Starting phenix.real_space_refine on Thu Jun 4 07:01:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w24_65565/06_2026/9w24_65565.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w24_65565/06_2026/9w24_65565.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9w24_65565/06_2026/9w24_65565.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w24_65565/06_2026/9w24_65565.map" model { file = "/net/cci-nas-00/data/ceres_data/9w24_65565/06_2026/9w24_65565.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w24_65565/06_2026/9w24_65565.cif" } resolution = 3.8 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= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 80 5.16 5 C 6944 2.51 5 N 1902 2.21 5 O 2062 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10988 Number of models: 1 Model: "" Number of chains: 4 Chain: "a" Number of atoms: 2807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2807 Classifications: {'peptide': 352} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 335} Chain: "b" Number of atoms: 2687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2687 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 16, 'TRANS': 319} Chain: "B" Number of atoms: 2807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2807 Classifications: {'peptide': 352} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 335} Chain: "A" Number of atoms: 2687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2687 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 16, 'TRANS': 319} Time building chain proxies: 2.77, per 1000 atoms: 0.25 Number of scatterers: 10988 At special positions: 0 Unit cell: (105.347, 121.451, 89.243, 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 80 16.00 O 2062 8.00 N 1902 7.00 C 6944 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS a 4 " - pdb=" SG CYS a 15 " distance=2.03 Simple disulfide: pdb=" SG CYS a 55 " - pdb=" SG CYS a 143 " distance=2.03 Simple disulfide: pdb=" SG CYS a 179 " - pdb=" SG CYS a 223 " distance=2.03 Simple disulfide: pdb=" SG CYS a 280 " - pdb=" SG CYS a 329 " distance=2.03 Simple disulfide: pdb=" SG CYS a 291 " - pdb=" SG CYS a 312 " distance=2.03 Simple disulfide: pdb=" SG CYS a 313 " - pdb=" SG CYS a 316 " distance=2.03 Simple disulfide: pdb=" SG CYS b 55 " - pdb=" SG CYS b 143 " distance=2.03 Simple disulfide: pdb=" SG CYS b 179 " - pdb=" SG CYS b 223 " distance=2.03 Simple disulfide: pdb=" SG CYS b 280 " - pdb=" SG CYS b 329 " distance=2.03 Simple disulfide: pdb=" SG CYS b 291 " - pdb=" SG CYS b 312 " distance=2.03 Simple disulfide: pdb=" SG CYS B 4 " - pdb=" SG CYS B 15 " distance=2.03 Simple disulfide: pdb=" SG CYS B 55 " - pdb=" SG CYS B 143 " distance=2.03 Simple disulfide: pdb=" SG CYS B 179 " - pdb=" SG CYS B 223 " distance=2.03 Simple disulfide: pdb=" SG CYS B 280 " - pdb=" SG CYS B 329 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 312 " distance=2.03 Simple disulfide: pdb=" SG CYS B 313 " - pdb=" SG CYS B 316 " distance=2.03 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 143 " distance=2.03 Simple disulfide: pdb=" SG CYS A 179 " - pdb=" SG CYS A 223 " distance=2.03 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 329 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 312 " distance=2.03 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 316 " distance=2.03 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: 0.79 Conformation dependent library (CDL) restraints added in 563.8 milliseconds 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2560 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 25 sheets defined 17.4% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'a' and resid 38 through 53 removed outlier: 4.199A pdb=" N SER a 44 " --> pdb=" O SER a 40 " (cutoff:3.500A) Processing helix chain 'a' and resid 61 through 82 Proline residue: a 73 - end of helix Processing helix chain 'a' and resid 144 through 146 No H-bonds generated for 'chain 'a' and resid 144 through 146' Processing helix chain 'a' and resid 226 through 230 Processing helix chain 'a' and resid 244 through 248 Processing helix chain 'a' and resid 252 through 256 removed outlier: 3.857A pdb=" N ASN a 255 " --> pdb=" O SER a 252 " (cutoff:3.500A) Processing helix chain 'b' and resid 38 through 53 Processing helix chain 'b' and resid 61 through 82 Proline residue: b 73 - end of helix Processing helix chain 'b' and resid 144 through 146 No H-bonds generated for 'chain 'b' and resid 144 through 146' Processing helix chain 'b' and resid 226 through 230 Processing helix chain 'b' and resid 244 through 248 Processing helix chain 'b' and resid 252 through 256 Processing helix chain 'b' and resid 266 through 270 removed outlier: 4.382A pdb=" N HIS b 269 " --> pdb=" O GLY b 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 31 Processing helix chain 'B' and resid 38 through 52 Processing helix chain 'B' and resid 61 through 82 Proline residue: B 73 - end of helix Processing helix chain 'B' and resid 144 through 146 No H-bonds generated for 'chain 'B' and resid 144 through 146' Processing helix chain 'B' and resid 226 through 230 Processing helix chain 'B' and resid 244 through 248 Processing helix chain 'B' and resid 252 through 256 removed outlier: 3.791A pdb=" N ASN B 255 " --> pdb=" O SER B 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 53 removed outlier: 3.820A pdb=" N LEU A 42 " --> pdb=" O SER A 38 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA A 43 " --> pdb=" O PRO A 39 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER A 44 " --> pdb=" O SER A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 82 Proline residue: A 73 - end of helix Processing helix chain 'A' and resid 144 through 146 No H-bonds generated for 'chain 'A' and resid 144 through 146' Processing helix chain 'A' and resid 226 through 230 removed outlier: 3.580A pdb=" N HIS A 229 " --> pdb=" O PRO A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 248 Processing helix chain 'A' and resid 252 through 256 Processing helix chain 'A' and resid 341 through 345 removed outlier: 3.765A pdb=" N LEU A 345 " --> pdb=" O GLU A 342 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'a' and resid 4 through 5 removed outlier: 3.691A pdb=" N VAL a 5 " --> pdb=" O LYS a 14 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS a 14 " --> pdb=" O VAL a 5 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'a' and resid 20 through 23 removed outlier: 3.507A pdb=" N PHE a 20 " --> pdb=" O THR b 22 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ILE b 19 " --> pdb=" O GLU b 30 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 56 through 58 Processing sheet with id=AA4, first strand: chain 'a' and resid 87 through 90 removed outlier: 6.832A pdb=" N THR a 87 " --> pdb=" O PHE a 133 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ILE a 135 " --> pdb=" O THR a 87 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N MET a 89 " --> pdb=" O ILE a 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'a' and resid 154 through 160 removed outlier: 5.917A pdb=" N VAL a 155 " --> pdb=" O LYS a 170 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LYS