Starting phenix.real_space_refine on Fri Aug 7 11:59:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/36hw_77588/08_2026/36hw_77588.cif Found real_map, /net/cci-nas-00/data/ceres_data/36hw_77588/08_2026/36hw_77588.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/36hw_77588/08_2026/36hw_77588.cif" } default_model = "/net/cci-nas-00/data/ceres_data/36hw_77588/08_2026/36hw_77588.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/36hw_77588/08_2026/36hw_77588.map" default_real_map = "/net/cci-nas-00/data/ceres_data/36hw_77588/08_2026/36hw_77588.map" } resolution = 3.55 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.012 sd= 0.226 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 135 5.16 5 C 13644 2.51 5 N 3393 2.21 5 O 3609 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20781 Number of models: 1 Model: "" Number of chains: 1 Chain: "A2" Number of atoms: 2309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2309 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 9, 'TRANS': 301} Restraints were copied for chains: B2, C2, D2, E2, F2, G2, H2, I2 Time building chain proxies: 2.60, per 1000 atoms: 0.13 Number of scatterers: 20781 At special positions: 0 Unit cell: (137.55, 135.45, 95.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 135 16.00 O 3609 8.00 N 3393 7.00 C 13644 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.21 Conformation dependent library (CDL) restraints added in 797.7 milliseconds 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5004 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 0 sheets defined 87.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A2' and resid 22 through 37 Processing helix chain 'A2' and resid 40 through 64 removed outlier: 3.549A pdb=" N LEUA2 44 " --> pdb=" O PROA2 40 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N LEUA2 46 " --> pdb=" O PHEA2 42 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N THRA2 49 " --> pdb=" O ASPA2 45 " (cutoff:3.500A) Processing helix chain 'A2' and resid 67 through 71 removed outlier: 3.549A pdb=" N PHEA2 71 " --> pdb=" O THRA2 68 " (cutoff:3.500A) Processing helix chain 'A2' and resid 73 through 98 Processing helix chain 'A2' and resid 108 through 119 Processing helix chain 'A2' and resid 123 through 140 removed outlier: 6.024A pdb=" N VALA2 129 " --> pdb=" O ILEA2 125 " (cutoff:3.500A) Processing helix chain 'A2' and resid 140 through 173 Proline residue: A2 161 - end of helix Processing helix chain 'A2' and resid 177 through 231 removed outlier: 3.820A pdb=" N ASPA2 199 " --> pdb=" O TYRA2 195 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLYA2 200 " --> pdb=" O GLYA2 196 " (cutoff:3.500A) Processing helix chain 'A2' and resid 234 through 268 removed outlier: 3.894A pdb=" N ALAA2 238 " --> pdb=" O SERA2 234 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N SERA2 241 " --> pdb=" O SERA2 237 " (cutoff:3.500A) Proline residue: A2 256 - end of helix Processing helix chain 'A2' and resid 276 through 286 Processing helix chain 'A2' and resid 289 through 304 removed outlier: 4.815A pdb=" N ALAA2 295 " --> pdb=" O VALA2 291 " (cutoff:3.500A) Processing helix chain 'A2' and resid 310 through 327 Processing helix chain 'B2' and resid 22 through 37 Processing helix chain 'B2' and resid 40 through 64 removed outlier: 3.550A pdb=" N LEUB2 44 " --> pdb=" O PROB2 40 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N LEUB2 46 " --> pdb=" O PHEB2 42 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THRB2 49 " --> pdb=" O ASPB2 45 " (cutoff:3.500A) Processing helix chain 'B2' and resid 67 through 71 removed outlier: 3.549A pdb=" N PHEB2 71 " --> pdb=" O THRB2 68 " (cutoff:3.500A) Processing helix chain 'B2' and resid 73 through 98 Processing helix chain 'B2' and resid 108 through 119 Processing helix chain 'B2' and resid 123 through 140 removed outlier: 6.024A pdb=" N VALB2 129 " --> pdb=" O ILEB2 125 " (cutoff:3.500A) Processing helix chain 'B2' and resid 140 through 173 Proline residue: B2 161 - end of helix Processing helix chain 'B2' and resid 177 through 231 removed outlier: 3.820A pdb=" N ASPB2 199 " --> pdb=" O TYRB2 195 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLYB2 200 " --> pdb=" O GLYB2 196 " (cutoff:3.500A) Processing helix chain 'B2' and resid 234 through 268 removed outlier: 3.894A pdb=" N ALAB2 238 " --> pdb=" O SERB2 234 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N SERB2 241 " --> pdb=" O SERB2 237 " (cutoff:3.500A) Proline residue: B2 256 - end of helix Processing helix chain 'B2' and resid 276 through 286 Processing helix chain 'B2' and resid 289 through 304 removed outlier: 4.815A pdb=" N ALAB2 295 " --> pdb=" O VALB2 291 " (cutoff:3.500A) Processing helix chain 'B2' and resid 310 through 327 Processing helix chain 'C2' and resid 22 through 37 Processing helix chain 'C2' and resid 40 through 64 removed outlier: 3.550A pdb=" N LEUC2 44 " --> pdb=" O PROC2 40 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N LEUC2 46 " --> pdb=" O PHEC2 42 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THRC2 49 " --> pdb=" O ASPC2 45 " (cutoff:3.500A) Processing helix chain 'C2' and resid 67 through 71 removed outlier: 3.548A pdb=" N PHEC2 71 " --> pdb=" O THRC2 68 " (cutoff:3.500A) Processing helix chain 'C2' and resid 73 through 98 Processing helix chain 'C2' and resid 108 through 119 Processing helix chain 'C2' and resid 123 through 140 removed outlier: 6.024A pdb=" N VALC2 129 " --> pdb=" O ILEC2 125 " (cutoff:3.500A) Processing helix chain 'C2' and resid 140 through 173 Proline residue: C2 161 - end of helix Processing helix chain 'C2' and resid 177 through 231 removed outlier: 3.821A pdb=" N ASPC2 199 " --> pdb=" O TYRC2 195 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLYC2 200 " --> pdb=" O GLYC2 196 " (cutoff:3.500A) Processing helix chain 'C2' and resid 234 through 268 removed outlier: 3.895A pdb=" N ALAC2 238 " --> pdb=" O SERC2 234 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N SERC2 241 " --> pdb=" O SERC2 237 " (cutoff:3.500A) Proline residue: C2 256 - end of helix Processing helix chain 'C2' and resid 276 through 286 Processing helix chain 'C2' and resid 289 through 304 removed outlier: 4.816A pdb=" N ALAC2 295 " --> pdb=" O VALC2 291 " (cutoff:3.500A) Processing helix chain 'C2' and resid 310 through 327 Processing helix chain 'D2' and resid 22 through 37 Processing helix chain 'D2' and resid 40 through 64 removed outlier: 3.550A pdb=" N LEUD2 44 " --> pdb=" O PROD2 40 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N LEUD2 46 " --> pdb=" O PHED2 42 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THRD2 49 " --> pdb=" O ASPD2 45 " (cutoff:3.500A) Processing helix chain 'D2' and resid 67 through 71 removed outlier: 3.548A pdb=" N PHED2 71 " --> pdb=" O THRD2 68 " (cutoff:3.500A) Processing helix chain 'D2' and resid 73 through 98 Processing helix chain 'D2' and resid 108 through 119 Processing helix chain 'D2' and resid 123 through 140 removed outlier: 6.023A pdb=" N VALD2 129 " --> pdb=" O ILED2 125 " (cutoff:3.500A) Processing helix chain 'D2' and resid 140 through 173 Proline residue: D2 161 - end of helix Processing helix chain 'D2' and resid 177 through 231 removed outlier: 3.820A pdb=" N ASPD2 199 " --> pdb=" O TYRD2 195 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLYD2 200 " --> pdb=" O GLYD2 196 " (cutoff:3.500A) Processing helix chain 'D2' and resid 234 through 268 removed outlier: 3.895A pdb=" N ALAD2 238 " --> pdb=" O SERD2 234 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N SERD2 241 " --> pdb=" O SERD2 237 " (cutoff:3.500A) Proline residue: D2 256 - end of helix Processing helix chain 'D2' and resid 276 through 286 Processing helix chain 'D2' and resid 289 through 304 removed outlier: 4.816A pdb=" N ALAD2 295 " --> pdb=" O VALD2 291 " (cutoff:3.500A) Processing helix chain 'D2' and resid 310 through 327 Processing helix chain 'E2' and resid 22 through 37 Processing helix chain 'E2' and resid 40 through 64 removed outlier: 3.549A pdb=" N LEUE2 44 " --> pdb=" O PROE2 40 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N LEUE2 46 " --> pdb=" O PHEE2 42 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THRE2 49 " --> pdb=" O ASPE2 45 " (cutoff:3.500A) Processing helix chain 'E2' and resid 67 through 71 removed outlier: 3.548A pdb=" N PHEE2 71 " --> pdb=" O THRE2 68 " (cutoff:3.500A) Processing helix chain 'E2' and resid 73 through 98 Processing helix chain 'E2' and resid 108 through 119 Processing helix chain 'E2' and resid 123 through 140 removed outlier: 6.024A pdb=" N VALE2 129 " --> pdb=" O ILEE2 125 " (cutoff:3.500A) Processing helix chain 'E2' and resid 140 through 173 Proline residue: E2 161 - end of helix Processing helix chain 'E2' and resid 177 through 231 removed outlier: 3.820A pdb=" N ASPE2 199 " --> pdb=" O TYRE2 195 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLYE2 200 " --> pdb=" O GLYE2 196 " (cutoff:3.500A) Processing helix chain 'E2' and resid 234 through 268 removed outlier: 3.894A pdb=" N ALAE2 238 " --> pdb=" O SERE2 234 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N SERE2 241 " --> pdb=" O SERE2 237 " (cutoff:3.500A) Proline residue: E2 256 - end of helix Processing helix chain 'E2' and resid 276 through 286 Processing helix chain 'E2' and resid 289 through 304 removed outlier: 4.816A pdb=" N ALAE2 295 " --> pdb=" O VALE2 291 " (cutoff:3.500A) Processing helix chain 'E2' and resid 310 through 327 Processing helix chain 'F2' and resid 22 through 37 Processing helix chain 'F2' and resid 40 through 64 removed outlier: 3.549A pdb=" N LEUF2 44 " --> pdb=" O PROF2 40 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N LEUF2 46 " --> pdb=" O PHEF2 42 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N THRF2 49 " --> pdb=" O ASPF2 45 " (cutoff:3.500A) Processing helix chain 'F2' and resid 67 through 71 removed outlier: 3.549A pdb=" N PHEF2 71 " --> pdb=" O THRF2 68 " (cutoff:3.500A) Processing helix chain 'F2' and resid 73 through 98 Processing helix chain 'F2' and resid 108 through 119 Processing helix chain 'F2' and resid 123 through 140 removed outlier: 6.024A pdb=" N VALF2 129 " --> pdb=" O ILEF2 125 " (cutoff:3.500A) Processing helix chain 'F2' and resid 140 through 173 Proline residue: F2 161 - end of helix Processing helix chain 'F2' and resid 177 through 231 removed outlier: 3.820A pdb=" N ASPF2 199 " --> pdb=" O TYRF2 195 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLYF2 200 " --> pdb=" O GLYF2 196 " (cutoff:3.500A) Processing helix chain 'F2' and resid 234 through 268 removed outlier: 3.895A pdb=" N ALAF2 238 " --> pdb=" O SERF2 234 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N SERF2 241 " --> pdb=" O SERF2 237 " (cutoff:3.500A) Proline residue: F2 256 - end of helix Processing helix chain 'F2' and resid 276 through 286 Processing helix chain 'F2' and resid 289 through 304 removed outlier: 4.815A pdb=" N ALAF2 295 " --> pdb=" O VALF2 291 " (cutoff:3.500A) Processing helix chain 'F2' and resid 310 through 327 Processing helix chain 'G2' and resid 22 through 37 Processing helix chain 'G2' and resid 40 through 64 removed outlier: 3.549A pdb=" N LEUG2 44 " --> pdb=" O PROG2 40 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N LEUG2 46 " --> pdb=" O PHEG2 42 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THRG2 49 " --> pdb=" O