final: 0.7316 (p) REVERT: c 51 MET cc_start: 0.8851 (mmp) cc_final: 0.8629 (mmm) REVERT: c 52 LYS cc_start: 0.7868 (mppt) cc_final: 0.7585 (mppt) outliers start: 10 outliers final: 5 residues processed: 212 average time/residue: 2.8168 time to fit residues: 634.5699 Evaluate side-chains 215 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 209 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 331 MET Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain E residue 430 SER Chi-restraints excluded: chain F residue 391 LYS 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 43 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 34 optimal weight: 0.5980 chunk 106 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- 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 = 0.3202 r_free = 0.3202 target = 0.079812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2574 r_free = 0.2574 target = 0.049246 restraints weight = 57428.092| |-----------------------------------------------------------------------------| r_work (start): 0.2565 rms_B_bonded: 3.35 r_work: 0.2413 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.4237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8952 Z= 0.198 Angle : 0.564 7.448 12084 Z= 0.303 Chirality : 0.046 0.148 1449 Planarity : 0.004 0.059 1578 Dihedral : 6.750 82.437 1260 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 1.91 % Allowed : 15.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.24), residues: 1188 helix: 1.85 (0.37), residues: 231 sheet: 0.25 (0.25), residues: 384 loop : 0.65 (0.25), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP b 48 HIS 0.004 0.002 HIS b 33 PHE 0.017 0.001 PHE a 36 TYR 0.006 0.001 TYR b 34 ARG 0.007 0.001 ARG A 286 Details of bonding type rmsd hydrogen bonds : bond 0.03620 ( 405) hydrogen bonds : angle 5.13956 ( 1062) covalent geometry : bond 0.00445 ( 8952) covalent geometry : angle 0.56374 (12084) *********************** 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 227 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 209 time to evaluate : 1.400 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: A 23 MET cc_start: 0.9271 (mtm) cc_final: 0.9003 (mtm) REVERT: A 133 ARG cc_start: 0.8809 (mmm-85) cc_final: 0.8240 (mmm-85) REVERT: A 191 ASN cc_start: 0.8317 (t0) cc_final: 0.8025 (t0) REVERT: A 193 GLU cc_start: 0.9218 (mm-30) cc_final: 0.8823 (tp30) REVERT: A 207 ARG cc_start: 0.8446 (mmm-85) cc_final: 0.8212 (mtm-85) REVERT: A 254 MET cc_start: 0.8972 (mtt) cc_final: 0.8736 (mtt) REVERT: A 271 GLU cc_start: 0.8824 (mt-10) cc_final: 0.8194 (mm-30) REVERT: B 133 ARG cc_start: 0.8766 (mmm-85) cc_final: 0.8052 (mmm-85) REVERT: B 191 ASN cc_start: 0.8190 (t0) cc_final: 0.7886 (t0) REVERT: B 193 GLU cc_start: 0.9227 (mm-30) cc_final: 0.8628 (tp30) REVERT: B 271 GLU cc_start: 0.8897 (OUTLIER) cc_final: 0.8186 (mm-30) REVERT: C 85 MET cc_start: 0.8796 (mtp) cc_final: 0.8562 (mtm) REVERT: C 191 ASN cc_start: 0.8223 (t0) cc_final: 0.7602 (t0) REVERT: C 193 GLU cc_start: 0.9298 (mm-30) cc_final: 0.8814 (tp30) REVERT: C 264 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7635 (mt-10) REVERT: C 268 MET cc_start: 0.8790 (mmm) cc_final: 0.8010 (mmm) REVERT: C 331 MET cc_start: 0.9431 (OUTLIER) cc_final: 0.9146 (mtp) REVERT: D 389 ASN cc_start: 0.8796 (t0) cc_final: 0.8451 (t0) REVERT: D 415 VAL cc_start: 0.8902 (t) cc_final: 0.8554 (p) REVERT: D 426 ASP cc_start: 0.9599 (m-30) cc_final: 0.9324 (p0) REVERT: D 437 GLN cc_start: 0.8389 (mt0) cc_final: 0.8007 (tm130) REVERT: E 376 MET cc_start: 0.7591 (pmt) cc_final: 0.6747 (pmm) REVERT: E 378 ASN cc_start: 0.8462 (m-40) cc_final: 0.8205 (t0) REVERT: E 413 GLN cc_start: 0.8905 (mm-40) cc_final: 0.8450 (mm-40) REVERT: E 436 ILE cc_start: 0.7995 (OUTLIER) cc_final: 0.7687 (pp) REVERT: E 437 GLN cc_start: 0.8471 (mt0) cc_final: 0.7870 (tm130) REVERT: E 438 ARG cc_start: 0.8052 (mtm-85) cc_final: 0.7648 (mtt180) REVERT: E 447 MET cc_start: 0.8485 (tmm) cc_final: 0.8164 (tmm) REVERT: F 376 MET cc_start: 0.5794 (pmt) cc_final: 0.5532 (pmt) REVERT: F 378 ASN cc_start: 0.8536 (m-40) cc_final: 0.8248 (t0) REVERT: F 389 ASN cc_start: 0.8819 (t0) cc_final: 0.8511 (t0) REVERT: F 415 VAL cc_start: 0.8924 (t) cc_final: 0.8571 (p) REVERT: F 437 GLN cc_start: 0.8395 (mt0) cc_final: 0.8001 (tm130) REVERT: a 52 LYS cc_start: 0.8690 (mtpt) cc_final: 0.8448 (mppt) REVERT: b 51 MET cc_start: 0.8957 (mmm) cc_final: 0.8112 (mmm) REVERT: b 52 LYS cc_start: 0.8308 (mppt) cc_final: 0.8088 (mppt) REVERT: b 53 LYS cc_start: 0.9233 (ttpp) cc_final: 0.8866 (tppp) REVERT: c 50 THR cc_start: 0.7736 (p) cc_final: 0.7361 (p) REVERT: c 51 MET cc_start: 0.8873 (mmp) cc_final: 0.8617 (mmm) REVERT: c 52 LYS cc_start: 0.8160 (mppt) cc_final: 0.7844 (mppt) outliers start: 18 outliers final: 9 residues processed: 209 average time/residue: 2.8119 time to fit residues: 625.7427 Evaluate side-chains 220 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 207 time to evaluate : 1.440 ------------------------------------------------------------------------------- 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 C residue 331 MET 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 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 Chi-restraints excluded: chain F residue 430 SER Chi-restraints excluded: chain F residue 446 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 67 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 49 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3214 r_free = 0.3214 target = 0.080523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.050767 restraints weight = 56514.580| |-----------------------------------------------------------------------------| r_work (start): 0.2598 rms_B_bonded: 3.27 r_work: 0.2449 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.4374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8952 Z= 0.124 Angle : 0.558 8.657 12084 Z= 0.293 Chirality : 0.046 0.153 1449 Planarity : 0.004 0.059 1578 Dihedral : 6.676 81.132 1260 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.17 % Allowed : 16.67 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.24), residues: 1188 helix: 1.90 (0.37), residues: 231 sheet: 0.46 (0.27), residues: 348 loop : 0.66 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP a 48 HIS 0.004 0.002 HIS b 33 PHE 0.015 0.001 PHE a 36 TYR 0.003 0.001 TYR F 444 ARG 0.008 0.001 ARG A 286 Details of bonding type rmsd hydrogen bonds : bond 0.03325 ( 405) hydrogen bonds : angle 5.03629 ( 1062) covalent geometry : bond 0.00284 ( 8952) covalent geometry : angle 0.55799 (12084) *********************** 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 225 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 214 time to evaluate : 1.393 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: 