a 170 " --> pdb=" O VAL a 155 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP a 157 " --> pdb=" O TRP a 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'a' and resid 210 through 212 Processing sheet with id=AA7, first strand: chain 'a' and resid 210 through 212 removed outlier: 4.143A pdb=" N ALA a 193 " --> pdb=" O SER a 204 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER a 185 " --> pdb=" O ALA a 196 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA A 186 " --> pdb=" O ILE a 188 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N TRP A 201 " --> pdb=" O ALA A 215 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ALA A 215 " --> pdb=" O TRP A 201 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N GLU A 203 " --> pdb=" O GLU A 213 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS A 211 " --> pdb=" O ALA A 205 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU A 273 " --> pdb=" O PHE A 217 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASP A 276 " --> pdb=" O ARG A 322 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'a' and resid 274 through 277 removed outlier: 3.581A pdb=" N ASP a 276 " --> pdb=" O ARG a 322 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'a' and resid 284 through 287 removed outlier: 3.520A pdb=" N TRP a 311 " --> pdb=" O THR a 284 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N CYS a 313 " --> pdb=" O VAL a 286 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'b' and resid 32 through 35 removed outlier: 3.854A pdb=" N LYS b 33 " --> pdb=" O THR b 165 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU b 169 " --> pdb=" O GLN b 35 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASP b 157 " --> pdb=" O TRP b 168 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LYS b 170 " --> pdb=" O VAL b 155 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N VAL b 155 " --> pdb=" O LYS b 170 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'b' and resid 56 through 57 removed outlier: 6.861A pdb=" N GLY b 56 " --> pdb=" O ALA b 149 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'b' and resid 87 through 90 removed outlier: 3.528A pdb=" N PHE b 133 " --> pdb=" O THR b 87 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET b 89 " --> pdb=" O PHE b 133 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'b' and resid 273 through 276 removed outlier: 6.070A pdb=" N ILE b 212 " --> pdb=" O ALA b 205 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ALA b 205 " --> pdb=" O ILE b 212 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS b 214 " --> pdb=" O GLU b 203 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA B 186 " --> pdb=" O ILE b 188 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER B 185 " --> pdb=" O ALA B 196 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA B 193 " --> pdb=" O SER B 204 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'b' and resid 273 through 276 removed outlier: 6.070A pdb=" N ILE b 212 " --> pdb=" O ALA b 205 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ALA b 205 " --> pdb=" O ILE b 212 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS b 214 " --> pdb=" O GLU b 203 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA B 186 " --> pdb=" O ILE b 188 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER B 185 " --> pdb=" O ALA B 196 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA B 193 " --> pdb=" O SER B 204 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'b' and resid 285 through 287 removed outlier: 3.781A pdb=" N CYS b 313 " --> pdb=" O VAL b 286 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 4 through 5 removed outlier: 3.575A pdb=" N VAL B 5 " --> pdb=" O LYS B 14 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS B 14 " --> pdb=" O VAL B 5 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 20 through 22 removed outlier: 9.715A pdb=" N THR A 165 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N GLN A 31 " --> pdb=" O THR A 165 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N ILE A 167 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LYS A 33 " --> pdb=" O ILE A 167 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N LEU A 169 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLN A 35 " --> pdb=" O LEU A 169 " (cutoff:3.500A) removed outlier: 8.781A pdb=" N LEU A 171 " --> pdb=" O GLN A 35 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASP A 157 " --> pdb=" O TRP A 168 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LYS A 170 " --> pdb=" O VAL A 155 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N VAL A 155 " --> pdb=" O LYS A 170 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 56 through 58 removed outlier: 7.383A pdb=" N GLY B 56 " --> pdb=" O ALA B 149 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 87 through 89 removed outlier: 3.587A pdb=" N MET B 89 " --> pdb=" O PHE B 133 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 154 through 158 removed outlier: 5.865A pdb=" N VAL B 155 " --> pdb=" O LYS B 170 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LYS B 170 " --> pdb=" O VAL B 155 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP B 157 " --> pdb=" O TRP B 168 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 276 through 277 Processing sheet with id=AC4, first strand: chain 'B' and resid 284 through 287 removed outlier: 4.039A pdb=" N CYS B 313 " --> pdb=" O VAL B 286 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 56 through 57 removed outlier: 6.675A pdb=" N GLY A 56 " --> pdb=" O ALA A 149 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'A' and resid 87 through 90 removed outlier: 6.540A pdb=" N THR A 87 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ILE A 135 " --> pdb=" O THR A 87 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N MET A 89 " --> pdb=" O ILE A 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'A' and resid 285 through 287 removed outlier: 6.251A pdb=" N VAL A 286 " --> pdb=" O CYS A 313 " (cutoff:3.500A) 258 hydrogen bonds defined for protein. 