ASPG2 45 " (cutoff:3.500A) Processing helix chain 'G2' and resid 67 through 71 removed outlier: 3.549A pdb=" N PHEG2 71 " --> pdb=" O THRG2 68 " (cutoff:3.500A) Processing helix chain 'G2' and resid 73 through 98 Processing helix chain 'G2' and resid 108 through 119 Processing helix chain 'G2' and resid 123 through 140 removed outlier: 6.024A pdb=" N VALG2 129 " --> pdb=" O ILEG2 125 " (cutoff:3.500A) Processing helix chain 'G2' and resid 140 through 173 Proline residue: G2 161 - end of helix Processing helix chain 'G2' and resid 177 through 231 removed outlier: 3.820A pdb=" N ASPG2 199 " --> pdb=" O TYRG2 195 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLYG2 200 " --> pdb=" O GLYG2 196 " (cutoff:3.500A) Processing helix chain 'G2' and resid 234 through 268 removed outlier: 3.895A pdb=" N ALAG2 238 " --> pdb=" O SERG2 234 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N SERG2 241 " --> pdb=" O SERG2 237 " (cutoff:3.500A) Proline residue: G2 256 - end of helix Processing helix chain 'G2' and resid 276 through 286 Processing helix chain 'G2' and resid 289 through 304 removed outlier: 4.816A pdb=" N ALAG2 295 " --> pdb=" O VALG2 291 " (cutoff:3.500A) Processing helix chain 'G2' and resid 310 through 327 Processing helix chain 'H2' and resid 22 through 37 Processing helix chain 'H2' and resid 40 through 64 removed outlier: 3.549A pdb=" N LEUH2 44 " --> pdb=" O PROH2 40 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N LEUH2 46 " --> pdb=" O PHEH2 42 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THRH2 49 " --> pdb=" O ASPH2 45 " (cutoff:3.500A) Processing helix chain 'H2' and resid 67 through 71 removed outlier: 3.549A pdb=" N PHEH2 71 " --> pdb=" O THRH2 68 " (cutoff:3.500A) Processing helix chain 'H2' and resid 73 through 98 Processing helix chain 'H2' and resid 108 through 119 Processing helix chain 'H2' and resid 123 through 140 removed outlier: 6.023A pdb=" N VALH2 129 " --> pdb=" O ILEH2 125 " (cutoff:3.500A) Processing helix chain 'H2' and resid 140 through 173 Proline residue: H2 161 - end of helix Processing helix chain 'H2' and resid 177 through 231 removed outlier: 3.820A pdb=" N ASPH2 199 " --> pdb=" O TYRH2 195 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLYH2 200 " --> pdb=" O GLYH2 196 " (cutoff:3.500A) Processing helix chain 'H2' and resid 234 through 268 removed outlier: 3.896A pdb=" N ALAH2 238 " --> pdb=" O SERH2 234 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N SERH2 241 " --> pdb=" O SERH2 237 " (cutoff:3.500A) Proline residue: H2 256 - end of helix Processing helix chain 'H2' and resid 276 through 286 Processing helix chain 'H2' and resid 289 through 304 removed outlier: 4.815A pdb=" N ALAH2 295 " --> pdb=" O VALH2 291 " (cutoff:3.500A) Processing helix chain 'H2' and resid 310 through 327 Processing helix chain 'I2' and resid 22 through 37 Processing helix chain 'I2' and resid 40 through 64 removed outlier: 3.549A pdb=" N LEUI2 44 " --> pdb=" O PROI2 40 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N LEUI2 46 " --> pdb=" O PHEI2 42 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THRI2 49 " --> pdb=" O ASPI2 45 " (cutoff:3.500A) Processing helix chain 'I2' and resid 67 through 71 removed outlier: 3.548A pdb=" N PHEI2 71 " --> pdb=" O THRI2 68 " (cutoff:3.500A) Processing helix chain 'I2' and resid 73 through 98 Processing helix chain 'I2' and resid 108 through 119 Processing helix chain 'I2' and resid 123 through 140 removed outlier: 6.024A pdb=" N VALI2 129 " --> pdb=" O ILEI2 125 " (cutoff:3.500A) Processing helix chain 'I2' and resid 140 through 173 Proline residue: I2 161 - end of helix Processing helix chain 'I2' and resid 177 through 231 removed outlier: 3.821A pdb=" N ASPI2 199 " --> pdb=" O TYRI2 195 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLYI2 200 " --> pdb=" O GLYI2 196 " (cutoff:3.500A) Processing helix chain 'I2' and resid 234 through 268 removed outlier: 3.895A pdb=" N ALAI2 238 " --> pdb=" O SERI2 234 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N SERI2 241 " --> pdb=" O SERI2 237 " (cutoff:3.500A) Proline residue: I2 256 - end of helix Processing helix chain 'I2' and resid 276 through 286 Processing helix chain 'I2' and resid 289 through 304 removed outlier: 4.815A pdb=" N ALAI2 295 " --> pdb=" O VALI2 291 " (cutoff:3.500A) Processing helix chain 'I2' and resid 310 through 327 1872 hydrogen bonds defined for protein. 5589 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.54 Time building geometry restraints manager: 1.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6615 1.34 - 1.45: 3193 1.45 - 1.57: 11036 1.57 - 1.69: 0 1.69 - 1.80: 270 Bond restraints: 21114 Sorted by residual: bond pdb=" CA ILEI2 255 " pdb=" CB ILEI2 255 " ideal model delta sigma weight residual 1.539 1.531 0.008 5.40e-03 3.43e+04 2.17e+00 bond pdb=" C VALG2 268 " pdb=" N THRG2 269 " ideal model delta sigma weight residual 1.332 1.312 0.020 1.40e-02 5.10e+03 2.08e+00 bond pdb=" CA ILEH2 255 " pdb=" CB ILEH2 255 " ideal model delta sigma weight residual 1.539 1.531 0.008 5.40e-03 3.43e+04 2.07e+00 bond pdb=" CA ILEA2 255 " pdb=" CB ILEA2 255 " ideal model delta sigma weight residual 1.539 1.531 0.008 5.40e-03 3.43e+04 2.05e+00 bond pdb=" C VALD2 268 " pdb=" N THRD2 269 " ideal model delta sigma weight residual 1.332 1.313 0.020 1.40e-02 5.10e+03 2.02e+00 ... (remaining 21109 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.79: 28033 2.79 - 5.57: 595 5.57 - 8.36: 46 8.36 - 11.14: 0 11.14 - 13.93: 9 Bond angle restraints: 28683 Sorted by residual: angle pdb=" N GLYF2 103 " pdb=" CA GLYF2 103 " pdb=" C GLYF2 103 " ideal model delta sigma weight residual 113.18 99.25 13.93 2.37e+00 1.78e-01 3.45e+01 angle pdb=" N GLYC2 103 " pdb=" CA GLYC2 103 " pdb=" C GLYC2 103 " ideal model delta sigma weight residual 113.18 99.26 13.92 2.37e+00 1.78e-01 3.45e+01 angle pdb=" N GLYE2 103 " pdb=" CA GLYE2 103 " pdb=" C GLYE2 103 " ideal model delta sigma weight residual 113.18 99.27 13.91 2.37e+00 1.78e-01 3.45e+01 angle pdb=" N GLYG2 103 " pdb=" CA GLYG2 103 " pdb=" C GLYG2 103 " ideal model delta sigma weight residual 113.18 99.27 13.91 2.37e+00 1.78e-01 3.44e+01 angle pdb=" N GLYH2 103 " pdb=" CA GLYH2 103 " pdb=" C GLYH2 103 " ideal model delta sigma weight residual 113.18 99.29 13.89 2.37e+00 1.78e-01 3.44e+01 ... (remaining 28678 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.54: 10068 12.54 - 25.09: 1488 25.09 - 37.63: 585 37.63 - 50.17: 216 50.17 - 62.71: 54 Dihedral angle restraints: 12411 sinusoidal: 4599 harmonic: 7812 Sorted by residual: dihedral pdb=" CA THRA2 102 " pdb=" C THRA2 102 " pdb=" N GLYA2 103 " pdb=" CA GLYA2 103 " ideal model delta harmonic sigma weight residual -180.00 -129.60 -50.40 0 5.00e+00 4.00e-02 1.02e+02 dihedral pdb=" CA THRB2 102 " pdb=" C THRB2 102 " pdb=" N GLYB2 103 " pdb=" CA GLYB2 103 " ideal model delta harmonic sigma weight residual 180.00 -129.63 -50.37 0 5.00e+00 4.00e-02 1.02e+02 dihedral pdb=" CA THRH2 102 " pdb=" C THRH2 102 " pdb=" N GLYH2 103 " pdb=" CA GLYH2 103 " ideal model delta harmonic sigma weight residual -180.00 -129.63 -50.37 0 5.00e+00 4.00e-02 1.02e+02 ... (remaining 12408 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1867 0.033 - 0.065: 1085 0.065 - 0.097: 435 0.097 - 0.130: 177 0.130 - 0.162: 45 Chirality restraints: 3609 Sorted by residual: chirality pdb=" CA HISF2 116 " pdb=" N HISF2 116 " pdb=" C HISF2 116 " pdb=" CB HISF2 116 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.60e-01 chirality pdb=" CA HISH2 116 " pdb=" N HISH2 116 " pdb=" C HISH2 116 " pdb=" CB HISH2 116 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.50e-01 chirality pdb=" CA HISG2 116 " pdb=" N HISG2 116 " pdb=" C HISG2 116 " pdb=" CB HISG2 116 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.49e-01 ... (remaining 3606 not shown) Planarity restraints: 3555 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLYB2 24 " -0.046 5.00e-02 4.00e+02 7.01e-02 7.85e+00 pdb=" N PROB2 25 " 0.121 5.00e-02 4.00e+02 pdb=" CA PROB2 25 " -0.036 5.00e-02 4.00e+02 pdb=" CD PROB2 25 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLYI2 24 " -0.046 5.00e-02 4.00e+02 6.99e-02 7.82e+00 pdb=" N PROI2 25 " 0.121 5.00e-02 4.00e+02 pdb=" CA PROI2 25 " -0.036 5.00e-02 4.00e+02 pdb=" CD PROI2 25 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLYF2 24 " 0.046 5.00e-02 4.00e+02 6.99e-02 7.81e+00 pdb=" N PROF2 25 " -0.121 5.00e-02 4.00e+02 pdb=" CA PROF2 25 " 0.036 5.00e-02 4.00e+02 pdb=" CD PROF2 25 " 0.039 5.00e-02 4.00e+02 ... (remaining 3552 not shown) Histogram of nonbonded interaction distances: 2.46 - 2.94: 11397 2.94 - 3.43: 25384 3.43 - 3.92: 33788 3.92 - 4.41: 39817 4.41 - 4.90: 61437 Nonbonded interactions: 171823 Sorted by model distance: nonbonded pdb=" N GLYD2 103 " pdb=" N ALAD2 104 " model vdw 2.456 2.560 nonbonded pdb=" N GLYF2 103 " pdb=" N ALAF2 104 " model vdw 2.456 2.560 nonbonded pdb=" N GLYB2 103 " pdb=" N ALAB2 104 " model vdw 2.456 2.560 nonbonded pdb=" N GLYI2 103 " pdb=" N ALAI2 104 " model vdw 2.456 2.560 nonbonded pdb=" N GLYC2 103 " pdb=" N ALAC2 104 " model vdw 2.456 2.560 ... (remaining 171818 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A2' selection = chain 'B2' selection = chain 'C2' selection = chain 'D2' selection = chain 'E2' selection = chain 'F2' selection = chain 'G2' selection = chain 'H2' selection = chain 'I2' } 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 group one per residue 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: 9.270 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: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 15.770 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 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 : 0.010 0.052 21114 Z= 0.451 Angle : 0.996 13.927 28683 Z= 0.522 Chirality : 0.050 0.162 3609 Planarity : 0.007 0.070 3555 Dihedral : 15.326 62.712 7407 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 18.