0.9262 (mtm) cc_final: 0.9025 (mmm) REVERT: A 133 ARG cc_start: 0.8818 (mmm-85) cc_final: 0.8301 (mmm-85) REVERT: A 191 ASN cc_start: 0.8273 (t0) cc_final: 0.8001 (t0) REVERT: A 193 GLU cc_start: 0.9194 (mm-30) cc_final: 0.8818 (tp30) REVERT: A 207 ARG cc_start: 0.8447 (mmm-85) cc_final: 0.8201 (mtm-85) REVERT: A 271 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8219 (mm-30) REVERT: B 133 ARG cc_start: 0.8756 (mmm-85) cc_final: 0.8356 (mmm-85) REVERT: B 191 ASN cc_start: 0.8122 (t0) cc_final: 0.7849 (t0) REVERT: B 193 GLU cc_start: 0.9213 (mm-30) cc_final: 0.8754 (tp30) REVERT: B 271 GLU cc_start: 0.8902 (OUTLIER) cc_final: 0.8201 (mm-30) REVERT: B 286 ARG cc_start: 0.8428 (mtt-85) cc_final: 0.7985 (mtt-85) REVERT: C 85 MET cc_start: 0.8725 (mtp) cc_final: 0.8494 (mtm) REVERT: C 191 ASN cc_start: 0.8250 (t0) cc_final: 0.7475 (t0) REVERT: C 193 GLU cc_start: 0.9288 (mm-30) cc_final: 0.8790 (tp30) REVERT: C 268 MET cc_start: 0.8807 (mmm) cc_final: 0.8058 (mmm) REVERT: C 331 MET cc_start: 0.9413 (OUTLIER) cc_final: 0.9110 (mtp) REVERT: D 426 ASP cc_start: 0.9590 (m-30) cc_final: 0.9349 (p0) REVERT: D 437 GLN cc_start: 0.8416 (mt0) cc_final: 0.8018 (tm130) REVERT: E 376 MET cc_start: 0.7608 (pmt) cc_final: 0.6785 (pmm) REVERT: E 378 ASN cc_start: 0.8485 (m-40) cc_final: 0.8219 (t0) REVERT: E 391 LYS cc_start: 0.8488 (mppt) cc_final: 0.8187 (mmmt) REVERT: E 413 GLN cc_start: 0.8951 (mm-40) cc_final: 0.8471 (mm-40) REVERT: E 437 GLN cc_start: 0.8464 (mt0) cc_final: 0.7877 (tm130) REVERT: E 438 ARG cc_start: 0.8085 (mtm-85) cc_final: 0.7709 (mtt180) REVERT: E 447 MET cc_start: 0.8464 (tmm) cc_final: 0.8173 (tmm) REVERT: F 378 ASN cc_start: 0.8539 (m-40) cc_final: 0.8262 (t0) REVERT: F 389 ASN cc_start: 0.8873 (t0) cc_final: 0.8650 (t0) REVERT: F 415 VAL cc_start: 0.8938 (t) cc_final: 0.8620 (p) REVERT: F 437 GLN cc_start: 0.8367 (mt0) cc_final: 0.8060 (tm130) REVERT: a 52 LYS cc_start: 0.8673 (mtpt) cc_final: 0.8456 (mppt) REVERT: b 51 MET cc_start: 0.8986 (mmm) cc_final: 0.8212 (mmm) REVERT: c 50 THR cc_start: 0.7792 (p) cc_final: 0.7566 (t) REVERT: c 51 MET cc_start: 0.8860 (mmp) cc_final: 0.8609 (mmm) REVERT: c 52 LYS cc_start: 0.8101 (mppt) cc_final: 0.7810 (mppt) outliers start: 11 outliers final: 4 residues processed: 215 average time/residue: 2.7993 time to fit residues: 639.7657 Evaluate side-chains 214 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 207 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain C residue 331 MET Chi-restraints excluded: chain D residue 422 ARG Chi-restraints excluded: chain D residue 436 ILE 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 77 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 101 optimal weight: 0.8980 chunk 116 optimal weight: 9.9990 chunk 74 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 75 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3223 r_free = 0.3223 target = 0.080960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.050759 restraints weight = 56911.097| |-----------------------------------------------------------------------------| r_work (start): 0.2601 rms_B_bonded: 3.33 r_work: 0.2450 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.4475 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= 0.123 Angle : 0.561 9.668 12084 Z= 0.295 Chirality : 0.045 0.146 1449 Planarity : 0.004 0.061 1578 Dihedral : 6.602 79.307 1260 