654 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: 1.59 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3571 1.34 - 1.46: 2641 1.46 - 1.58: 4944 1.58 - 1.70: 0 1.70 - 1.82: 116 Bond restraints: 11272 Sorted by residual: bond pdb=" CA SER A 228 " pdb=" C SER A 228 " ideal model delta sigma weight residual 1.522 1.498 0.024 1.72e-02 3.38e+03 1.97e+00 bond pdb=" C THR A 72 " pdb=" N PRO A 73 " ideal model delta sigma weight residual 1.335 1.351 -0.016 1.30e-02 5.92e+03 1.57e+00 bond pdb=" C VAL b 177 " pdb=" O VAL b 177 " ideal model delta sigma weight residual 1.236 1.225 0.011 1.19e-02 7.06e+03 8.56e-01 bond pdb=" C CYS A 143 " pdb=" O CYS A 143 " ideal model delta sigma weight residual 1.238 1.248 -0.010 1.28e-02 6.10e+03 6.44e-01 bond pdb=" CB PRO A 320 " pdb=" CG PRO A 320 " ideal model delta sigma weight residual 1.492 1.530 -0.038 5.00e-02 4.00e+02 5.92e-01 ... (remaining 11267 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.24: 14860 1.24 - 2.47: 341 2.47 - 3.71: 74 3.71 - 4.95: 8 4.95 - 6.18: 3 Bond angle restraints: 15286 Sorted by residual: angle pdb=" N VAL A 60 " pdb=" CA VAL A 60 " pdb=" C VAL A 60 " ideal model delta sigma weight residual 111.45 109.26 2.19 9.30e-01 1.16e+00 5.56e+00 angle pdb=" N THR a 309 " pdb=" CA THR a 309 " pdb=" C THR a 309 " ideal model delta sigma weight residual 114.04 111.26 2.78 1.24e+00 6.50e-01 5.02e+00 angle pdb=" C TRP a 115 " pdb=" N LYS a 116 " pdb=" CA LYS a 116 " ideal model delta sigma weight residual 121.54 125.60 -4.06 1.91e+00 2.74e-01 4.52e+00 angle pdb=" C LYS B 122 " pdb=" N MET B 123 " pdb=" CA MET B 123 " ideal model delta sigma weight residual 121.54 125.54 -4.00 1.91e+00 2.74e-01 4.39e+00 angle pdb=" N ILE b 218 " pdb=" CA ILE b 218 " pdb=" C ILE b 218 " ideal model delta sigma weight residual 113.07 110.32 2.75 1.37e+00 5.33e-01 4.03e+00 ... (remaining 15281 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 6372 17.72 - 35.43: 323 35.43 - 53.15: 51 53.15 - 70.87: 12 70.87 - 88.58: 3 Dihedral angle restraints: 6761 sinusoidal: 2797 harmonic: 3964 Sorted by residual: dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 312 " pdb=" CB CYS A 312 " ideal model delta sinusoidal sigma weight residual -86.00 -126.66 40.66 1 1.00e+01 1.00e-02 2.32e+01 dihedral pdb=" CA VAL b 194 " pdb=" C VAL b 194 " pdb=" N HIS b 195 " pdb=" CA HIS b 195 " ideal model delta harmonic sigma weight residual 180.00 162.95 17.05 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA LYS a 9 " pdb=" C LYS a 9 " pdb=" N ASN a 10 " pdb=" CA ASN a 10 " ideal model delta harmonic sigma weight residual 180.00 163.87 16.13 0 5.00e+00 4.00e-02 1.04e+01 ... (remaining 6758 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1125 0.033 - 0.067: 356 0.067 - 0.100: 106 0.100 - 0.133: 58 0.133 - 0.166: 1 Chirality restraints: 1646 Sorted by residual: chirality pdb=" CA THR B 72 " pdb=" N THR B 72 " pdb=" C THR B 72 " pdb=" CB THR B 72 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.17 2.00e-01 2.50e+01 6.90e-01 chirality pdb=" CA ILE A 243 " pdb=" N ILE A 243 " pdb=" C ILE A 243 " pdb=" CB ILE A 243 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.42e-01 chirality pdb=" CA ILE a 57 " pdb=" N ILE a 57 " pdb=" C ILE a 57 " pdb=" CB ILE a 57 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.06e-01 ... (remaining 1643 not shown) Planarity restraints: 1944 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG a 257 " 0.027 5.00e-02 4.00e+02 4.05e-02 2.63e+00 pdb=" N PRO a 258 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO a 258 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO a 258 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO b 319 " 0.023 5.00e-02 4.00e+02 3.46e-02 1.92e+00 pdb=" N PRO b 320 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO b 320 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO b 320 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 257 " -0.022 5.00e-02 4.00e+02 3.35e-02 1.80e+00 pdb=" N PRO B 258 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO B 258 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 258 " -0.019 5.00e-02 4.00e+02 ... (remaining 1941 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1712 2.77 - 3.30: 9873 3.30 - 3.83: 16652 3.83 - 4.37: 18983 4.37 - 4.90: 34192 Nonbonded interactions: 81412 Sorted by model distance: nonbonded pdb=" OG1 THR A 283 " pdb=" OH TYR A 331 " model vdw 2.233 3.040 nonbonded pdb=" O GLY b 266 " pdb=" OG SER b 348 " model vdw 2.265 3.040 nonbonded pdb=" O CYS A 291 " pdb=" NH2 ARG A 314 " model vdw 2.304 3.120 nonbonded pdb=" NH2 ARG B 336 " pdb=" OE2 GLU B 342 " model vdw 2.317 3.120 nonbonded pdb=" NH1 ARG a 294 " pdb=" OE2 GLU a 334 " model vdw 2.319 3.120 ... (remaining 81407 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 17 through 352) selection = (chain 'a' and resid 17 through 352) selection = chain 'b' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 4.320 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: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 10.910 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 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 : 0.002 0.038 11293 Z= 0.106 Angle : 0.481 6.185 15328 Z= 0.266 Chirality : 0.040 0.166 1646 Planarity : 0.003 0.041 1944 Dihedral : 10.781 88.583 4138 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 3.73 % Allowed : 6.95 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.23), residues: 1368 helix: 2.26 (0.46), residues: 148 sheet: -2.32 (0.32), residues: 240 loop : -1.50 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG b 257 TYR 0.005 0.001 TYR A 331 PHE 0.010 0.001 PHE A 279 TRP 0.009 0.001 TRP a 330 HIS 0.003 0.000 HIS a 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.11 (11272) covalent geometry : angle 0.47989 / 0.27 (15286) SS BOND : bond 0.00188 / 0.12 ( 21) SS BOND : angle 0.69119 / 0.48 ( 42) hydrogen bonds : bond 0.22598 / 15.41 ( 232) hydrogen bonds : angle 8.87919 / 5.92 ( 654) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 193 time to evaluate : 0.313 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: a 50 HIS cc_start: 0.8140 (t70) cc_final: 0.7861 (t-170) REVERT: a 118 TRP cc_start: 0.7184 (m100) cc_final: 0.6836 (m100) REVERT: a 123 MET cc_start: 0.7067 (OUTLIER) cc_final: 0.6862 (ptm) REVERT: a 157 ASP cc_start: 0.7886 (t0) cc_final: 0.7504 (m-30) REVERT: a 253 GLN cc_start: 0.7674 (mt0) cc_final: 0.7463 (tt0) REVERT: a 333 MET cc_start: 0.8440 (mtp) cc_final: 0.8219 (mtp) REVERT: B 50 HIS cc_start: 0.8350 (t-90) cc_final: 0.8082 (t-170) REVERT: B 86 LEU cc_start: 0.6835 (tp) cc_final: 0.6501 (tp) REVERT: B 106 PRO cc_start: 0.8640 (Cg_exo) cc_final: 0.8367 (Cg_endo) REVERT: B 157 ASP cc_start: 0.7860 (m-30) cc_final: 0.7636 (m-30) REVERT: B 213 GLU cc_start: 0.7363 (tt0) cc_final: 0.7133 (tp30) REVERT: A 127 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7758 (mp0) REVERT: A 231 LEU cc_start: 0.7804 (OUTLIER) cc_final: 0.7404 (pt) REVERT: A 323 TYR cc_start: 0.6762 (m-80) cc_final: 0.5824 (m-80) REVERT: A 333 MET cc_start: 0.8161 (mtm) cc_final: 0.7833 (mtp) outliers start: 45 outliers final: 13 residues processed: 230 average time/residue: 0.1004 time to fit residues: 33.0655 Evaluate side-chains 130 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 123 MET Chi-restraints excluded: chain a residue 209 THR Chi-restraints excluded: chain b residue 26 HIS Chi-restraints excluded: chain b residue 74 GLU Chi-restraints excluded: chain b residue 171 LEU Chi-restraints excluded: chain b residue 209 THR Chi-restraints excluded: chain b residue 231 LEU Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 290 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 20.0000 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 50 HIS a 65 ASN ** a 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 26 HIS b 65 ASN b 293 ASN B 31 GLN B 35 GLN ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 26 HIS ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 129 HIS ** A 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.138101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.107978 restraints weight = 24335.