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.36 % Favored : 89.64 % Rotamer: Outliers : 0.41 % Allowed : 17.89 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.52 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.16), residues: 2781 helix: 0.16 (0.11), residues: 2223 sheet: None (None), residues: 0 loop : -4.26 (0.22), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARGC2 67 TYR 0.010 0.003 TYRE2 195 PHE 0.021 0.002 PHEA2 316 TRP 0.007 0.002 TRPG2 19 HIS 0.010 0.005 HISD2 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00999 / 0.45 (21114) covalent geometry : angle 0.99590 / 0.52 (28683) hydrogen bonds : bond 0.10821 / 7.33 ( 1872) hydrogen bonds : angle 6.62956 / 4.75 ( 5589) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 546 time to evaluate : 0.687 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: A2 317 THR cc_start: 0.8695 (m) cc_final: 0.8443 (t) REVERT: B2 18 GLN cc_start: 0.8211 (mp-120) cc_final: 0.7732 (pp30) REVERT: B2 275 GLN cc_start: 0.8862 (mp-120) cc_final: 0.8646 (mp10) REVERT: B2 292 MET cc_start: 0.8233 (mtt) cc_final: 0.8009 (mtt) REVERT: C2 206 ARG cc_start: 0.9094 (ttm-80) cc_final: 0.8696 (ttm-80) REVERT: D2 206 ARG cc_start: 0.9060 (ttm-80) cc_final: 0.8846 (ttm-80) REVERT: D2 230 GLN cc_start: 0.7674 (pt0) cc_final: 0.7366 (pt0) REVERT: E2 203 LYS cc_start: 0.9303 (mmmm) cc_final: 0.8943 (mmmm) REVERT: E2 230 GLN cc_start: 0.7722 (pt0) cc_final: 0.7447 (pt0) REVERT: E2 275 GLN cc_start: 0.8655 (mp-120) cc_final: 0.8420 (mp10) REVERT: E2 292 MET cc_start: 0.8547 (mtt) cc_final: 0.8240 (mtt) REVERT: E2 317 THR cc_start: 0.8735 (m) cc_final: 0.8529 (t) REVERT: F2 199 ASP cc_start: 0.7814 (t70) cc_final: 0.6216 (t0) REVERT: F2 206 ARG cc_start: 0.9065 (ttm-80) cc_final: 0.8797 (ttm-80) REVERT: F2 275 GLN cc_start: 0.8672 (mp-120) cc_final: 0.8428 (mp10) REVERT: F2 317 THR cc_start: 0.8808 (m) cc_final: 0.8521 (t) REVERT: G2 191 GLU cc_start: 0.8726 (tm-30) cc_final: 0.8426 (tp30) REVERT: G2 230 GLN cc_start: 0.7468 (pt0) cc_final: 0.7232 (pt0) REVERT: H2 109 LYS cc_start: 0.8439 (mttm) cc_final: 0.8185 (tptt) REVERT: H2 191 GLU cc_start: 0.8757 (tm-30) cc_final: 0.8425 (tm-30) REVERT: H2 195 TYR cc_start: 0.8915 (m-10) cc_final: 0.8416 (m-80) REVERT: H2 199 ASP cc_start: 0.7925 (t70) cc_final: 0.7525 (t0) REVERT: H2 204 PHE cc_start: 0.8019 (m-80) cc_final: 0.7797 (m-10) REVERT: H2 206 ARG cc_start: 0.8994 (ttm-80) cc_final: 0.8708 (ttm-80) REVERT: I2 57 MET cc_start: 0.8510 (ttt) cc_final: 0.8228 (tmm) outliers start: 9 outliers final: 1 residues processed: 555 average time/residue: 0.1840 time to fit residues: 145.7643 Evaluate side-chains 435 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 434 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F2 residue 37 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.4980 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A2 172 ASN ** A2 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2 172 ASN ** B2 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2 275 GLN ** B2 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2 172 ASN ** C2 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 172 ASN ** D2 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2 51 ASN E2 172 ASN E2 275 GLN ** E2 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F2 18 GLN F2 172 ASN F2 275 GLN F2 288 ASN G2 18 GLN G2 172 ASN ** G2 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H2 18 GLN H2 172 ASN H2 230 GLN H2 231 HIS ** H2 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I2 172 ASN I2 230 GLN ** I2 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.057146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.049159 restraints weight = 88286.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.050611 restraints weight = 47083.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.051538 restraints weight = 30481.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.052155 restraints weight = 22664.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.052520 restraints weight = 18446.632| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 21114 Z= 0.206 Angle : 0.829 12.259 28683 Z= 0.427 Chirality : 0.044 0.190 3609 Planarity : 0.006 0.067 3555 Dihedral : 6.823 48.969 2909 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 3.18 % Allowed : 25.31 % Favored : 71.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.66 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.16), residues: 2781 helix: 0.77 (0.11), residues: 2169 sheet: None (None), residues: 0 loop : -3.74 (0.22), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARGG2 184 TYR 0.018 0.003 TYRI2 195 PHE 0.023 0.002 PHEG2 316 TRP 0.007 0.001 TRPG2 325 HIS 0.012 0.003 HISB2 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.21 (21114) covalent geometry : angle 0.82853 / 0.43 (28683) hydrogen bonds : bond 0.06172 / 4.23 ( 1872) hydrogen bonds : angle 5.14818 / 3.70 ( 5589) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 515 time to evaluate : 0.733 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: A2 57 MET cc_start: 0.7959 (tmm) cc_final: 0.7223 (tmm) REVERT: A2 233 MET cc_start: 0.6881 (ptp) cc_final: 0.6513 (ptp) REVERT: B2 158 ASP cc_start: 0.7678 (p0) cc_final: 0.7459 (p0) REVERT: C2 57 MET cc_start: 0.7723 (tmm) cc_final: 0.7207 (tmm) REVERT: C2 184 ARG cc_start: 0.7917 (ttm-80) cc_final: 0.7668 (mtt90) REVERT: D2 275 GLN cc_start: 0.8033 (mp10) cc_final: 0.7811 (mp10) REVERT: E2 67 ARG cc_start: 0.6762 (ttp80) cc_final: 0.6495 (ttp80) REVERT: E2 184 ARG cc_start: 0.7800 (ttm110) cc_final: 0.7314 (mtt90) REVERT: E2 199 ASP cc_start: 0.7539 (t70) cc_final: 0.6845 (t0) REVERT: E2 203 LYS cc_start: 0.9099 (mmmm) cc_final: 0.8734 (mmmm) REVERT: E2 206 ARG cc_start: 0.8455 (ttm-80) cc_final: 0.8090 (tpp-160) REVERT: E2 301 LEU cc_start: 0.9194 (pp) cc_final: 0.8987 (pp) REVERT: F2 147 ARG cc_start: 0.8517 (mmm-85) cc_final: 0.8276 (mmm-85) REVERT: F2 317 THR cc_start: 0.8584 (m) cc_final: 0.8373 (t) REVERT: G2 240 GLU cc_start: 0.8450 (pp20) cc_final: 0.8218 (pp20) REVERT: H2 57 MET cc_start: 0.7313 (tmm) cc_final: 0.6856 (tmm) REVERT: H2 109 LYS cc_start: 0.8379 (mttm) cc_final: 0.8111 (tptt) REVERT: H2 195 TYR cc_start: 0.8967 (m-10) cc_final: 0.8299 (m-10) REVERT: H2 230 GLN cc_start: 0.6780 (pt0) cc_final: 0.6170 (pt0) REVERT: I2 292 MET cc_start: 0.8013 (mtt) cc_final: 0.7748 (mtt) outliers start: 69 outliers final: 24 residues processed: 555 average time/residue: 0.1717 time to fit residues: 140.6823 Evaluate side-chains 473 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 449 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A2 residue 116 HIS Chi-restraints excluded: chain A2 residue 136 ILE Chi-restraints excluded: chain A2 residue 323 LEU Chi-restraints excluded: chain B2 residue 136 ILE Chi-restraints excluded: chain C2 residue 136 ILE Chi-restraints excluded: chain C2 residue 150 GLU Chi-restraints excluded: chain D2 residue 136 ILE Chi-restraints excluded: chain D2 residue 176 ILE Chi-restraints excluded: chain E2 residue 51 ASN Chi-restraints excluded: chain E2 residue 136 ILE Chi-restraints excluded: chain F2 residue 18 GLN Chi-restraints excluded: chain F2 residue 136 ILE Chi-restraints excluded: chain G2 residue 102 THR Chi-restraints excluded: chain G2 residue 136 ILE Chi-restraints excluded: chain G2 residue 176 ILE Chi-restraints excluded: chain G2 residue 179 ASP Chi-restraints excluded: chain G2 residue 285 LEU Chi-restraints excluded: chain H2 residue 18 GLN Chi-restraints excluded: chain H2 residue 136 ILE Chi-restraints excluded: chain H2 residue 311 LEU Chi-restraints excluded: chain I2 residue 136 ILE Chi-restraints excluded: chain I2 residue 140 VAL Chi-restraints excluded: chain I2 residue 143 LYS Chi-restraints excluded: chain I2 residue 160 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 202 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 chunk 160 optimal weight: 0.9990 chunk 265 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 81 optimal weight: 0.6980 chunk 263 optimal weight: 2.9990 chunk 175 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 137 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A2 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2 51 ASN ** E2 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F2 18 GLN ** G2 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H2 18 GLN H2 164 GLN ** H2 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.056727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.048684 restraints weight = 88537.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.050151 restraints weight = 45269.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.051091 restraints weight = 28678.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.051702 restraints weight = 21041.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.052100 restraints weight = 17007.175| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 21114 Z= 0.209 Angle : 0.827 11.622 28683 Z= 0.422 Chirality : 0.043 0.152 3609 Planarity : 0.006 0.065 3555 Dihedral : 6.588 46.500 2907 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 4.61 % Allowed : 25.63 % Favored : 69.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.66 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.16), residues: 2781 helix: 0.94 (0.11), residues: 2160 sheet: None (None), residues: 0 loop : -3.33 (0.24), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARGC2 67 TYR 0.025 0.002 TYRI2 195 PHE 0.024 0.002 PHEF2 316 TRP 0.007 0.001 TRPG2 325 HIS 0.007 0.002 HISD2 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.21 (21114) covalent geometry : angle 0.82654 / 0.42 (28683) hydrogen bonds : bond 0.06028 / 4.13 ( 1872) hydrogen bonds : angle 5.03036 / 3.61 ( 5589) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 496 time to evaluate : 0.716 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: A2 57 MET cc_start: 0.8013 (tmm) cc_final: 0.7420 (tmm) REVERT: A2 233 MET cc_start: 0.6699 (ptp) cc_final: 0.6092 (ptp) REVERT: C2 57 MET cc_start: 0.7768 (tmm) cc_final: 0.7250 (tmm) REVERT: D2 275 GLN cc_start: 0.8104 (mp10) cc_final: 0.7850 (mp10) REVERT: E2 67 ARG cc_start: 0.6806 (ttp80) cc_final: 0.6574 (ttp80) REVERT: E2 206 ARG cc_start: 0.8480 (ttm-80) cc_final: 0.8124 (tpp-160) REVERT: E2 275 GLN cc_start: 0.7939 (mp10) cc_final: 0.7704 (mp10) REVERT: F2 191 GLU cc_start: 0.8019 (tp30) cc_final: 0.7754 (tp30) REVERT: F2 281 MET cc_start: 0.8480 (mtm) cc_final: 0.8257 (ttm) REVERT: F2 317 THR cc_start: 0.8541 (m) cc_final: 0.8328 (t) REVERT: G2 191 GLU cc_start: 0.7829 (tp30) cc_final: 0.7217 (tp30) REVERT: G2 195 TYR cc_start: 0.9047 (m-10) cc_final: 0.8619 (m-10) REVERT: G2 240 GLU cc_start: 0.8448 (pp20) cc_final: 0.8235 (pp20) REVERT: H2 57 MET cc_start: 0.7506 (tmm) cc_final: 0.6988 (tmm) REVERT: H2 109 LYS cc_start: 0.8368 (mttm) cc_final: 0.8097 (tptt) REVERT: H2 158 ASP cc_start: 0.8507 (t0) cc_final: 0.8259 (t0) REVERT: H2 191 GLU cc_start: 0.8006 (tm-30) cc_final: 0.7432 (tp30) REVERT: H2 195 TYR cc_start: 0.9020 (m-10) cc_final: 0.8657 (m-10) REVERT: I2 292 MET cc_start: 0.7827 (mtt) cc_final: 0.7526 (mtt) outliers start: 100 outliers final: 37 residues processed: 562 average time/residue: 0.1700 time to fit residues: 140.2969 Evaluate side-chains 505 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 468 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A2 residue 102 THR Chi-restraints excluded: chain A2 residue 116 HIS Chi-restraints excluded: chain A2 residue 136 ILE Chi-restraints excluded: chain A2 residue 285 LEU Chi-restraints excluded: chain A2 residue 311 LEU Chi-restraints excluded: chain A2 residue 323 LEU Chi-restraints excluded: chain B2 residue 102 THR Chi-restraints excluded: chain B2 residue 116 HIS Chi-restraints excluded: chain B2 residue 136 ILE Chi-restraints excluded: chain B2 residue 317 THR Chi-restraints excluded: chain C2 residue 46 LEU Chi-restraints excluded: chain C2 residue 102 THR Chi-restraints excluded: chain C2 residue 116 HIS Chi-restraints excluded: chain C2 residue 136 ILE Chi-restraints excluded: chain D2 residue 102 THR Chi-restraints excluded: chain D2 residue 136 ILE Chi-restraints excluded: chain D2 residue 311 LEU Chi-restraints excluded: chain E2 residue 54 LEU Chi-restraints excluded: chain E2 residue 102 THR Chi-restraints excluded: chain E2 residue 136 ILE Chi-restraints excluded: chain E2 residue 150 GLU Chi-restraints excluded: chain E2 residue 311 LEU Chi-restraints excluded: chain F2 residue 102 THR Chi-restraints excluded: chain F2 residue 116 HIS Chi-restraints excluded: chain F2 residue 136 ILE Chi-restraints excluded: chain G2 residue 136 ILE Chi-restraints excluded: chain G2 residue 176 ILE Chi-restraints excluded: chain G2 residue 179 ASP Chi-restraints excluded: chain G2 residue 285 LEU Chi-restraints excluded: chain H2 residue 116 HIS Chi-restraints excluded: chain H2 residue 136 ILE Chi-restraints excluded: chain H2 residue 311 LEU Chi-restraints excluded: chain I2 residue 37 LEU Chi-restraints excluded: chain I2 residue 102 THR Chi-restraints excluded: chain I2 residue 136 ILE Chi-restraints excluded: chain I2 residue 140 VAL Chi-restraints excluded: chain I2 residue 160 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 66 optimal weight: 1.9990 chunk 180 optimal weight: 0.0060 chunk 215 optimal weight: 0.7980 chunk 75 optimal weight: 0.2980 chunk 152 optimal weight: 0.9980 chunk 269 optimal weight: 2.9990 chunk 96 optimal weight: 0.5980 chunk 185 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 187 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A2 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G2 288 ASN H2 18 GLN ** H2 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I2 288 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.058249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.050305 restraints weight = 87355.