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.96 % Allowed : 17.73 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.24), residues: 1188 helix: 1.98 (0.37), residues: 231 sheet: 0.50 (0.27), residues: 351 loop : 0.69 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP c 48 HIS 0.004 0.002 HIS b 33 PHE 0.014 0.001 PHE a 36 TYR 0.003 0.001 TYR D 444 ARG 0.007 0.001 ARG A 286 Details of bonding type rmsd hydrogen bonds : bond 0.03203 ( 405) hydrogen bonds : angle 4.96557 ( 1062) covalent geometry : bond 0.00283 ( 8952) covalent geometry : angle 0.56137 (12084) *********************** 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 222 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 213 time to evaluate : 1.533 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: 0.9246 (mtm) cc_final: 0.8910 (mmm) REVERT: A 133 ARG cc_start: 0.8830 (mmm-85) cc_final: 0.8308 (mmm-85) REVERT: A 191 ASN cc_start: 0.8248 (t0) cc_final: 0.7978 (t0) REVERT: A 193 GLU cc_start: 0.9212 (mm-30) cc_final: 0.8851 (tp30) REVERT: A 207 ARG cc_start: 0.8490 (mmm-85) cc_final: 0.8255 (mtm-85) REVERT: A 271 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8252 (mm-30) REVERT: B 133 ARG cc_start: 0.8763 (mmm-85) cc_final: 0.8363 (mmm-85) REVERT: B 191 ASN cc_start: 0.8122 (t0) cc_final: 0.7783 (t0) REVERT: B 193 GLU cc_start: 0.9219 (mm-30) cc_final: 0.8773 (tp30) REVERT: B 271 GLU cc_start: 0.8945 (OUTLIER) cc_final: 0.8267 (mm-30) REVERT: C 85 MET cc_start: 0.8691 (mtp) cc_final: 0.8458 (mtm) REVERT: C 191 ASN cc_start: 0.8163 (t0) cc_final: 0.7549 (t0) REVERT: C 193 GLU cc_start: 0.9290 (mm-30) cc_final: 0.8794 (tp30) REVERT: C 205 ILE cc_start: 0.8779 (mt) cc_final: 0.8479 (pt) REVERT: C 268 MET cc_start: 0.8777 (mmm) cc_final: 0.8247 (mmm) REVERT: C 331 MET cc_start: 0.9441 (OUTLIER) cc_final: 0.9128 (mtp) REVERT: D 376 MET cc_start: 0.7176 (pmt) cc_final: 0.6689 (pmm) REVERT: D 422 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.8193 (mmt90) REVERT: D 426 ASP cc_start: 0.9597 (m-30) cc_final: 0.9344 (p0) REVERT: D 437 GLN cc_start: 0.8413 (mt0) cc_final: 0.7980 (tm130) REVERT: E 376 MET cc_start: 0.7577 (pmt) cc_final: 0.6731 (pmm) REVERT: E 378 ASN cc_start: 0.8524 (m-40) cc_final: 0.8268 (t0) REVERT: E 413 GLN cc_start: 0.8972 (mm-40) cc_final: 0.8597 (mm-40) REVERT: E 437 GLN cc_start: 0.8487 (mt0) cc_final: 0.7877 (tm130) REVERT: E 438 ARG cc_start: 0.8191 (mtm-85) cc_final: 0.7779 (mtt180) REVERT: E 447 MET cc_start: 0.8472 (tmm) cc_final: 0.8177 (tmm) REVERT: F 376 MET cc_start: 0.5752 (pmt) cc_final: 0.5157 (pmm) REVERT: F 378 ASN cc_start: 0.8672 (m-40) cc_final: 0.8383 (t0) REVERT: F 415 VAL cc_start: 0.8926 (t) cc_final: 0.8588 (p) REVERT: F 437 GLN cc_start: 0.8389 (mt0) cc_final: 0.7938 (tm130) REVERT: b 36 PHE cc_start: 0.7779 (p90) cc_final: 0.7569 (p90) REVERT: b 51 MET cc_start: 0.8989 (mmm) cc_final: 0.8158 (mmm) REVERT: b 53 LYS cc_start: 0.9235 (ttpp) cc_final: 0.8847 (tppp) REVERT: c 50 THR cc_start: 0.7782 (p) cc_final: 0.7530 (t) REVERT: c 51 MET cc_start: 0.8846 (mmp) cc_final: 0.8596 (mmm) REVERT: c 52 LYS cc_start: 0.8072 (mppt) cc_final: 0.7773 (mppt) outliers start: 9 outliers final: 5 residues processed: 214 average time/residue: 2.8606 time to fit residues: 649.9543 Evaluate side-chains 218 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 209 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain C residue 331 