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.110104 restraints weight = 33003.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.111829 restraints weight = 17996.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.114262 restraints weight = 12750.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.114554 restraints weight = 10421.639| |-----------------------------------------------------------------------------| r_work (final): 0.3933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 11293 Z= 0.301 Angle : 0.735 8.043 15328 Z= 0.384 Chirality : 0.049 0.260 1646 Planarity : 0.005 0.054 1944 Dihedral : 7.151 80.494 1493 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.75 % Favored : 89.25 % Rotamer: Outliers : 5.05 % Allowed : 11.18 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.41 (0.22), residues: 1368 helix: 1.65 (0.44), residues: 156 sheet: -2.76 (0.35), residues: 188 loop : -2.05 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG b 324 TYR 0.015 0.002 TYR b 32 PHE 0.024 0.003 PHE b 217 TRP 0.021 0.003 TRP b 201 HIS 0.010 0.002 HIS b 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00690 / 0.30 (11272) covalent geometry : angle 0.73201 / 0.38 (15286) SS BOND : bond 0.00473 / 0.28 ( 21) SS BOND : angle 1.39393 / 0.92 ( 42) hydrogen bonds : bond 0.04508 / 3.00 ( 232) hydrogen bonds : angle 6.53856 / 4.58 ( 654) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 120 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 47 GLN cc_start: 0.8874 (OUTLIER) cc_final: 0.8471 (pp30) REVERT: a 89 MET cc_start: 0.8413 (ppp) cc_final: 0.8149 (ppp) REVERT: a 157 ASP cc_start: 0.7645 (t0) cc_final: 0.7378 (m-30) REVERT: a 333 MET cc_start: 0.8521 (mtp) cc_final: 0.7999 (mtp) REVERT: b 26 HIS cc_start: 0.6081 (OUTLIER) cc_final: 0.4722 (t-170) REVERT: b 28 TRP cc_start: 0.6705 (p90) cc_final: 0.6202 (p90) REVERT: b 35 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.8159 (mm110) REVERT: B 47 GLN cc_start: 0.8844 (OUTLIER) cc_final: 0.8441 (pp30) REVERT: B 50 HIS cc_start: 0.8612 (t-90) cc_final: 0.8330 (t-170) REVERT: B 111 LEU cc_start: 0.8743 (mt) cc_final: 0.8542 (mp) REVERT: A 127 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7693 (mp0) REVERT: A 230 THR cc_start: 0.8619 (OUTLIER) cc_final: 0.8215 (p) outliers start: 61 outliers final: 31 residues processed: 164 average time/residue: 0.0894 time to fit residues: 21.9569 Evaluate side-chains 146 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 109 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 21 ILE Chi-restraints excluded: chain a residue 47 GLN Chi-restraints excluded: chain a residue 54 ILE Chi-restraints excluded: chain a residue 97 MET Chi-restraints excluded: chain a residue 184 MET Chi-restraints excluded: chain a residue 209 THR Chi-restraints excluded: chain a residue 230 THR Chi-restraints excluded: chain a residue 241 MET Chi-restraints excluded: chain b residue 26 HIS Chi-restraints excluded: chain b residue 35 GLN Chi-restraints excluded: chain b residue 75 LEU Chi-restraints excluded: chain b residue 171 LEU Chi-restraints excluded: chain b residue 184 MET Chi-restraints excluded: chain b residue 209 THR Chi-restraints excluded: chain b residue 212 ILE Chi-restraints excluded: chain b residue 351 THR Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 47 GLN Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 184 MET Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 241 MET Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain A residue 26 HIS Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 286 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 42 optimal weight: 0.9990 chunk 125 optimal weight: 0.0980 chunk 105 optimal weight: 4.9990 chunk 30 optimal weight: 8.9990 chunk 90 optimal weight: 0.6980 chunk 12 optimal weight: 40.0000 chunk 23 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 98 optimal weight: 10.0000 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 35 GLN ** a 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN A 26 HIS ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 GLN A 263 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.143606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.112399 restraints weight = 24090.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.117795 restraints weight = 27422.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.118052 restraints weight = 13361.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.119408 restraints weight = 10666.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.119942 restraints weight = 9260.479| |-----------------------------------------------------------------------------| r_work (final): 0.4003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11293 Z= 0.118 Angle : 0.569 7.378 15328 Z= 0.292 Chirality : 0.044 0.259 1646 Planarity : 0.003 0.049 1944 Dihedral : 6.086 79.613 1479 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 3.73 % Allowed : 13.33 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.12 (0.22), residues: 1368 helix: 1.91 (0.45), residues: 156 sheet: -2.39 (0.34), residues: 206 loop : -1.88 (0.18), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 314 TYR 0.009 0.001 TYR B 256 PHE 0.010 0.001 PHE a 279 TRP 0.020 0.001 TRP A 28 HIS 0.013 0.001 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (11272) covalent geometry : angle 0.56797 / 0.29 (15286) SS BOND : bond 0.00214 / 0.13 ( 21) SS BOND : angle 0.82437 / 0.56 ( 42) hydrogen bonds : bond 0.03714 / 2.47 ( 232) hydrogen bonds : angle 5.76531 / 4.05 ( 654) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 116 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 12 GLU cc_start: 0.7702 (tp30) cc_final: 0.7136 (pt0) REVERT: a 47 GLN cc_start: 0.8909 (OUTLIER) cc_final: 0.8553 (pp30) REVERT: a 89 MET cc_start: 0.8401 (ppp) cc_final: 0.8077 (ppp) REVERT: a 206 LEU cc_start: 0.7853 (tp) cc_final: 0.7570 (tp) REVERT: b 26 HIS cc_start: 0.5903 (OUTLIER) cc_final: 0.5534 (t-170) REVERT: b 35 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7977 (mm110) REVERT: b 74 GLU cc_start: 0.8904 (OUTLIER) cc_final: 0.8122 (tm-30) REVERT: b 288 THR cc_start: 0.8187 (OUTLIER) cc_final: 0.7903 (p) REVERT: B 47 GLN cc_start: 0.8886 (OUTLIER) cc_final: 0.8579 (pp30) REVERT: B 206 LEU cc_start: 0.7952 (tp) cc_final: 0.7676 (tp) REVERT: A 28 TRP cc_start: 0.6990 (p90) cc_final: 0.6737 (p90) REVERT: A 127 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7670 (mp0) REVERT: A 230 THR cc_start: 0.8513 (OUTLIER) cc_final: 0.8295 (p) outliers start: 45 outliers final: 23 residues processed: 149 average time/residue: 0.0881 time to fit residues: 19.8752 Evaluate side-chains 140 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 109 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 21 ILE Chi-restraints excluded: chain a residue 47 GLN Chi-restraints excluded: chain a residue 54 ILE Chi-restraints excluded: chain a residue 79 LEU Chi-restraints excluded: chain a residue 97 MET Chi-restraints excluded: chain a residue 184 MET Chi-restraints excluded: chain a residue 209 THR Chi-restraints