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.051804 restraints weight = 43687.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.052757 restraints weight = 27280.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.053388 restraints weight = 19762.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.053781 restraints weight = 15807.456| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 21114 Z= 0.177 Angle : 0.787 10.379 28683 Z= 0.399 Chirality : 0.041 0.157 3609 Planarity : 0.006 0.063 3555 Dihedral : 6.242 44.398 2907 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 4.24 % Allowed : 27.06 % Favored : 68.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.59 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.16), residues: 2781 helix: 1.14 (0.11), residues: 2151 sheet: None (None), residues: 0 loop : -3.18 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARGI2 67 TYR 0.014 0.002 TYRF2 195 PHE 0.022 0.002 PHEG2 316 TRP 0.008 0.001 TRPB2 325 HIS 0.012 0.002 HISC2 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.18 (21114) covalent geometry : angle 0.78734 / 0.40 (28683) hydrogen bonds : bond 0.05648 / 3.87 ( 1872) hydrogen bonds : angle 4.88027 / 3.51 ( 5589) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 518 time to evaluate : 0.777 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: A2 57 MET cc_start: 0.7955 (tmm) cc_final: 0.7585 (tmm) REVERT: A2 233 MET cc_start: 0.6491 (ptp) cc_final: 0.5883 (ptp) REVERT: C2 57 MET cc_start: 0.7807 (tmm) cc_final: 0.7320 (tmm) REVERT: D2 57 MET cc_start: 0.8134 (tpp) cc_final: 0.7752 (tpp) REVERT: D2 67 ARG cc_start: 0.6876 (ttp80) cc_final: 0.6663 (ttp80) REVERT: D2 69 LEU cc_start: 0.8493 (tp) cc_final: 0.8286 (tp) REVERT: D2 273 THR cc_start: 0.7777 (t) cc_final: 0.7438 (t) REVERT: D2 275 GLN cc_start: 0.8055 (mp10) cc_final: 0.7774 (mp10) REVERT: E2 206 ARG cc_start: 0.8470 (ttm-80) cc_final: 0.8198 (tpp-160) REVERT: E2 275 GLN cc_start: 0.7928 (mp10) cc_final: 0.7711 (mp10) REVERT: F2 18 GLN cc_start: 0.7969 (mp10) cc_final: 0.7743 (mp10) REVERT: F2 147 ARG cc_start: 0.8638 (mmm-85) cc_final: 0.8392 (mmm-85) REVERT: F2 240 GLU cc_start: 0.7855 (pp20) cc_final: 0.7548 (pp20) REVERT: F2 275 GLN cc_start: 0.7853 (mp10) cc_final: 0.7648 (mp10) REVERT: F2 317 THR cc_start: 0.8475 (m) cc_final: 0.8204 (t) REVERT: G2 20 GLN cc_start: 0.8208 (mp10) cc_final: 0.7993 (mp10) REVERT: G2 191 GLU cc_start: 0.7858 (tp30) cc_final: 0.7629 (tp30) REVERT: G2 206 ARG cc_start: 0.8849 (ttm-80) cc_final: 0.8342 (ttt-90) REVERT: G2 275 GLN cc_start: 0.7865 (mp10) cc_final: 0.7579 (mp10) REVERT: H2 57 MET cc_start: 0.7544 (tmm) cc_final: 0.6954 (tmm) REVERT: H2 139 MET cc_start: 0.7292 (ptm) cc_final: 0.7078 (ptm) REVERT: H2 150 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7479 (mm-30) REVERT: H2 158 ASP cc_start: 0.8483 (t0) cc_final: 0.8163 (t0) REVERT: H2 191 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7347 (tp30) REVERT: H2 195 TYR cc_start: 0.9025 (OUTLIER) cc_final: 0.8626 (m-10) REVERT: H2 240 GLU cc_start: 0.8405 (pp20) cc_final: 0.7974 (pp20) REVERT: I2 191 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7639 (tm-30) REVERT: I2 206 ARG cc_start: 0.8560 (ttm170) cc_final: 0.8341 (ttt90) REVERT: I2 292 MET cc_start: 0.7656 (mtt) cc_final: 0.7370 (mtt) outliers start: 92 outliers final: 46 residues processed: 589 average time/residue: 0.1765 time to fit residues: 152.1483 Evaluate side-chains 530 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 483 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A2 residue 46 LEU Chi-restraints excluded: chain A2 residue 60 LEU Chi-restraints excluded: chain A2 residue 116 HIS Chi-restraints excluded: chain A2 residue 136 ILE Chi-restraints excluded: chain A2 residue 285 LEU Chi-restraints excluded: chain A2 residue 311 LEU Chi-restraints excluded: chain B2 residue 54 LEU Chi-restraints excluded: chain B2 residue 68 THR Chi-restraints excluded: chain B2 residue 116 HIS Chi-restraints excluded: chain B2 residue 136 ILE Chi-restraints excluded: chain B2 residue 301 LEU Chi-restraints excluded: chain B2 residue 317 THR Chi-restraints excluded: chain C2 residue 116 HIS Chi-restraints excluded: chain C2 residue 136 ILE Chi-restraints excluded: chain D2 residue 46 LEU Chi-restraints excluded: chain D2 residue 54 LEU Chi-restraints excluded: chain D2 residue 102 THR Chi-restraints excluded: chain D2 residue 136 ILE Chi-restraints excluded: chain D2 residue 301 LEU Chi-restraints excluded: chain D2 residue 311 LEU Chi-restraints excluded: chain E2 residue 46 LEU Chi-restraints excluded: chain E2 residue 136 ILE Chi-restraints excluded: chain E2 residue 139 MET Chi-restraints excluded: chain E2 residue 195 TYR Chi-restraints excluded: chain E2 residue 311 LEU Chi-restraints excluded: chain F2 residue 76 THR Chi-restraints excluded: chain F2 residue 77 ILE Chi-restraints excluded: chain F2 residue 102 THR Chi-restraints excluded: chain F2 residue 116 HIS Chi-restraints excluded: chain F2 residue 136 ILE Chi-restraints excluded: chain G2 residue 46 LEU Chi-restraints excluded: chain G2 residue 102 THR Chi-restraints excluded: chain G2 residue 136 ILE Chi-restraints excluded: chain G2 residue 179 ASP Chi-restraints excluded: chain G2 residue 285 LEU Chi-restraints excluded: chain H2 residue 46 LEU Chi-restraints excluded: chain H2 residue 102 THR Chi-restraints excluded: chain H2 residue 116 HIS Chi-restraints excluded: chain H2 residue 136 ILE Chi-restraints excluded: chain H2 residue 195 TYR Chi-restraints excluded: chain H2 residue 311 LEU Chi-restraints excluded: chain H2 residue 312 VAL Chi-restraints excluded: chain I2 residue 46 LEU Chi-restraints excluded: chain I2 residue 116 HIS Chi-restraints excluded: chain I2 residue 136 ILE Chi-restraints excluded: chain I2 residue 255 ILE Chi-restraints excluded: chain I2 residue 312 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 6 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 172 optimal weight: 0.8980 chunk 173 optimal weight: 0.5980 chunk 257 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 218 optimal weight: 0.9990 chunk 109 optimal weight: 0.5980 chunk 201 optimal weight: 1.9990 chunk 153 optimal weight: 0.0970 chunk 75 optimal weight: 0.6980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A2 51 ASN ** A2 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2 288 ASN F2 164 GLN G2 164 GLN H2 116 HIS ** H2 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.058387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.050430 restraints weight = 86390.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.051931 restraints weight = 43294.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.052881 restraints weight = 27082.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.053487 restraints weight = 19677.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.053904 restraints weight = 15891.229| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 21114 Z= 0.181 Angle : 0.795 10.223 28683 Z= 0.403 Chirality : 0.041 0.154 3609 Planarity : 0.006 0.064 3555 Dihedral : 6.152 42.715 2907 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 4.56 % Allowed : 27.62 % Favored : 67.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.59 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.16), residues: 2781 helix: 1.22 (0.11), residues: 2151 sheet: None (None), residues: 0 loop : -2.98 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARGB2 67 TYR 0.017 0.002 TYRI2 195 PHE 0.038 0.002 PHED2 117 TRP 0.007 0.001 TRPB2 325 HIS 0.010 0.002 HISC2 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.18 (21114) covalent geometry : angle 0.79524 / 0.40 (28683) hydrogen bonds : bond 0.05595 / 3.83 ( 1872) hydrogen bonds : angle 4.83480 / 3.47 ( 5589) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 509 time to evaluate : 0.735 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: A2 57 MET cc_start: 0.7957 (tmm) cc_final: 0.7415 (tmm) REVERT: A2 233 MET cc_start: 0.6411 (ptp) cc_final: 0.5779 (ptp) REVERT: B2 305 VAL cc_start: 0.8271 (OUTLIER) cc_final: 0.8057 (m) REVERT: C2 57 MET cc_start: 0.8080 (tmm) cc_final: 0.7381 (tmm) REVERT: C2 85 ARG cc_start: 0.8357 (ttp-110) cc_final: 0.8011 (ttp-110) REVERT: C2 233 MET cc_start: 0.6513 (ptp) cc_final: 0.6165 (ptp) REVERT: D2 114 PHE cc_start: 0.8677 (t80) cc_final: 0.8073 (m-80) REVERT: D2 275 GLN cc_start: 0.8053 (mp10) cc_final: 0.7835 (mp10) REVERT: E2 184 ARG cc_start: 0.8009 (tpp80) cc_final: 0.7763 (mpp80) REVERT: E2 206 ARG cc_start: 0.8454 (ttm-80) cc_final: 0.8191 (tpp-160) REVERT: F2 240 GLU cc_start: 0.7866 (pp20) cc_final: 0.7640 (pp20) REVERT: F2 275 GLN cc_start: 0.7953 (mp10) cc_final: 0.7737 (mp10) REVERT: F2 317 THR cc_start: 0.8470 (m) cc_final: 0.8189 (t) REVERT: G2 98 MET cc_start: 0.8447 (mtt) cc_final: 0.8178 (mtt) REVERT: G2 206 ARG cc_start: 0.8879 (ttm-80) cc_final: 0.8511 (ttm-80) REVERT: H2 57 MET cc_start: 0.7619 (OUTLIER) cc_final: 0.7010 (tmm) REVERT: H2 135 ILE cc_start: 0.9357 (OUTLIER) cc_final: 0.9156 (tp) REVERT: H2 158 ASP cc_start: 0.8497 (t0) cc_final: 0.8254 (t0) REVERT: H2 184 ARG cc_start: 0.7496 (mtt90) cc_final: 0.7258 (mtt90) REVERT: H2 191 GLU cc_start: 0.8018 (tm-30) cc_final: 0.7391 (tp30) REVERT: H2 195 TYR cc_start: 0.9040 (OUTLIER) cc_final: 0.8640 (m-10) REVERT: H2 240 GLU cc_start: 0.8370 (pp20) cc_final: 0.8028 (pp20) REVERT: I2 292 MET cc_start: 0.7585 (mtt) cc_final: 0.7295 (mtt) outliers start: 99 outliers final: 68 residues processed: 579 average time/residue: 0.1699 time to fit residues: 145.6655 Evaluate side-chains 565 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 493 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A2 residue 46 LEU Chi-restraints excluded: chain A2 residue 51 ASN Chi-restraints excluded: chain A2 residue 60 LEU Chi-restraints excluded: chain A2 residue 102 THR Chi-restraints excluded: chain A2 residue 116 HIS Chi-restraints excluded: chain A2 residue 136 ILE Chi-restraints excluded: chain A2 residue 285 LEU Chi-restraints excluded: chain A2 residue 305 VAL Chi-restraints excluded: chain A2 residue 311 LEU Chi-restraints excluded: chain