MET Chi-restraints excluded: chain D residue 422 ARG Chi-restraints excluded: chain E residue 430 SER Chi-restraints excluded: chain F residue 391 LYS Chi-restraints excluded: chain F residue 426 ASP Chi-restraints excluded: chain F residue 430 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 25 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 22 optimal weight: 0.3980 chunk 53 optimal weight: 3.9990 chunk 90 optimal weight: 7.9990 chunk 77 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- 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 = 0.3205 r_free = 0.3205 target = 0.079917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.049870 restraints weight = 57094.828| |-----------------------------------------------------------------------------| r_work (start): 0.2579 rms_B_bonded: 3.29 r_work: 0.2426 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.4506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8952 Z= 0.226 Angle : 0.599 10.701 12084 Z= 0.316 Chirality : 0.046 0.143 1449 Planarity : 0.004 0.061 1578 Dihedral : 6.586 78.292 1260 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.17 % Allowed : 18.15 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.24), residues: 1188 helix: 1.96 (0.37), residues: 231 sheet: 0.33 (0.26), residues: 357 loop : 0.64 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP c 48 HIS 0.003 0.002 HIS b 33 PHE 0.014 0.001 PHE a 36 TYR 0.006 0.001 TYR b 34 ARG 0.008 0.001 ARG A 286 Details of bonding type rmsd hydrogen bonds : bond 0.03443 ( 405) hydrogen bonds : angle 4.98652 ( 1062) covalent geometry : bond 0.00512 ( 8952) covalent geometry : angle 0.59860 (12084) *********************** 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 218 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 207 time to evaluate : 1.345 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: 0.9273 (mtm) cc_final: 0.9039 (mmm) REVERT: A 133 ARG cc_start: 0.8842 (mmm-85) cc_final: 0.8332 (mmm-85) REVERT: A 191 ASN cc_start: 0.8319 (t0) cc_final: 0.7668 (t0) REVERT: A 193 GLU cc_start: 0.9215 (mm-30) cc_final: 0.8853 (tp30) REVERT: A 207 ARG cc_start: 0.8491 (mmm-85) cc_final: 0.8254 (mtm-85) REVERT: A 271 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8290 (mm-30) REVERT: B 133 ARG cc_start: 0.8782 (mmm-85) cc_final: 0.8099 (mmm-85) REVERT: B 191 ASN cc_start: 0.8146 (t0) cc_final: 0.7793 (t0) REVERT: B 193 GLU cc_start: 0.9221 (mm-30) cc_final: 0.8660 (tp30) REVERT: B 271 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8224 (mm-30) REVERT: B 286 ARG cc_start: 0.8454 (mtt-85) cc_final: 0.8023 (mtt-85) REVERT: C 85 MET cc_start: 0.8799 (mtp) cc_final: 0.8567 (mtm) REVERT: C 191 ASN cc_start: 0.8275 (t0) cc_final: 0.7616 (t0) REVERT: C 193 GLU cc_start: 0.9307 (mm-30) cc_final: 0.8815 (tp30) REVERT: C 268 MET cc_start: 0.8791 (mmm) cc_final: 0.8260 (mmm) REVERT: C 331 MET cc_start: 0.9495 (mtp) cc_final: 0.9206 (mtp) REVERT: D 376 MET cc_start: 0.7136 (pmt) cc_final: 0.6687 (pmm) REVERT: D 422 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.8197 (mmt90) REVERT: D 426 ASP cc_start: 0.9610 (m-30) cc_final: 0.9332 (p0) REVERT: D 437 GLN cc_start: 0.8390 (mt0) cc_final: 0.7972 (tm130) REVERT: E 376 MET cc_start: 0.7595 (pmt) cc_final: 0.6745 (pmm) REVERT: E 378 ASN cc_start: 0.8519 (m-40) cc_final: 0.8254 (t0) REVERT: E 413 GLN cc_start: 0.9002 (mm-40) cc_final: 0.8634 (mm-40) REVERT: E 436 ILE cc_start: 0.7977 (OUTLIER) cc_final: 0.7708 (pp) REVERT: E 437 GLN cc_start: 0.8495 (mt0) cc_final: 0.7859 (tm130) REVERT: E 438 ARG cc_start: 0.8115 (mtm-85) cc_final: 0.7674 (mtt180) REVERT: E 447 MET cc_start: 0.8493 (tmm) cc_final: 0.8200 (tmm) REVERT: F 376 MET cc_start: 0.5912 (pmt) cc_final: 0.5304 (pmm) REVERT: F 378 ASN cc_start: 0.8631 (m-40) cc_final: 0.8386 (t0) REVERT: F 415 VAL cc_start: 0.8942 (t) cc_final: 0.8610 (p) REVERT: F 437 GLN cc_start: 0.8494 (mt0) cc_final: 0.8017 (tm130) REVERT: b 51 MET cc_start: 0.8961 (mmm) cc_final: 0.8188 (mmm) REVERT: b 53 LYS cc_start: 0.9253 (ttpp) cc_final: 0.8859 (tppp) REVERT: c 50 THR cc_start: 0.7829 (p) cc_final: 0.7580 (t) REVERT: c 51 MET cc_start: 0.8885 (mmp) cc_final: 0.8609 (mmm) REVERT: c 52 LYS cc_start: 0.8221 (mppt) cc_final: 0.7916 (mppt) outliers start: 11 outliers final: 4 residues processed: 208 average time/residue: 2.8790 time to fit residues: 635.4558 Evaluate side-chains 215 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 207 time to evaluate : 1.430 ------------------------------------------------------------------------------- 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 405 ASP Chi-restraints excluded: chain D residue 422 ARG 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 39 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 22 optimal weight: 0.3980 chunk 105 optimal weight: 8.9990 chunk 106 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3228 r_free = 0.3228 target = 0.081164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.050953 restraints weight = 56768.953| |-----------------------------------------------------------------------------| r_work (start): 0.2605 rms_B_bonded: 3.32 r_work: 0.2451 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.4604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8952 Z= 0.118 Angle : 0.595 12.063 12084 Z= 0.309 Chirality : 0.045 0.147 1449 Planarity : 0.004 0.063 1578 Dihedral : 6.520 79.941 1260 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 0.85 % Allowed : 18.79 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.24), residues: 1188 helix: 1.99 (0.37), residues: 231 sheet: 0.51 (0.27), residues: 351 loop : 0.72 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP a 48 HIS 0.005 0.002 HIS b 33 PHE 0.014 0.001 PHE a 36 TYR 0.003 0.000 TYR F 444 ARG 0.008 0.001 ARG B 286 Details of bonding type rmsd hydrogen bonds : bond 0.03162 ( 405) hydrogen bonds : angle 4.89157 ( 1062) covalent geometry : bond 0.00276 ( 8952) covalent geometry : angle 0.59466 (12084) ********************** 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 219 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 211 time to evaluate : 1.730 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: 0.9253 (mtm) cc_final: 0.8934 (mmm) REVERT: A 133 ARG cc_start: 0.8834 (mmm-85) cc_final: 0.8302 (mmm-85) REVERT: A 191 ASN cc_start: 0.8266 (t0) cc_final: 0.7993 (t0) REVERT: A 193 GLU cc_start: 0.9216 (mm-30) cc_final: 0.8837 (tp30) REVERT: A 207 ARG cc_start: 0.8487 (mmm-85) cc_final: 0.8253 (mtm-85) REVERT: A 271 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8175 (mm-30) REVERT: B 133 ARG cc_start: 0.8788 (mmm-85) cc_final: 0.8083 (mmm-85) REVERT: B 191 ASN cc_start: 0.8056 (t0) cc_final: 0.7757 (t0) REVERT: B 193 GLU cc_start: 0.9217 (mm-30) cc_final: 0.8665 (tp30) REVERT: B 271 