excluded: chain a residue 349 LEU Chi-restraints excluded: chain b residue 26 HIS Chi-restraints excluded: chain b residue 35 GLN Chi-restraints excluded: chain b residue 74 GLU Chi-restraints excluded: chain b residue 171 LEU Chi-restraints excluded: chain b residue 209 THR Chi-restraints excluded: chain b residue 288 THR Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 47 GLN Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 184 MET Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 241 MET Chi-restraints excluded: chain B residue 329 CYS Chi-restraints excluded: chain A residue 26 HIS Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 333 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 43 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 97 optimal weight: 8.9990 chunk 5 optimal weight: 8.9990 chunk 131 optimal weight: 10.0000 chunk 11 optimal weight: 20.0000 chunk 71 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 1 optimal weight: 0.9980 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 77 HIS ** a 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 263 GLN B 263 GLN A 26 HIS ** A 35 GLN ** 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 = 0.4324 r_free = 0.4324 target = 0.142417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.112432 restraints weight = 23949.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.114501 restraints weight = 28708.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.115409 restraints weight = 18277.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.117498 restraints weight = 12559.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.118034 restraints weight = 10405.018| |-----------------------------------------------------------------------------| r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11293 Z= 0.192 Angle : 0.605 6.830 15328 Z= 0.314 Chirality : 0.044 0.195 1646 Planarity : 0.004 0.045 1944 Dihedral : 6.250 78.582 1479 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % Rotamer: Outliers : 4.14 % Allowed : 14.24 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.28 (0.21), residues: 1368 helix: 1.82 (0.45), residues: 156 sheet: -2.51 (0.36), residues: 186 loop : -2.02 (0.18), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 314 TYR 0.016 0.002 TYR b 260 PHE 0.015 0.002 PHE b 217 TRP 0.020 0.002 TRP b 28 HIS 0.011 0.001 HIS a 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 (11272) covalent geometry : angle 0.60413 / 0.31 (15286) SS BOND : bond 0.00322 / 0.20 ( 21) SS BOND : angle 0.95074 / 0.62 ( 42) hydrogen bonds : bond 0.03727 / 2.46 ( 232) hydrogen bonds : angle 5.73082 / 4.02 ( 654) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 108 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 47 GLN cc_start: 0.8928 (OUTLIER) cc_final: 0.8614 (pp30) REVERT: a 67 MET cc_start: 0.8162 (tmm) cc_final: 0.7938 (tmm) REVERT: a 89 MET cc_start: 0.8387 (ppp) cc_final: 0.8077 (ppp) REVERT: b 26 HIS cc_start: 0.5512 (OUTLIER) cc_final: 0.4485 (t-170) REVERT: b 28 TRP cc_start: 0.6686 (p90) cc_final: 0.6055 (p90) REVERT: b 35 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.8026 (mm110) REVERT: b 74 GLU cc_start: 0.8941 (OUTLIER) cc_final: 0.8141 (tm-30) REVERT: B 47 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.8571 (pp30) REVERT: A 127 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7736 (mp0) REVERT: A 230 THR cc_start: 0.8480 (OUTLIER) cc_final: 0.8157 (p) outliers start: 50 outliers final: 29 residues processed: 145 average time/residue: 0.0916 time to fit residues: 19.6951 Evaluate side-chains 143 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 107 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 21 ILE Chi-restraints excluded: chain a residue 47 GLN Chi-restraints excluded: chain a residue 54 ILE Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain a residue 79 LEU Chi-restraints excluded: chain a residue 97 MET Chi-restraints excluded: chain a residue 184 MET Chi-restraints excluded: chain a residue 209 THR Chi-restraints excluded: chain a residue 212 ILE Chi-restraints excluded: chain a residue 230 THR Chi-restraints excluded: chain a residue 241 MET Chi-restraints excluded: chain a residue 300 THR Chi-restraints excluded: chain a residue 349 LEU Chi-restraints excluded: chain b residue 26 HIS Chi-restraints excluded: chain b residue 35 GLN Chi-restraints excluded: chain b residue 74 GLU Chi-restraints excluded: chain b residue 171 LEU Chi-restraints excluded: chain b residue 212 ILE Chi-restraints excluded: chain b residue 351 THR Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 47 GLN Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 184 MET Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 241 MET Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 329 CYS Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 333 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 27 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 chunk 24 optimal weight: 0.7980 chunk 38 optimal weight: 6.9990 chunk 9 optimal weight: 8.9990 chunk 45 optimal weight: 10.0000 chunk 121 optimal weight: 0.9990 chunk 132 optimal weight: 10.0000 chunk 124 optimal weight: 0.4980 chunk 90 optimal weight: 0.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 147 ASN ** A 35 GLN ** 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 = 0.4342 r_free = 0.4342 target = 0.143541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.112563 restraints weight = 24016.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.117235 restraints weight = 28764.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.117715 restraints weight = 14820.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.119544 restraints weight = 11631.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.119737 restraints weight = 10293.903| |-----------------------------------------------------------------------------| r_work (final): 0.4000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11293 Z= 0.116 Angle : 0.554 7.135 15328 Z= 0.285 Chirality : 0.043 0.280 1646 Planarity : 0.003 0.041 1944 Dihedral : 5.901 78.412 1478 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 3.31 % Allowed : 15.81 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.21), residues: 1368 helix: 1.88 (0.45), residues: 156 sheet: -2.33 (0.36), residues: 196 loop : -1.92 (0.18), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 314 TYR 0.024 0.001 TYR b 260 PHE 0.009 0.001 PHE b 217 TRP 0.022 0.001 TRP A 28 HIS 0.005 0.001 HIS B 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (11272) covalent geometry : angle 0.55327 / 0.28 (15286) SS BOND : bond 0.00214 / 0.13 ( 21) SS BOND : angle 0.74552 / 0.51 ( 42) hydrogen bonds : bond 0.03378 / 2.24 ( 232) hydrogen bonds : angle 5.40033 / 3.80 ( 654) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 118 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 47 GLN cc_start: 0.8909 (OUTLIER) cc_final: 0.8567 (pp30) REVERT: a 89 MET cc_start: 0.8382 (ppp) cc_final: 0.8089 (ppp) REVERT: b 26 HIS cc_start: 0.5482 (OUTLIER) cc_final: 0.5130 (t-170) REVERT: b 35 