A2 residue 312 VAL Chi-restraints excluded: chain B2 residue 68 THR Chi-restraints excluded: chain B2 residue 102 THR Chi-restraints excluded: chain B2 residue 116 HIS Chi-restraints excluded: chain B2 residue 136 ILE Chi-restraints excluded: chain B2 residue 301 LEU Chi-restraints excluded: chain B2 residue 305 VAL Chi-restraints excluded: chain B2 residue 312 VAL Chi-restraints excluded: chain C2 residue 46 LEU Chi-restraints excluded: chain C2 residue 102 THR Chi-restraints excluded: chain C2 residue 136 ILE Chi-restraints excluded: chain D2 residue 46 LEU Chi-restraints excluded: chain D2 residue 54 LEU Chi-restraints excluded: chain D2 residue 68 THR Chi-restraints excluded: chain D2 residue 102 THR Chi-restraints excluded: chain D2 residue 116 HIS Chi-restraints excluded: chain D2 residue 136 ILE Chi-restraints excluded: chain D2 residue 285 LEU Chi-restraints excluded: chain D2 residue 301 LEU Chi-restraints excluded: chain D2 residue 311 LEU Chi-restraints excluded: chain E2 residue 46 LEU Chi-restraints excluded: chain E2 residue 54 LEU Chi-restraints excluded: chain E2 residue 102 THR Chi-restraints excluded: chain E2 residue 116 HIS Chi-restraints excluded: chain E2 residue 136 ILE Chi-restraints excluded: chain E2 residue 179 ASP Chi-restraints excluded: chain E2 residue 195 TYR Chi-restraints excluded: chain E2 residue 311 LEU Chi-restraints excluded: chain F2 residue 76 THR Chi-restraints excluded: chain F2 residue 77 ILE Chi-restraints excluded: chain F2 residue 116 HIS Chi-restraints excluded: chain F2 residue 136 ILE Chi-restraints excluded: chain F2 residue 235 ILE Chi-restraints excluded: chain G2 residue 46 LEU Chi-restraints excluded: chain G2 residue 102 THR Chi-restraints excluded: chain G2 residue 136 ILE Chi-restraints excluded: chain G2 residue 164 GLN Chi-restraints excluded: chain G2 residue 176 ILE Chi-restraints excluded: chain G2 residue 179 ASP Chi-restraints excluded: chain G2 residue 285 LEU Chi-restraints excluded: chain G2 residue 311 LEU Chi-restraints excluded: chain G2 residue 312 VAL Chi-restraints excluded: chain H2 residue 46 LEU Chi-restraints excluded: chain H2 residue 57 MET Chi-restraints excluded: chain H2 residue 76 THR Chi-restraints excluded: chain H2 residue 102 THR Chi-restraints excluded: chain H2 residue 114 PHE Chi-restraints excluded: chain H2 residue 116 HIS Chi-restraints excluded: chain H2 residue 135 ILE Chi-restraints excluded: chain H2 residue 136 ILE Chi-restraints excluded: chain H2 residue 176 ILE Chi-restraints excluded: chain H2 residue 195 TYR Chi-restraints excluded: chain H2 residue 235 ILE Chi-restraints excluded: chain H2 residue 311 LEU Chi-restraints excluded: chain I2 residue 46 LEU Chi-restraints excluded: chain I2 residue 102 THR Chi-restraints excluded: chain I2 residue 116 HIS Chi-restraints excluded: chain I2 residue 136 ILE Chi-restraints excluded: chain I2 residue 160 MET Chi-restraints excluded: chain I2 residue 179 ASP Chi-restraints excluded: chain I2 residue 199 ASP Chi-restraints excluded: chain I2 residue 255 ILE Chi-restraints excluded: chain I2 residue 312 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 277 optimal weight: 2.9990 chunk 160 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 89 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 105 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A2 51 ASN A2 190 GLN ** A2 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H2 164 GLN ** H2 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.057707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.049751 restraints weight = 86736.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.051239 restraints weight = 43477.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.052192 restraints weight = 27209.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.052817 restraints weight = 19755.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.053228 restraints weight = 15862.437| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 21114 Z= 0.207 Angle : 0.829 10.686 28683 Z= 0.423 Chirality : 0.042 0.173 3609 Planarity : 0.006 0.064 3555 Dihedral : 6.218 42.375 2907 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 5.07 % Allowed : 28.22 % Favored : 66.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.52 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.16), residues: 2781 helix: 1.20 (0.11), residues: 2151 sheet: None (None), residues: 0 loop : -2.90 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARGD2 185 TYR 0.018 0.002 TYRA2 195 PHE 0.026 0.002 PHEF2 117 TRP 0.007 0.001 TRPD2 325 HIS 0.007 0.002 HISF2 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.21 (21114) covalent geometry : angle 0.82944 / 0.42 (28683) hydrogen bonds : bond 0.05736 / 3.92 ( 1872) hydrogen bonds : angle 4.86764 / 3.50 ( 5589) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 517 time to evaluate : 0.653 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: A2 57 MET cc_start: 0.7971 (tmm) cc_final: 0.7422 (tmm) REVERT: A2 233 MET cc_start: 0.6482 (ptp) cc_final: 0.5762 (ptp) REVERT: B2 305 VAL cc_start: 0.8315 (OUTLIER) cc_final: 0.8101 (m) REVERT: C2 57 MET cc_start: 0.8157 (tmm) cc_final: 0.7461 (tmm) REVERT: C2 85 ARG cc_start: 0.8373 (ttp-110) cc_final: 0.8023 (ttp-110) REVERT: C2 191 GLU cc_start: 0.7854 (tp30) cc_final: 0.7577 (tp30) REVERT: C2 233 MET cc_start: 0.6562 (ptp) cc_final: 0.5909 (ptp) REVERT: E2 184 ARG cc_start: 0.8062 (tpp80) cc_final: 0.7822 (mpp80) REVERT: F2 240 GLU cc_start: 0.7828 (pp20) cc_final: 0.7560 (pp20) REVERT: F2 275 GLN cc_start: 0.8077 (mp10) cc_final: 0.7856 (mp10) REVERT: F2 317 THR cc_start: 0.8487 (m) cc_final: 0.8186 (t) REVERT: G2 98 MET cc_start: 0.8465 (mtt) cc_final: 0.8182 (mtt) REVERT: G2 195 TYR cc_start: 0.9050 (m-80) cc_final: 0.8775 (m-10) REVERT: H2 57 MET cc_start: 0.7681 (OUTLIER) cc_final: 0.7055 (tmm) REVERT: H2 116 HIS cc_start: 0.8571 (OUTLIER) cc_final: 0.8264 (t-90) REVERT: H2 150 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7683 (mm-30) REVERT: H2 158 ASP cc_start: 0.8547 (t0) cc_final: 0.8302 (t0) REVERT: H2 191 GLU cc_start: 0.7992 (tm-30) cc_final: 0.7371 (tp30) REVERT: H2 195 TYR cc_start: 0.9053 (OUTLIER) cc_final: 0.8671 (m-10) REVERT: H2 240 GLU cc_start: 0.8402 (pp20) cc_final: 0.8026 (pp20) REVERT: I2 292 MET cc_start: 0.7572 (mtt) cc_final: 0.7278 (mtt) outliers start: 110 outliers final: 80 residues processed: 602 average time/residue: 0.1750 time to fit residues: 154.3098 Evaluate side-chains 577 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 493 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A2 residue 46 LEU Chi-restraints excluded: chain A2 residue 51 ASN Chi-restraints excluded: chain A2 residue 102 THR Chi-restraints excluded: chain A2 residue 116 HIS Chi-restraints excluded: chain A2 residue 136 ILE Chi-restraints excluded: chain A2 residue 285 LEU Chi-restraints excluded: chain A2 residue 305 VAL Chi-restraints excluded: chain A2 residue 311 LEU Chi-restraints excluded: chain A2 residue 312 VAL Chi-restraints excluded: chain B2 residue 54 LEU Chi-restraints excluded: chain B2 residue 59 LEU Chi-restraints excluded: chain B2 residue 68 THR Chi-restraints excluded: chain B2 residue 102 THR Chi-restraints excluded: chain B2 residue 116 HIS Chi-restraints excluded: chain B2 residue 136 ILE Chi-restraints excluded: chain B2 residue 301 LEU Chi-restraints excluded: chain B2 residue 305 VAL Chi-restraints excluded: chain B2 residue 312 VAL Chi-restraints excluded: chain B2 residue 317 THR Chi-restraints excluded: chain C2 residue 46 LEU Chi-restraints excluded: chain C2 residue 76 THR Chi-restraints excluded: chain C2 residue 77 ILE Chi-restraints excluded: chain C2 residue 102 THR Chi-restraints excluded: chain C2 residue 116 HIS Chi-restraints excluded: chain C2 residue 136 ILE Chi-restraints excluded: chain C2 residue 311 LEU Chi-restraints excluded: chain C2 residue 312 VAL Chi-restraints excluded: chain D2 residue 46 LEU Chi-restraints excluded: chain D2 residue 54 LEU Chi-restraints excluded: chain D2 residue 68 THR Chi-restraints excluded: chain D2 residue 102 THR Chi-restraints excluded: chain D2 residue 116 HIS Chi-restraints excluded: chain D2 residue 119 VAL Chi-restraints excluded: chain D2 residue 136 ILE Chi-restraints excluded: chain D2 residue 285 LEU Chi-restraints excluded: chain D2 residue 301 LEU Chi-restraints excluded: chain D2 residue 311 LEU Chi-restraints excluded: chain D2 residue 312 VAL Chi-restraints excluded: chain E2 residue 46 LEU Chi-restraints excluded: chain E2 residue 77 ILE Chi-restraints excluded: chain E2 residue 102 THR Chi-restraints excluded: chain E2 residue 116 HIS Chi-restraints excluded: chain E2 residue 136 ILE Chi-restraints excluded: chain E2 residue 179 ASP Chi-restraints excluded: chain E2 residue 195 TYR Chi-restraints excluded: chain E2 residue 311 LEU Chi-restraints excluded: chain F2 residue 76 THR Chi-restraints excluded: chain F2 residue 77 ILE Chi-restraints excluded: chain F2 residue 102 THR Chi-restraints excluded: chain F2 residue 116 HIS Chi-restraints excluded: chain F2 residue 136 ILE Chi-restraints excluded: chain F2 residue 235 ILE Chi-restraints excluded: chain F2 residue 312 VAL Chi-restraints excluded: chain G2 residue 46 LEU Chi-restraints excluded: chain G2 residue 102 THR Chi-restraints excluded: chain G2 residue 136 ILE Chi-restraints excluded: chain G2 residue 176 ILE Chi-restraints excluded: chain G2 residue 179 ASP Chi-restraints excluded: chain G2 residue 235 ILE Chi-restraints excluded: chain G2 residue 285 LEU Chi-restraints excluded: chain G2 residue 311 LEU Chi-restraints excluded: chain G2 residue 312 VAL Chi-restraints excluded: chain G2 residue 314 LEU Chi-restraints excluded: chain H2 residue 46 LEU Chi-restraints excluded: chain H2 residue 57 MET Chi-restraints excluded: chain H2 residue 68 THR Chi-restraints excluded: chain H2 residue 76 THR Chi-restraints excluded: chain H2 residue 77 ILE Chi-restraints excluded: chain H2 residue 102 THR Chi-restraints excluded: chain H2 residue 116 HIS Chi-restraints excluded: chain H2 residue 136 ILE Chi-restraints excluded: chain H2 residue 176 ILE Chi-restraints excluded: chain H2 residue 195 TYR Chi-restraints excluded: chain H2 residue 235 ILE Chi-restraints excluded: chain H2 residue 311 LEU Chi-restraints excluded: chain H2 residue 312 VAL Chi-restraints excluded: chain I2 residue 46 LEU Chi-restraints excluded: chain I2 residue 102 THR Chi-restraints excluded: chain I2 residue 116 HIS Chi-restraints excluded: chain I2 residue 136 ILE Chi-restraints excluded: chain I2 residue 160 MET Chi-restraints excluded: chain I2 residue 179 ASP Chi-restraints excluded: chain I2 residue 255 ILE Chi-restraints excluded: chain I2 residue 312 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 152 optimal weight: 0.6980 chunk 66 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 252 optimal weight: 0.9980 chunk 243 optimal weight: 0.5980 chunk 12 optimal weight: 0.0670 chunk 25 optimal weight: 0.7980 chunk 269 optimal weight: 0.3980 chunk 239 optimal weight: 0.5980 chunk 221 optimal weight: 2.9990 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A2 51 ASN A2 190 GLN ** A2 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F2 164 GLN F2 190 GLN G2 164 GLN H2 116 HIS ** H2 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.059175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.051001 restraints weight = 86208.