GLU cc_start: 0.8933 (OUTLIER) cc_final: 0.8255 (mm-30) REVERT: B 286 ARG cc_start: 0.8423 (mtt-85) cc_final: 0.7993 (mtt-85) REVERT: C 85 MET cc_start: 0.8684 (mtp) cc_final: 0.8457 (mtm) REVERT: C 191 ASN cc_start: 0.8197 (t0) cc_final: 0.7477 (t0) REVERT: C 193 GLU cc_start: 0.9296 (mm-30) cc_final: 0.8782 (tp30) REVERT: C 205 ILE cc_start: 0.8788 (mt) cc_final: 0.8475 (pt) REVERT: C 268 MET cc_start: 0.8753 (mmm) cc_final: 0.8206 (mmm) REVERT: C 331 MET cc_start: 0.9466 (OUTLIER) cc_final: 0.9167 (mtp) REVERT: D 376 MET cc_start: 0.7089 (pmt) cc_final: 0.6707 (pmm) REVERT: D 426 ASP cc_start: 0.9593 (m-30) cc_final: 0.9345 (p0) REVERT: D 437 GLN cc_start: 0.8434 (mt0) cc_final: 0.8018 (tm130) REVERT: E 376 MET cc_start: 0.7544 (pmt) cc_final: 0.6674 (pmm) REVERT: E 378 ASN cc_start: 0.8609 (m-40) cc_final: 0.8370 (t0) REVERT: E 437 GLN cc_start: 0.8494 (mt0) cc_final: 0.7863 (tm130) REVERT: E 438 ARG cc_start: 0.8232 (mtm-85) cc_final: 0.7802 (mtt180) REVERT: E 447 MET cc_start: 0.8483 (tmm) cc_final: 0.8185 (tmm) REVERT: F 378 ASN cc_start: 0.8648 (m-40) cc_final: 0.8393 (t0) REVERT: F 415 VAL cc_start: 0.8910 (t) cc_final: 0.8583 (p) REVERT: F 437 GLN cc_start: 0.8605 (mt0) cc_final: 0.8196 (tm130) REVERT: b 51 MET cc_start: 0.8974 (mmm) cc_final: 0.8199 (mmm) REVERT: b 53 LYS cc_start: 0.9240 (ttpp) cc_final: 0.8877 (tppp) REVERT: c 50 THR cc_start: 0.7818 (p) cc_final: 0.7576 (t) REVERT: c 51 MET cc_start: 0.8877 (mmp) cc_final: 0.8609 (mmm) REVERT: c 52 LYS cc_start: 0.8125 (mppt) cc_final: 0.7834 (mppt) outliers start: 8 outliers final: 5 residues processed: 212 average time/residue: 2.8164 time to fit residues: 634.9082 Evaluate side-chains 215 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 207 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain C residue 331 MET Chi-restraints excluded: chain D residue 375 GLU Chi-restraints excluded: chain D residue 405 ASP Chi-restraints excluded: chain E residue 430 SER Chi-restraints excluded: chain F residue 391 LYS Chi-restraints excluded: chain F residue 430 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 102 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 = 0.3242 r_free = 0.3242 target = 0.081244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.052741 restraints weight = 57690.781| |-----------------------------------------------------------------------------| r_work (start): 0.2616 rms_B_bonded: 3.31 r_work: 0.2464 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.4672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8952 Z= 0.160 Angle : 0.614 12.148 12084 Z= 0.316 Chirality : 0.045 0.159 1449 Planarity : 0.004 0.073 1578 Dihedral : 6.518 81.355 1260 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.96 % Allowed : 19.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.25), residues: 1188 helix: 2.03 (0.37), residues: 228 sheet: 0.41 (0.26), residues: 381 loop : 0.79 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP c 48 HIS 0.004 0.002 HIS b 33 PHE 0.014 0.001 PHE a 36 TYR 0.004 0.001 TYR F 444 ARG 0.007 0.001 ARG A 286 Details of bonding type rmsd hydrogen bonds : bond 0.03268 ( 405) hydrogen bonds : angle 4.96244 ( 1062) covalent geometry : bond 0.00371 ( 8952) covalent geometry : angle 0.61430 (12084) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15296.60 seconds wall clock time: 258 minutes 27.57 seconds (15507.57 seconds total)