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.7971 (mm110) REVERT: b 74 GLU cc_start: 0.8961 (OUTLIER) cc_final: 0.8182 (tm-30) REVERT: B 47 GLN cc_start: 0.8845 (pt0) cc_final: 0.8449 (pp30) REVERT: A 28 TRP cc_start: 0.6857 (p90) cc_final: 0.6402 (p90) REVERT: A 127 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7698 (mp0) REVERT: A 230 THR cc_start: 0.8607 (OUTLIER) cc_final: 0.8348 (p) outliers start: 40 outliers final: 25 residues processed: 144 average time/residue: 0.0944 time to fit residues: 20.0001 Evaluate side-chains 143 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 112 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 21 ILE Chi-restraints excluded: chain a residue 47 GLN Chi-restraints excluded: chain a residue 54 ILE Chi-restraints excluded: chain a residue 79 LEU Chi-restraints excluded: chain a residue 97 MET Chi-restraints excluded: chain a residue 209 THR Chi-restraints excluded: chain a residue 212 ILE Chi-restraints excluded: chain a residue 241 MET Chi-restraints excluded: chain a residue 260 TYR Chi-restraints excluded: chain a residue 300 THR Chi-restraints excluded: chain a residue 349 LEU Chi-restraints excluded: chain b residue 26 HIS Chi-restraints excluded: chain b residue 35 GLN Chi-restraints excluded: chain b residue 74 GLU Chi-restraints excluded: chain b residue 171 LEU Chi-restraints excluded: chain b residue 351 THR Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 241 MET Chi-restraints excluded: chain A residue 26 HIS Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 333 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 126 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 124 optimal weight: 0.9980 chunk 47 optimal weight: 6.9990 chunk 123 optimal weight: 4.9990 chunk 52 optimal weight: 0.3980 chunk 72 optimal weight: 2.9990 chunk 24 optimal weight: 0.0970 chunk 75 optimal weight: 7.9990 chunk 69 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 overall best weight: 1.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.142094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.113140 restraints weight = 24219.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.113029 restraints weight = 29371.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.115270 restraints weight = 20406.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.116087 restraints weight = 13482.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.117676 restraints weight = 11533.236| |-----------------------------------------------------------------------------| r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11293 Z= 0.150 Angle : 0.577 9.010 15328 Z= 0.298 Chirality : 0.044 0.244 1646 Planarity : 0.003 0.039 1944 Dihedral : 5.934 77.721 1478 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 3.89 % Allowed : 16.06 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.17 (0.21), residues: 1368 helix: 1.89 (0.45), residues: 156 sheet: -2.40 (0.37), residues: 186 loop : -1.94 (0.17), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 314 TYR 0.022 0.001 TYR b 260 PHE 0.012 0.001 PHE b 217 TRP 0.027 0.001 TRP b 28 HIS 0.006 0.001 HIS B 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (11272) covalent geometry : angle 0.57623 / 0.30 (15286) SS BOND : bond 0.00259 / 0.16 ( 21) SS BOND : angle 0.79348 / 0.53 ( 42) hydrogen bonds : bond 0.03417 / 2.26 ( 232) hydrogen bonds : angle 5.36820 / 3.78 ( 654) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 115 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 47 GLN cc_start: 0.8934 (OUTLIER) cc_final: 0.8582 (pp30) REVERT: a 50 HIS cc_start: 0.8569 (t70) cc_final: 0.8334 (t70) REVERT: a 206 LEU cc_start: 0.7840 (tp) cc_final: 0.7564 (tp) REVERT: b 26 HIS cc_start: 0.5184 (OUTLIER) cc_final: 0.4649 (t-170) REVERT: b 28 TRP cc_start: 0.6694 (p90) cc_final: 0.6155 (p90) REVERT: b 74 GLU cc_start: 0.8975 (OUTLIER) cc_final: 0.8737 (tm-30) REVERT: b 275 MET cc_start: 0.8781 (ttt) cc_final: 0.8270 (ttm) REVERT: B 47 GLN cc_start: 0.8834 (pt0) cc_final: 0.8536 (pp30) REVERT: B 182 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8225 (mptp) REVERT: B 206 LEU cc_start: 0.7945 (tp) cc_final: 0.7687 (tp) REVERT: A 127 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7735 (mp0) REVERT: A 209 THR cc_start: 0.8335 (OUTLIER) cc_final: 0.7842 (p) REVERT: A 230 THR cc_start: 0.8495 (OUTLIER) cc_final: 0.8186 (p) outliers start: 47 outliers final: 30 residues processed: 151 average time/residue: 0.0985 time to fit residues: 22.1969 Evaluate side-chains 147 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 110 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 21 ILE Chi-restraints excluded: chain a residue 47 GLN Chi-restraints excluded: chain a residue 54 ILE Chi-restraints excluded: chain a residue 79 LEU Chi-restraints excluded: chain a residue 97 MET Chi-restraints excluded: chain a residue 209 THR Chi-restraints excluded: chain a residue 212 ILE Chi-restraints excluded: chain a residue 241 MET Chi-restraints excluded: chain a residue 260 TYR Chi-restraints excluded: chain a residue 283 THR Chi-restraints excluded: chain a residue 300 THR Chi-restraints excluded: chain a residue 349 LEU Chi-restraints excluded: chain b residue 26 HIS Chi-restraints excluded: chain b residue 74 GLU Chi-restraints excluded: chain b residue 171 LEU Chi-restraints excluded: chain b residue 212 ILE Chi-restraints excluded: chain b residue 312 CYS Chi-restraints excluded: chain b residue 351 THR Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 241 MET Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 329 CYS Chi-restraints excluded: chain A residue 26 HIS Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 333 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 41 optimal weight: 8.9990 chunk 115 optimal weight: 0.9990 chunk 76 optimal weight: 9.9990 chunk 128 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 52 optimal weight: 0.4980 chunk 121 optimal weight: 0.7980 chunk 106 optimal weight: 7.9990 chunk 57 optimal weight: 0.1980 chunk 30 optimal weight: 0.6980 chunk 93 optimal weight: 4.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.145865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.115683 restraints weight = 24147.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.118574 restraints weight = 28116.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.119930 restraints weight = 16922.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.120694 restraints weight = 12145.