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.052518 restraints weight = 43533.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.053484 restraints weight = 27397.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.054115 restraints weight = 20050.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.054525 restraints weight = 16197.607| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 21114 Z= 0.177 Angle : 0.823 10.049 28683 Z= 0.417 Chirality : 0.042 0.197 3609 Planarity : 0.006 0.062 3555 Dihedral : 6.113 39.092 2907 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 4.66 % Allowed : 29.55 % Favored : 65.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.52 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.16), residues: 2781 helix: 1.27 (0.11), residues: 2151 sheet: None (None), residues: 0 loop : -2.80 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARGB2 67 TYR 0.013 0.002 TYRA2 195 PHE 0.039 0.002 PHEC2 117 TRP 0.007 0.001 TRPB2 325 HIS 0.007 0.002 HISC2 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.18 (21114) covalent geometry : angle 0.82294 / 0.42 (28683) hydrogen bonds : bond 0.05495 / 3.76 ( 1872) hydrogen bonds : angle 4.77275 / 3.44 ( 5589) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 513 time to evaluate : 0.772 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: A2 57 MET cc_start: 0.7947 (tmm) cc_final: 0.7403 (tmm) REVERT: B2 191 GLU cc_start: 0.7872 (tp30) cc_final: 0.7480 (tp30) REVERT: B2 305 VAL cc_start: 0.8153 (OUTLIER) cc_final: 0.7928 (m) REVERT: B2 328 ARG cc_start: 0.6403 (tmm160) cc_final: 0.5805 (tmt170) REVERT: C2 57 MET cc_start: 0.8127 (tmm) cc_final: 0.7435 (tmm) REVERT: C2 85 ARG cc_start: 0.8371 (ttp-110) cc_final: 0.8009 (ttp-110) REVERT: C2 233 MET cc_start: 0.6527 (ptp) cc_final: 0.5806 (ptp) REVERT: D2 191 GLU cc_start: 0.8105 (tp30) cc_final: 0.7193 (tp30) REVERT: D2 195 TYR cc_start: 0.9005 (OUTLIER) cc_final: 0.8509 (m-10) REVERT: E2 184 ARG cc_start: 0.8046 (tpp80) cc_final: 0.7764 (mpp80) REVERT: E2 206 ARG cc_start: 0.8662 (ttm-80) cc_final: 0.8373 (ttm-80) REVERT: F2 114 PHE cc_start: 0.8711 (OUTLIER) cc_final: 0.8328 (m-80) REVERT: F2 184 ARG cc_start: 0.7517 (OUTLIER) cc_final: 0.7100 (mpp80) REVERT: F2 317 THR cc_start: 0.8325 (m) cc_final: 0.8067 (t) REVERT: G2 98 MET cc_start: 0.8479 (mtt) cc_final: 0.8181 (mtt) REVERT: G2 195 TYR cc_start: 0.9094 (m-80) cc_final: 0.8792 (m-10) REVERT: G2 206 ARG cc_start: 0.8873 (ttm-80) cc_final: 0.8513 (ttm-80) REVERT: H2 57 MET cc_start: 0.7684 (OUTLIER) cc_final: 0.7136 (tmm) REVERT: H2 67 ARG cc_start: 0.7381 (tmm-80) cc_final: 0.6910 (tmm-80) REVERT: H2 158 ASP cc_start: 0.8499 (t0) cc_final: 0.8219 (t0) REVERT: H2 191 GLU cc_start: 0.7985 (tm-30) cc_final: 0.7281 (tp30) REVERT: H2 195 TYR cc_start: 0.9070 (OUTLIER) cc_final: 0.8635 (m-10) REVERT: I2 187 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8444 (mm-30) REVERT: I2 292 MET cc_start: 0.7436 (mtt) cc_final: 0.7115 (mtt) outliers start: 101 outliers final: 74 residues processed: 588 average time/residue: 0.1744 time to fit residues: 150.6859 Evaluate side-chains 576 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 496 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A2 residue 46 LEU Chi-restraints excluded: chain A2 residue 76 THR Chi-restraints excluded: chain A2 residue 102 THR Chi-restraints excluded: chain A2 residue 116 HIS Chi-restraints excluded: chain A2 residue 136 ILE Chi-restraints excluded: chain A2 residue 285 LEU Chi-restraints excluded: chain A2 residue 305 VAL Chi-restraints excluded: chain A2 residue 311 LEU Chi-restraints excluded: chain A2 residue 312 VAL Chi-restraints excluded: chain B2 residue 54 LEU Chi-restraints excluded: chain B2 residue 59 LEU Chi-restraints excluded: chain B2 residue 68 THR Chi-restraints excluded: chain B2 residue 102 THR Chi-restraints excluded: chain B2 residue 116 HIS Chi-restraints excluded: chain B2 residue 136 ILE Chi-restraints excluded: chain B2 residue 301 LEU Chi-restraints excluded: chain B2 residue 305 VAL Chi-restraints excluded: chain B2 residue 312 VAL Chi-restraints excluded: chain B2 residue 317 THR Chi-restraints excluded: chain C2 residue 46 LEU Chi-restraints excluded: chain C2 residue 76 THR Chi-restraints excluded: chain C2 residue 77 ILE Chi-restraints excluded: chain C2 residue 102 THR Chi-restraints excluded: chain C2 residue 116 HIS Chi-restraints excluded: chain C2 residue 136 ILE Chi-restraints excluded: chain C2 residue 301 LEU Chi-restraints excluded: chain C2 residue 311 LEU Chi-restraints excluded: chain D2 residue 46 LEU Chi-restraints excluded: chain D2 residue 54 LEU Chi-restraints excluded: chain D2 residue 102 THR Chi-restraints excluded: chain D2 residue 136 ILE Chi-restraints excluded: chain D2 residue 195 TYR Chi-restraints excluded: chain D2 residue 301 LEU Chi-restraints excluded: chain D2 residue 311 LEU Chi-restraints excluded: chain D2 residue 312 VAL Chi-restraints excluded: chain E2 residue 54 LEU Chi-restraints excluded: chain E2 residue 77 ILE Chi-restraints excluded: chain E2 residue 102 THR Chi-restraints excluded: chain E2 residue 116 HIS Chi-restraints excluded: chain E2 residue 136 ILE Chi-restraints excluded: chain E2 residue 179 ASP Chi-restraints excluded: chain E2 residue 195 TYR Chi-restraints excluded: chain E2 residue 311 LEU Chi-restraints excluded: chain F2 residue 76 THR Chi-restraints excluded: chain F2 residue 77 ILE Chi-restraints excluded: chain F2 residue 102 THR Chi-restraints excluded: chain F2 residue 114 PHE Chi-restraints excluded: chain F2 residue 116 HIS Chi-restraints excluded: chain F2 residue 136 ILE Chi-restraints excluded: chain F2 residue 184 ARG Chi-restraints excluded: chain F2 residue 235 ILE Chi-restraints excluded: chain F2 residue 312 VAL Chi-restraints excluded: chain G2 residue 46 LEU Chi-restraints excluded: chain G2 residue 102 THR Chi-restraints excluded: chain G2 residue 136 ILE Chi-restraints excluded: chain G2 residue 176 ILE Chi-restraints excluded: chain G2 residue 179 ASP Chi-restraints excluded: chain G2 residue 285 LEU Chi-restraints excluded: chain G2 residue 311 LEU Chi-restraints excluded: chain G2 residue 312 VAL Chi-restraints excluded: chain H2 residue 46 LEU Chi-restraints excluded: chain H2 residue 57 MET Chi-restraints excluded: chain H2 residue 68 THR Chi-restraints excluded: chain H2 residue 76 THR Chi-restraints excluded: chain H2 residue 77 ILE Chi-restraints excluded: chain H2 residue 102 THR Chi-restraints excluded: chain H2 residue 114 PHE Chi-restraints excluded: chain H2 residue 116 HIS Chi-restraints excluded: chain H2 residue 136 ILE Chi-restraints excluded: chain H2 residue 176 ILE Chi-restraints excluded: chain H2 residue 195 TYR Chi-restraints excluded: chain H2 residue 235 ILE Chi-restraints excluded: chain H2 residue 311 LEU Chi-restraints excluded: chain H2 residue 312 VAL Chi-restraints excluded: chain I2 residue 46 LEU Chi-restraints excluded: chain I2 residue 102 THR Chi-restraints excluded: chain I2 residue 116 HIS Chi-restraints excluded: chain I2 residue 136 ILE Chi-restraints excluded: chain I2 residue 179 ASP Chi-restraints excluded: chain I2 residue 255 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 1 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 210 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 229 optimal weight: 0.7980 chunk 71 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 221 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A2 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H2 116 HIS ** H2 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I2 190 GLN ** I2 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.059056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.050908 restraints weight = 86180.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.052430 restraints weight = 43767.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.053391 restraints weight = 27616.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.054023 restraints weight = 20214.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.054434 restraints weight = 16343.829| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 21114 Z= 0.195 Angle : 0.862 14.165 28683 Z= 0.438 Chirality : 0.043 0.220 3609 Planarity : 0.006 0.066 3555 Dihedral : 6.192 38.318 2907 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 4.61 % Allowed : 31.21 % Favored : 64.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.52 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.16), residues: 2781 helix: 1.20 (0.11), residues: 2151 sheet: None (None), residues: 0 loop : -2.78 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARGI2 67 TYR 0.024 0.002 TYRI2 195 PHE 0.039 0.002 PHED2 117 TRP 0.007 0.001 TRPG2 325 HIS 0.010 0.002 HISH2 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.19 (21114) covalent geometry : angle 0.86215 / 0.44 (28683) hydrogen bonds : bond 0.05604 / 3.83 ( 1872) hydrogen bonds : angle 4.80090 / 3.46 ( 5589) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 507 time to evaluate : 0.550 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: A2 57 MET cc_start: 0.7927 (tmm) cc_final: 0.7349 (tmm) REVERT: B2 195 TYR cc_start: 0.8957 (m-80) cc_final: 0.8501 (m-10) REVERT: B2 305 VAL cc_start: 0.8084 (OUTLIER) cc_final: 0.7856 (m) REVERT: B2 328 ARG cc_start: 0.6437 (tmm160) cc_final: 0.6022 (tmt170) REVERT: C2 57 MET cc_start: 0.8143 (tmm) cc_final: 0.7447 (tmm) REVERT: C2 85 ARG cc_start: 0.8355 (ttp-110) cc_final: 0.7995 (ttp-110) REVERT: D2 185 ARG cc_start: 0.8339 (ptt-90) cc_final: 0.8121 (ptp-170) REVERT: E2 99 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7740 (mm-30) REVERT: E2 184 ARG cc_start: 0.8034 (tpp80) cc_final: 0.7753 (mpp80) REVERT: E2 206 ARG cc_start: 0.8688 (ttm-80) cc_final: 0.8388 (ttm-80) REVERT: E2 231 HIS cc_start: 0.7077 (OUTLIER) cc_final: 0.6419 (m-70) REVERT: F2 57 MET cc_start: 0.8100 (tpp) cc_final: 0.7780 (tpt) REVERT: F2 114 PHE cc_start: 0.8807 (OUTLIER) cc_final: 0.8410 (m-80) REVERT: F2 184 ARG cc_start: 0.7454 (OUTLIER) cc_final: 0.6968 (mpp80) REVERT: F2 216 MET cc_start: 0.8711 (tpp) cc_final: 0.8411 (tpp) REVERT: F2 317 THR cc_start: 0.8362 (m) cc_final: 0.8069 (t) REVERT: G2 98 MET cc_start: 0.8525 (mtt) cc_final: 0.8244 (mtt) REVERT: G2 191 GLU cc_start: 0.8035 (tp30) cc_final: 0.7735 (tp30) REVERT: G2 195 TYR cc_start: 0.9093 (m-80) cc_final: 0.8520 (m-10) REVERT: H2 57 MET cc_start: 0.7718 (OUTLIER) cc_final: 0.7138 (tmm) REVERT: H2 116 HIS cc_start: 0.8670 (OUTLIER) cc_final: 0.8080 (t70) REVERT: H2 158 ASP cc_start: 0.8511 (t0) cc_final: 0.8237 (t0) REVERT: H2 191 GLU cc_start: 0.8029 (tm-30) cc_final: 0.7244 (tp30) REVERT: H2 195 TYR cc_start: 0.9070 (OUTLIER) cc_final: 0.8695 (m-10) REVERT: H2 206 ARG cc_start: 0.8470 (ttm-80) cc_final: 0.8114 (tpt170) REVERT: I2 139 MET cc_start: 0.6935 (ptm) cc_final: 0.6635 (ptt) REVERT: I2 187 GLU cc_start: 0.8710 (mm-30) cc_final: 0.8492 (mm-30) REVERT: I2 191 GLU cc_start: 0.8527 (tp30) cc_final: 0.8082 (tp30) REVERT: I2 292 MET cc_start: 0.7408 (mtt) cc_final: 0.7080 (mtt) outliers start: 100 outliers final: 74 residues processed: 585 average time/residue: 0.1639 time to fit residues: 141.5551 