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.122108 restraints weight = 10326.845| |-----------------------------------------------------------------------------| r_work (final): 0.4025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11293 Z= 0.093 Angle : 0.537 8.738 15328 Z= 0.273 Chirality : 0.042 0.156 1646 Planarity : 0.003 0.034 1944 Dihedral : 5.579 77.709 1478 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.06 % Allowed : 15.89 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.21), residues: 1368 helix: 1.87 (0.46), residues: 156 sheet: -2.28 (0.35), residues: 206 loop : -1.81 (0.18), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 314 TYR 0.015 0.001 TYR b 260 PHE 0.007 0.001 PHE B 20 TRP 0.019 0.001 TRP A 28 HIS 0.004 0.001 HIS B 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.09 (11272) covalent geometry : angle 0.53616 / 0.27 (15286) SS BOND : bond 0.00230 / 0.16 ( 21) SS BOND : angle 0.69548 / 0.44 ( 42) hydrogen bonds : bond 0.03178 / 2.10 ( 232) hydrogen bonds : angle 5.05573 / 3.56 ( 654) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 122 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 12 GLU cc_start: 0.7658 (tp30) cc_final: 0.7042 (pt0) REVERT: a 47 GLN cc_start: 0.8974 (pt0) cc_final: 0.8618 (pp30) REVERT: a 157 ASP cc_start: 0.7530 (t0) cc_final: 0.7272 (m-30) REVERT: a 206 LEU cc_start: 0.7823 (tp) cc_final: 0.7576 (tp) REVERT: b 26 HIS cc_start: 0.5308 (OUTLIER) cc_final: 0.4785 (t-170) REVERT: b 28 TRP cc_start: 0.6566 (p90) cc_final: 0.6099 (p90) REVERT: b 74 GLU cc_start: 0.9002 (OUTLIER) cc_final: 0.8754 (tm-30) REVERT: b 113 TYR cc_start: 0.7462 (t80) cc_final: 0.7032 (t80) REVERT: b 275 MET cc_start: 0.8893 (ttt) cc_final: 0.8683 (ttt) REVERT: B 47 GLN cc_start: 0.8863 (pt0) cc_final: 0.8492 (pp30) REVERT: B 206 LEU cc_start: 0.7980 (tp) cc_final: 0.7774 (tp) REVERT: A 28 TRP cc_start: 0.6660 (p90) cc_final: 0.6250 (p90) REVERT: A 127 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7721 (mp0) REVERT: A 230 THR cc_start: 0.8455 (OUTLIER) cc_final: 0.8232 (p) outliers start: 37 outliers final: 27 residues processed: 148 average time/residue: 0.0952 time to fit residues: 21.1823 Evaluate side-chains 145 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 114 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 54 ILE Chi-restraints excluded: chain a residue 79 LEU Chi-restraints excluded: chain a residue 97 MET Chi-restraints excluded: chain a residue 209 THR Chi-restraints excluded: chain a residue 212 ILE Chi-restraints excluded: chain a residue 241 MET Chi-restraints excluded: chain a residue 260 TYR Chi-restraints excluded: chain a residue 283 THR Chi-restraints excluded: chain a residue 300 THR Chi-restraints excluded: chain b residue 26 HIS Chi-restraints excluded: chain b residue 74 GLU Chi-restraints excluded: chain b residue 171 LEU Chi-restraints excluded: chain b residue 212 ILE Chi-restraints excluded: chain b residue 312 CYS Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 241 MET Chi-restraints excluded: chain B residue 329 CYS Chi-restraints excluded: chain A residue 26 HIS Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 230 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 42 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 95 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 70 optimal weight: 0.0170 chunk 123 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 22 optimal weight: 0.0170 chunk 68 optimal weight: 10.0000 overall best weight: 1.7860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 253 GLN ** b 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 GLN ** A 35 GLN ** 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 = 0.4339 r_free = 0.4339 target = 0.143367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.113871 restraints weight = 23971.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.114329 restraints weight = 29671.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.115779 restraints weight = 20998.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.118963 restraints weight = 13667.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.119327 restraints weight = 10182.079| |-----------------------------------------------------------------------------| r_work (final): 0.3992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11293 Z= 0.144 Angle : 0.582 9.462 15328 Z= 0.297 Chirality : 0.043 0.191 1646 Planarity : 0.003 0.033 1944 Dihedral : 5.726 77.270 1477 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 3.23 % Allowed : 16.14 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.21), residues: 1368 helix: 1.82 (0.46), residues: 156 sheet: -2.33 (0.37), residues: 194 loop : -1.84 (0.17), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 322 TYR 0.016 0.001 TYR b 260 PHE 0.013 0.001 PHE a 34 TRP 0.014 0.001 TRP a 68 HIS 0.006 0.001 HIS B 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 (11272) covalent geometry : angle 0.58088 / 0.30 (15286) SS BOND : bond 0.00247 / 0.15 ( 21) SS BOND : angle 0.77579 / 0.50 ( 42) hydrogen bonds : bond 0.03347 / 2.22 ( 232) hydrogen bonds : angle 5.19093 / 3.66 ( 654) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 115 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 47 GLN cc_start: 0.8923 (pt0) cc_final: 0.8046 (pp30) REVERT: a 123 MET cc_start: 0.6819 (ppp) cc_final: 0.6137 (ppp) REVERT: a 206 LEU cc_start: 0.7856 (tp) cc_final: 0.7557 (tp) REVERT: b 26 HIS cc_start: 0.5370 (OUTLIER) cc_final: 0.4671 (t-170) REVERT: b 28 TRP cc_start: 0.6531 (p90) cc_final: 0.6131 (p90) REVERT: b 74 GLU cc_start: 0.8985 (OUTLIER) cc_final: 0.8765 (tm-30) REVERT: b 113 TYR cc_start: 0.7482 (t80) cc_final: 0.7081 (t80) REVERT: b 275 MET cc_start: 0.8921 (ttt) cc_final: 0.8705 (ttt) REVERT: B 47 GLN cc_start: 0.8828 (pt0) cc_final: 0.8566 (pp30) REVERT: B 123 MET cc_start: 0.3270 (mmt) cc_final: 0.3062 (tpt) REVERT: B 206 LEU cc_start: 0.7903 (tp) cc_final: 0.7699 (tp) REVERT: A 127 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7722 (mp0) REVERT: A 230 THR cc_start: 0.8570 (OUTLIER) cc_final: 0.8270 (p) outliers start: 39 outliers final: 29 residues processed: 143 average time/residue: 0.0938 time to fit residues: 20.1010 Evaluate side-chains 146 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 113 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 54 ILE Chi-restraints excluded: chain a residue 79 LEU Chi-restraints excluded: chain a residue 97 MET Chi-restraints excluded: chain a residue 209 THR Chi-restraints excluded: chain a residue 212 ILE Chi-restraints excluded: chain a residue 241 MET Chi-restraints excluded: chain a residue 260 TYR Chi-restraints excluded: chain a residue 283 THR Chi-restraints excluded: chain a residue 300 THR Chi-restraints excluded: chain a residue 349 LEU Chi-restraints excluded: chain b residue 26 HIS Chi-restraints excluded: chain b residue 74 GLU Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain b residue 171 LEU Chi-restraints excluded: chain b residue 212 ILE Chi-restraints excluded: chain b residue 312 CYS Chi-restraints excluded: chain b residue 351 THR Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 241 MET Chi-restraints excluded: chain B residue 329 CYS Chi-restraints excluded: chain A residue 26 HIS Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 333 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 60 optimal weight: 0.3980 chunk 42 optimal weight: 5.9990 chunk 2 optimal weight: 0.2980 chunk 68 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 113 optimal weight: 8.9990 chunk 73 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 112 optimal weight: 8.