Evaluate side-chains 565 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 484 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A2 residue 46 LEU Chi-restraints excluded: chain A2 residue 76 THR Chi-restraints excluded: chain A2 residue 102 THR Chi-restraints excluded: chain A2 residue 116 HIS Chi-restraints excluded: chain A2 residue 136 ILE Chi-restraints excluded: chain A2 residue 285 LEU Chi-restraints excluded: chain A2 residue 305 VAL Chi-restraints excluded: chain A2 residue 311 LEU Chi-restraints excluded: chain A2 residue 312 VAL Chi-restraints excluded: chain B2 residue 54 LEU Chi-restraints excluded: chain B2 residue 59 LEU Chi-restraints excluded: chain B2 residue 102 THR Chi-restraints excluded: chain B2 residue 116 HIS Chi-restraints excluded: chain B2 residue 136 ILE Chi-restraints excluded: chain B2 residue 235 ILE Chi-restraints excluded: chain B2 residue 301 LEU Chi-restraints excluded: chain B2 residue 305 VAL Chi-restraints excluded: chain B2 residue 312 VAL Chi-restraints excluded: chain B2 residue 317 THR Chi-restraints excluded: chain C2 residue 46 LEU Chi-restraints excluded: chain C2 residue 76 THR Chi-restraints excluded: chain C2 residue 77 ILE Chi-restraints excluded: chain C2 residue 102 THR Chi-restraints excluded: chain C2 residue 116 HIS Chi-restraints excluded: chain C2 residue 136 ILE Chi-restraints excluded: chain C2 residue 235 ILE Chi-restraints excluded: chain C2 residue 301 LEU Chi-restraints excluded: chain C2 residue 311 LEU Chi-restraints excluded: chain C2 residue 312 VAL Chi-restraints excluded: chain D2 residue 46 LEU Chi-restraints excluded: chain D2 residue 54 LEU Chi-restraints excluded: chain D2 residue 102 THR Chi-restraints excluded: chain D2 residue 119 VAL Chi-restraints excluded: chain D2 residue 136 ILE Chi-restraints excluded: chain D2 residue 285 LEU Chi-restraints excluded: chain D2 residue 301 LEU Chi-restraints excluded: chain D2 residue 311 LEU Chi-restraints excluded: chain D2 residue 312 VAL Chi-restraints excluded: chain E2 residue 54 LEU Chi-restraints excluded: chain E2 residue 77 ILE Chi-restraints excluded: chain E2 residue 102 THR Chi-restraints excluded: chain E2 residue 116 HIS Chi-restraints excluded: chain E2 residue 136 ILE Chi-restraints excluded: chain E2 residue 179 ASP Chi-restraints excluded: chain E2 residue 231 HIS Chi-restraints excluded: chain E2 residue 235 ILE Chi-restraints excluded: chain E2 residue 311 LEU Chi-restraints excluded: chain F2 residue 76 THR Chi-restraints excluded: chain F2 residue 77 ILE Chi-restraints excluded: chain F2 residue 102 THR Chi-restraints excluded: chain F2 residue 114 PHE Chi-restraints excluded: chain F2 residue 136 ILE Chi-restraints excluded: chain F2 residue 184 ARG Chi-restraints excluded: chain F2 residue 235 ILE Chi-restraints excluded: chain F2 residue 312 VAL Chi-restraints excluded: chain G2 residue 46 LEU Chi-restraints excluded: chain G2 residue 102 THR Chi-restraints excluded: chain G2 residue 136 ILE Chi-restraints excluded: chain G2 residue 176 ILE Chi-restraints excluded: chain G2 residue 179 ASP Chi-restraints excluded: chain G2 residue 235 ILE Chi-restraints excluded: chain G2 residue 292 MET Chi-restraints excluded: chain G2 residue 311 LEU Chi-restraints excluded: chain G2 residue 312 VAL Chi-restraints excluded: chain H2 residue 46 LEU Chi-restraints excluded: chain H2 residue 57 MET Chi-restraints excluded: chain H2 residue 76 THR Chi-restraints excluded: chain H2 residue 102 THR Chi-restraints excluded: chain H2 residue 116 HIS Chi-restraints excluded: chain H2 residue 136 ILE Chi-restraints excluded: chain H2 residue 176 ILE Chi-restraints excluded: chain H2 residue 195 TYR Chi-restraints excluded: chain H2 residue 235 ILE Chi-restraints excluded: chain H2 residue 311 LEU Chi-restraints excluded: chain H2 residue 312 VAL Chi-restraints excluded: chain I2 residue 46 LEU Chi-restraints excluded: chain I2 residue 102 THR Chi-restraints excluded: chain I2 residue 116 HIS Chi-restraints excluded: chain I2 residue 136 ILE Chi-restraints excluded: chain I2 residue 179 ASP Chi-restraints excluded: chain I2 residue 312 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 6 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 218 optimal weight: 0.6980 chunk 160 optimal weight: 0.9990 chunk 264 optimal weight: 0.6980 chunk 184 optimal weight: 0.3980 chunk 24 optimal weight: 0.0670 chunk 187 optimal weight: 0.9980 chunk 102 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A2 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 231 HIS ** D2 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H2 116 HIS ** H2 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H2 190 GLN ** H2 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.059699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.051441 restraints weight = 85778.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.052963 restraints weight = 43524.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.053939 restraints weight = 27543.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.054581 restraints weight = 20197.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.055001 restraints weight = 16271.832| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 21114 Z= 0.184 Angle : 0.868 10.322 28683 Z= 0.438 Chirality : 0.043 0.211 3609 Planarity : 0.006 0.063 3555 Dihedral : 6.138 36.900 2907 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 4.38 % Allowed : 31.30 % Favored : 64.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.52 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.16), residues: 2781 helix: 1.22 (0.11), residues: 2151 sheet: None (None), residues: 0 loop : -2.79 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARGI2 185 TYR 0.029 0.003 TYRE2 195 PHE 0.033 0.002 PHED2 117 TRP 0.008 0.001 TRPG2 325 HIS 0.004 0.001 HISC2 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.18 (21114) covalent geometry : angle 0.86846 / 0.44 (28683) hydrogen bonds : bond 0.05542 / 3.79 ( 1872) hydrogen bonds : angle 4.78166 / 3.45 ( 5589) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 498 time to evaluate : 0.791 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: A2 57 MET cc_start: 0.8000 (tmm) cc_final: 0.7413 (tmm) REVERT: B2 305 VAL cc_start: 0.8052 (OUTLIER) cc_final: 0.7817 (m) REVERT: B2 328 ARG cc_start: 0.6385 (tmm160) cc_final: 0.6023 (tmt170) REVERT: C2 57 MET cc_start: 0.8225 (tmm) cc_final: 0.7630 (tmm) REVERT: C2 85 ARG cc_start: 0.8338 (ttp-110) cc_final: 0.7990 (ttp-110) REVERT: C2 184 ARG cc_start: 0.8552 (mmm-85) cc_final: 0.8347 (tpp80) REVERT: C2 233 MET cc_start: 0.6091 (ptp) cc_final: 0.5842 (ptp) REVERT: D2 57 MET cc_start: 0.7918 (tpp) cc_final: 0.7699 (tpp) REVERT: D2 191 GLU cc_start: 0.8093 (tp30) cc_final: 0.7248 (tp30) REVERT: D2 195 TYR cc_start: 0.9016 (OUTLIER) cc_final: 0.8539 (m-10) REVERT: D2 326 TRP cc_start: 0.8183 (t60) cc_final: 0.7525 (t-100) REVERT: E2 99 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7692 (mm-30) REVERT: E2 191 GLU cc_start: 0.7832 (tp30) cc_final: 0.7429 (tp30) REVERT: E2 231 HIS cc_start: 0.7076 (OUTLIER) cc_final: 0.6529 (m-70) REVERT: F2 57 MET cc_start: 0.8100 (tpp) cc_final: 0.7839 (tpt) REVERT: F2 114 PHE cc_start: 0.8808 (OUTLIER) cc_final: 0.8438 (m-80) REVERT: F2 184 ARG cc_start: 0.7514 (OUTLIER) cc_final: 0.7024 (mpp80) REVERT: F2 317 THR cc_start: 0.8333 (m) cc_final: 0.8050 (t) REVERT: G2 98 MET cc_start: 0.8487 (mtt) cc_final: 0.8224 (mtt) REVERT: G2 195 TYR cc_start: 0.9106 (m-80) cc_final: 0.8865 (m-10) REVERT: H2 57 MET cc_start: 0.7701 (OUTLIER) cc_final: 0.7121 (tmm) REVERT: H2 116 HIS cc_start: 0.8521 (OUTLIER) cc_final: 0.8010 (t70) REVERT: H2 158 ASP cc_start: 0.8509 (t0) cc_final: 0.8210 (t0) REVERT: H2 191 GLU cc_start: 0.8019 (tm-30) cc_final: 0.7251 (tp30) REVERT: H2 195 TYR cc_start: 0.9068 (OUTLIER) cc_final: 0.8630 (m-10) REVERT: H2 206 ARG cc_start: 0.8485 (ttm-80) cc_final: 0.8132 (tpt170) REVERT: I2 54 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8195 (mp) REVERT: I2 139 MET cc_start: 0.6964 (ptm) cc_final: 0.6669 (ptt) REVERT: I2 187 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8480 (mm-30) outliers start: 95 outliers final: 71 residues processed: 574 average time/residue: 0.1624 time to fit residues: 139.4775 Evaluate side-chains 564 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 484 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A2 residue 46 LEU Chi-restraints excluded: chain A2 residue 76 THR Chi-restraints excluded: chain A2 residue 102 THR Chi-restraints excluded: chain A2 residue 116 HIS Chi-restraints excluded: chain A2 residue 136 ILE Chi-restraints excluded: chain A2 residue 285 LEU Chi-restraints excluded: chain A2 residue 311 LEU Chi-restraints excluded: chain A2 residue 312 VAL Chi-restraints excluded: chain B2 residue 54 LEU Chi-restraints excluded: chain B2 residue 59 LEU Chi-restraints excluded: chain B2 residue 68 THR Chi-restraints excluded: chain B2 residue 102 THR Chi-restraints excluded: chain B2 residue 116 HIS Chi-restraints excluded: chain B2 residue 136 ILE Chi-restraints excluded: chain B2 residue 235 ILE Chi-restraints excluded: chain B2 residue 301 LEU Chi-restraints excluded: chain B2 residue 305 VAL Chi-restraints excluded: chain B2 residue 312 VAL Chi-restraints excluded: chain B2 residue 317 THR Chi-restraints excluded: chain C2 residue 46 LEU Chi-restraints excluded: chain C2 residue 76 THR Chi-restraints excluded: chain C2 residue 77 ILE Chi-restraints excluded: chain C2 residue 102 THR Chi-restraints excluded: chain C2 residue 136 ILE Chi-restraints excluded: chain C2 residue 235 ILE Chi-restraints excluded: chain C2 residue 301 LEU Chi-restraints excluded: chain C2 residue 311 LEU Chi-restraints excluded: chain C2 residue 312 VAL Chi-restraints excluded: chain D2 residue 46 LEU Chi-restraints excluded: chain D2 residue 54 LEU Chi-restraints excluded: chain D2 residue 102 THR Chi-restraints excluded: chain D2 residue 119 VAL Chi-restraints excluded: chain D2 residue 136 ILE Chi-restraints excluded: chain D2 residue 195 TYR Chi-restraints excluded: chain D2 residue 235 ILE Chi-restraints excluded: chain D2 residue 311 LEU Chi-restraints excluded: chain E2 residue 54 LEU Chi-restraints excluded: chain E2 residue 77 ILE Chi-restraints excluded: chain E2 residue 102 THR Chi-restraints excluded: chain E2 residue 116 HIS Chi-restraints excluded: chain E2 residue 136 ILE Chi-restraints excluded: chain E2 residue 179 ASP Chi-restraints excluded: chain E2 residue 231 HIS Chi-restraints excluded: chain E2 residue 235 ILE Chi-restraints excluded: chain E2 residue 311 LEU Chi-restraints excluded: chain F2 residue 76 THR Chi-restraints excluded: chain F2 residue 77 ILE Chi-restraints excluded: chain F2 residue 102 THR Chi-restraints excluded: chain F2 residue 114 PHE Chi-restraints excluded: chain F2 residue 136 ILE Chi-restraints excluded: chain F2 residue 184 ARG Chi-restraints excluded: chain F2 residue 312 VAL Chi-restraints excluded: chain G2 residue 46 LEU Chi-restraints excluded: chain G2 residue 102 THR Chi-restraints excluded: chain G2 residue 136 ILE Chi-restraints excluded: chain G2 residue 176 ILE Chi-restraints excluded: chain G2 residue 179 ASP Chi-restraints excluded: chain G2 residue 235 ILE Chi-restraints excluded: chain G2 residue 292 MET Chi-restraints excluded: chain G2 residue 311 LEU Chi-restraints excluded: chain G2 residue 312 VAL Chi-restraints excluded: chain H2 residue 46 LEU Chi-restraints excluded: chain H2 residue 57 MET Chi-restraints excluded: chain H2 residue 76 THR Chi-restraints excluded: chain H2 residue 102 THR Chi-restraints excluded: chain H2 residue 116 HIS Chi-restraints excluded: chain H2 residue 136 ILE Chi-restraints excluded: chain H2 residue 176 ILE Chi-restraints excluded: chain H2 residue 195 TYR Chi-restraints excluded: chain H2 residue 235 ILE Chi-restraints excluded: chain H2 residue 311 LEU Chi-restraints excluded: chain H2 residue 312 VAL Chi-restraints excluded: chain I2 residue 46 LEU Chi-restraints excluded: chain I2 residue 54 LEU Chi-restraints excluded: chain I2 residue 102 THR Chi-restraints excluded: chain I2 residue 116 HIS Chi-restraints excluded: chain I2 residue 136 ILE Chi-restraints excluded: chain I2 residue 179 ASP Chi-restraints excluded: chain I2 residue 255 ILE Chi-restraints excluded: chain I2 residue 312 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 139 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 151 optimal weight: 0.8980 chunk 130 optimal weight: 0.9980 chunk 273 optimal weight: 0.9980 chunk 231 optimal weight: 0.7980 chunk 185 optimal weight: 0.0980 chunk 172 optimal weight: 0.5980 chunk 89 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A2 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 231 HIS ** D2 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H2 116 HIS ** H2 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.059559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.051317 restraints weight = 85798.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.052849 restraints weight = 43673.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.053835 restraints weight = 27605.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.054472 restraints weight = 20190.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.054859 restraints weight = 16275.970| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 21114 Z= 0.192 Angle : 0.896 11.172 28683 Z= 0.457 Chirality : 0.044 0.227 3609 Planarity : 0.006 0.063 3555 Dihedral : 6.170 36.767 2907 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 4.29 % Allowed : 31.54 % Favored : 64.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.52 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.16), residues: 2781 helix: 1.17 (0.11), residues: 2151 sheet: None (None), residues: 0 loop : -2.83 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARGI2 185 TYR 0.027 0.002 TYRI2 195 PHE 0.033 0.002 PHED2 117 TRP 0.008 0.001 TRPG2 325 HIS 0.012 0.002 HISH2 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.19 (21114) covalent geometry : angle 0.89575 / 0.46 (28683) hydrogen bonds : bond 0.05621 / 3.85 ( 1872) hydrogen bonds : angle 4.85983 / 3.50 ( 5589) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 490 time to evaluate : 0.816 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: A2 57 MET cc_start: 0.7990 (tmm) cc_final: 0.7395 (tmm) REVERT: A2 99 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7579 (mm-30) REVERT: B2 305 VAL cc_start: 0.8046 (OUTLIER) cc_final: 0.7618 (t) REVERT: B2 328 ARG cc_start: 0.6439 (tmm160) cc_final: 0.6157 (tmt170) REVERT: C2 57 MET cc_start: 0.8248 (tmm) cc_final: 0.7650 (tmm) REVERT: C2 85 ARG cc_start: 0.8334 (ttp-110) cc_final: 0.7990 (ttp-110) REVERT: C2 184 ARG cc_start: 0.8561 (mmm-85) cc_final: 0.8354 (tpp80) REVERT: C2 195 TYR cc_start: 0.8988 (m-10) cc_final: 0.8489 (m-10) REVERT: C2 233 MET cc_start: 0.5854 (ptp) cc_final: 0.5612 (ptp) REVERT: D2 185 ARG cc_start: 0.8315 (ptt-90) cc_final: 0.8047 (ptp-170) REVERT: D2 191 GLU cc_start: 0.8076 (tp30) cc_final: 0.7180 (tp30) REVERT: D2 195 TYR cc_start: 0.9005 (OUTLIER) cc_final: 0.8504 (m-10) REVERT: D2 326 TRP cc_start: 0.8189 (t60) cc_final: 0.7525 (t-100) REVERT: E2 67 ARG cc_start: 0.7081 (ttp80) cc_final: 0.6732 (ttp80) REVERT: E2 99 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7673 (mm-30) REVERT: E2 191 GLU cc_start: 0.7731 (tp30) cc_final: 0.7434 (tp30) REVERT: E2 231 HIS cc_start: 0.6939 (OUTLIER) cc_final: 0.6468 (m-70) REVERT: F2 57 MET cc_start: 0.8123 (tpp) cc_final: 0.7861 (tpt) REVERT: F2 114 PHE cc_start: 0.8817 (OUTLIER) cc_final: 0.8431 (m-80) REVERT: F2 184 ARG cc_start: 0.7613 (OUTLIER) cc_final: 0.7111 (mpp80) REVERT: F2 317 THR cc_start: 0.8330 (m) cc_final: 0.8036 (t) REVERT: G2 98 MET cc_start: 0.8520 (mtt) cc_final: 0.8281 (mtt) REVERT: G2 187 GLU cc_start: 0.8712 (mm-30) cc_final: 0.8502 (mm-30) REVERT: G2 191 GLU cc_start: 0.7980 (tp30) cc_final: 0.7548 (tp30) REVERT: G2 195 TYR cc_start: 0.9064 (m-80) cc_final: 0.8587 (m-10) REVERT: G2 206 ARG cc_start: 0.8907 (ttm-80) cc_final: 0.8593 (ttm-80) REVERT: H2 57 MET cc_start: 0.7714 (OUTLIER) cc_final: 0.7138 (tmm) REVERT: H2 158 ASP cc_start: 0.8519 (t0) cc_final: 0.8198 (t0) REVERT: I2 139 MET cc_start: 0.6972 (ptm) cc_final: 0.6711 (ptt) REVERT: I2 187 GLU cc_start: 0.8738 (mm-30) cc_final: 0.8496 (mm-30) outliers start: 93 outliers final: 76 residues processed: 562 average time/residue: 0.1686 time to fit residues: 141.6114 Evaluate side-chains 569 residues out of total 2169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 487 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A2 residue 46 LEU Chi-restraints excluded: chain A2 residue 76 THR Chi-restraints excluded: chain A2 residue 116 HIS Chi-restraints excluded: chain A2 residue 136 ILE Chi-restraints excluded: chain A2 residue 285 LEU Chi-restraints excluded: chain A2 residue 311 LEU Chi-restraints excluded: chain A2 residue 312 VAL Chi-restraints excluded: chain B2 residue 54 LEU Chi-restraints excluded: chain B2 residue 59 LEU Chi-restraints excluded: chain B2 residue 68 THR Chi-restraints excluded: chain B2 residue 102 THR Chi-restraints excluded: chain B2 residue 116 HIS Chi-restraints excluded: chain B2 residue 136 ILE Chi-restraints excluded: chain B2 residue 235 ILE Chi-restraints excluded: chain B2 residue 301 LEU Chi-restraints excluded: chain B2 residue 305 VAL Chi-restraints excluded: chain B2 residue 312 VAL Chi-restraints excluded: chain B2 residue 317 THR Chi-restraints excluded: chain C2 residue 46 LEU Chi-restraints excluded: chain C2 residue 76 THR Chi-restraints excluded: chain C2 residue 77 ILE Chi-restraints excluded: chain C2 residue 102 THR Chi-restraints excluded: chain C2 residue 136 ILE Chi-restraints excluded: chain C2 residue 235 ILE Chi-restraints excluded: chain C2 residue 301 LEU Chi-restraints excluded: chain C2 residue 311 LEU Chi-restraints excluded: chain C2 residue 312 VAL Chi-restraints excluded: chain D2 residue 46 LEU Chi-restraints excluded: chain D2 residue 54 LEU Chi-restraints excluded: chain D2 residue 68 THR Chi-restraints excluded: chain D2 residue 102 THR Chi-restraints excluded: chain D2 residue 119 VAL Chi-restraints excluded: chain D2 residue 136 ILE Chi-restraints excluded: chain D2 residue 195 TYR Chi-restraints excluded: chain D2 residue 235 ILE Chi-restraints excluded: chain D2 residue 285 LEU Chi-restraints excluded: chain D2 residue 311 LEU Chi-restraints excluded: chain E2 residue 54 LEU Chi-restraints excluded: chain E2 residue 77 ILE Chi-restraints excluded: chain E2 residue 102 THR Chi-restraints excluded: chain E2 residue 116 HIS Chi-restraints excluded: chain E2 residue 136 ILE Chi-restraints excluded: chain E2 residue 179 ASP Chi-restraints excluded: chain E2 residue 231 HIS Chi-restraints excluded: chain E2 residue 235 ILE Chi-restraints excluded: chain E2 residue 311 LEU Chi-restraints excluded: chain F2 residue 76 THR Chi-restraints excluded: chain F2 residue 77 ILE Chi-restraints excluded: chain F2 residue 102 THR Chi-restraints excluded: chain F2 residue 114 PHE Chi-restraints excluded: chain F2 residue 136 ILE Chi-restraints excluded: chain F2 residue 184 ARG Chi-restraints excluded: chain F2 residue 312 VAL Chi-restraints excluded: chain G2 residue 46 LEU Chi-restraints excluded: chain G2 residue 102 THR Chi-restraints excluded: chain G2 residue 136 ILE Chi-restraints excluded: chain G2 residue 176 ILE Chi-restraints excluded: chain G2 residue 179 ASP Chi-restraints excluded: chain G2 residue 235 ILE Chi-restraints excluded: chain G2 residue 285 LEU Chi-restraints excluded: chain G2 residue 292 MET Chi-restraints excluded: chain G2 residue 311 LEU Chi-restraints excluded: chain G2 residue 312 VAL Chi-restraints excluded: chain H2 residue 46 LEU Chi-restraints excluded: chain H2 residue 57 MET Chi-restraints excluded: chain H2 residue 76 THR Chi-restraints excluded: chain H2 residue 102 THR Chi-restraints excluded: chain H2 residue 116 HIS Chi-restraints excluded: chain H2 residue 136 ILE Chi-restraints excluded: chain H2 residue 176 ILE Chi-restraints excluded: chain H2 residue 235 ILE Chi-restraints excluded: chain H2 residue 311 LEU Chi-restraints excluded: chain H2 residue 312 VAL Chi-restraints excluded: chain I2 residue 77 ILE Chi-restraints excluded: chain I2 residue 102 THR Chi-restraints excluded: chain I2 residue 116 HIS Chi-restraints excluded: chain I2 residue 136 ILE Chi-restraints excluded: chain I2 residue 179 ASP Chi-restraints excluded: chain I2 residue 235 ILE Chi-restraints excluded: chain I2 residue 255 ILE Chi-restraints excluded: chain I2 residue 311 LEU Chi-restraints excluded: chain I2 residue 312 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 133 optimal weight: 0.3980 chunk 57 optimal weight: 0.3980 chunk 176 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 212 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 45 optimal weight: 0.2980 chunk 43 optimal weight: 1.9990 chunk 174 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A2 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 231 HIS ** D2 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.059869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.051742 restraints weight = 85478.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.053248 restraints weight = 43821.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.054227 restraints weight = 27762.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.054871 restraints weight = 20302.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.055272 restraints weight = 16335.884| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 21114 Z= 0.190 Angle : 0.904 13.659 28683 Z= 0.458 Chirality : 0.044 0.234 3609 Planarity : 0.006 0.062 3555 Dihedral : 6.146 36.053 2907 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 4.15 % Allowed : 32.13 % Favored : 63.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.52 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.16), residues: 2781 helix: 1.20 (0.11), residues: 2151 sheet: None (None), residues: 0 loop : -2.80 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARGI2 185 TYR 0.026 0.002 TYRI2 195 PHE 0.032 0.002 PHED2 117 TRP 0.008 0.001 TRPG2 325 HIS 0.009 0.002 HISH2 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.19 (21114) covalent geometry : angle 0.90411 / 0.46 (28683) hydrogen bonds : bond 0.05584 / 3.82 ( 1872) hydrogen bonds : angle 4.86364 / 3.53 ( 5589) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3863.60 seconds wall clock time: 67 minutes 24.02 seconds (4044.02 seconds total)