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 253 GLN ** b 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 GLN ** A 35 GLN ** 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 = 0.4333 r_free = 0.4333 target = 0.142859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.112733 restraints weight = 23875.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.115576 restraints weight = 32177.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.116776 restraints weight = 19103.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.117410 restraints weight = 13799.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.119042 restraints weight = 11311.161| |-----------------------------------------------------------------------------| r_work (final): 0.3990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11293 Z= 0.154 Angle : 0.616 14.712 15328 Z= 0.311 Chirality : 0.043 0.191 1646 Planarity : 0.003 0.035 1944 Dihedral : 5.850 78.018 1477 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 3.15 % Allowed : 16.23 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.22), residues: 1368 helix: 1.74 (0.46), residues: 156 sheet: -2.32 (0.37), residues: 198 loop : -1.85 (0.18), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 322 TYR 0.022 0.001 TYR b 260 PHE 0.013 0.001 PHE b 217 TRP 0.021 0.002 TRP A 28 HIS 0.006 0.001 HIS B 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 (11272) covalent geometry : angle 0.61515 / 0.31 (15286) SS BOND : bond 0.00259 / 0.16 ( 21) SS BOND : angle 0.80053 / 0.52 ( 42) hydrogen bonds : bond 0.03465 / 2.31 ( 232) hydrogen bonds : angle 5.27836 / 3.72 ( 654) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 114 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 47 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.8468 (pp30) REVERT: a 157 ASP cc_start: 0.7551 (t0) cc_final: 0.7327 (m-30) REVERT: a 206 LEU cc_start: 0.7880 (tp) cc_final: 0.7595 (tp) REVERT: b 26 HIS cc_start: 0.5443 (OUTLIER) cc_final: 0.4758 (t-170) REVERT: b 28 TRP cc_start: 0.6430 (p90) cc_final: 0.6041 (p90) REVERT: b 275 MET cc_start: 0.8909 (ttt) cc_final: 0.8698 (ttt) REVERT: B 47 GLN cc_start: 0.8826 (pt0) cc_final: 0.8576 (pp30) REVERT: B 123 MET cc_start: 0.3296 (mmt) cc_final: 0.3078 (tpt) REVERT: B 206 LEU cc_start: 0.7902 (tp) cc_final: 0.7655 (tp) REVERT: A 28 TRP cc_start: 0.6713 (p90) cc_final: 0.6254 (p90) REVERT: A 127 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7731 (mp0) REVERT: A 230 THR cc_start: 0.8490 (OUTLIER) cc_final: 0.8160 (p) outliers start: 38 outliers final: 29 residues processed: 141 average time/residue: 0.0964 time to fit residues: 20.5075 Evaluate side-chains 140 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 107 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 47 GLN Chi-restraints excluded: chain a residue 54 ILE Chi-restraints excluded: chain a residue 79 LEU Chi-restraints excluded: chain a residue 97 MET Chi-restraints excluded: chain a residue 209 THR Chi-restraints excluded: chain a residue 212 ILE Chi-restraints excluded: chain a residue 241 MET Chi-restraints excluded: chain a residue 260 TYR Chi-restraints excluded: chain a residue 283 THR Chi-restraints excluded: chain a residue 300 THR Chi-restraints excluded: chain a residue 349 LEU Chi-restraints excluded: chain b residue 26 HIS Chi-restraints excluded: chain b residue 61 THR Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain b residue 171 LEU Chi-restraints excluded: chain b residue 212 ILE Chi-restraints excluded: chain b residue 219 GLU Chi-restraints excluded: chain b residue 312 CYS Chi-restraints excluded: chain b residue 351 THR Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 241 MET Chi-restraints excluded: chain B residue 329 CYS Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 333 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 23 optimal weight: 0.9980 chunk 127 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 chunk 124 optimal weight: 0.2980 chunk 11 optimal weight: 20.0000 chunk 91 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 chunk 14 optimal weight: 0.0970 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 253 GLN B 253 GLN ** A 35 GLN ** 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 = 0.4380 r_free = 0.4380 target = 0.146098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.118169 restraints weight = 23524.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.117795 restraints weight = 29842.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.119737 restraints weight = 20379.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.122170 restraints weight = 13137.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.122746 restraints weight = 10285.244| |-----------------------------------------------------------------------------| r_work (final): 0.4048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 11293 Z= 0.100 Angle : 0.578 13.908 15328 Z= 0.287 Chirality : 0.042 0.168 1646 Planarity : 0.003 0.033 1944 Dihedral : 5.477 77.502 1475 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.32 % Allowed : 17.47 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.92 (0.22), residues: 1368 helix: 1.76 (0.46), residues: 156 sheet: -2.13 (0.36), residues: 208 loop : -1.70 (0.18), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 314 TYR 0.014 0.001 TYR b 260 PHE 0.020 0.001 PHE a 34 TRP 0.025 0.001 TRP B 118 HIS 0.003 0.001 HIS B 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 (11272) covalent geometry : angle 0.57818 / 0.29 (15286) SS BOND : bond 0.00165 / 0.11 ( 21) SS BOND : angle 0.63653 / 0.41 ( 42) hydrogen bonds : bond 0.03207 / 2.15 ( 232) hydrogen bonds : angle 5.07849 / 3.58 ( 654) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 12 GLU cc_start: 0.7454 (tp30) cc_final: 0.7031 (pt0) REVERT: a 47 GLN cc_start: 0.8674 (pt0) cc_final: 0.8377 (pp30) REVERT: a 65 ASN cc_start: 0.8716 (t0) cc_final: 0.7986 (t0) REVERT: a 123 MET cc_start: 0.6741 (ppp) cc_final: 0.6241 (ppp) REVERT: a 206 LEU cc_start: 0.7732 (tp) cc_final: 0.7497 (tp) REVERT: a 253 GLN cc_start: 0.6875 (mt0) cc_final: 0.6611 (mt0) REVERT: b 26 HIS cc_start: 0.5280 (OUTLIER) cc_final: 0.4736 (t-170) REVERT: b 28 TRP cc_start: 0.6242 (p90) cc_final: 0.5956 (p90) REVERT: b 113 TYR cc_start: 0.7488 (t80) cc_final: 0.7190 (t80) REVERT: B 47 GLN cc_start: 0.8816 (pt0) cc_final: 0.8483 (pp30) REVERT: B 123 MET cc_start: 0.3025 (mmt) cc_final: 0.2806 (tpt) REVERT: A 28 TRP cc_start: 0.6632 (p90) cc_final: 0.6157 (p90) REVERT: A 127 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7730 (mp0) REVERT: A 232 TRP cc_start: 0.7789 (t60) cc_final: 0.7427 (t60) outliers start: 28 outliers final: 24 residues processed: 141 average time/residue: 0.0995 time to fit residues: 20.6043 Evaluate side-chains 139 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 79 LEU Chi-restraints excluded: chain a residue 97 MET Chi-restraints excluded: chain a residue 209 THR Chi-restraints excluded: chain a residue 212 ILE Chi-restraints excluded: chain a residue 241 MET Chi-restraints excluded: chain a residue 260 TYR Chi-restraints excluded: chain a residue 283 THR Chi-restraints excluded: chain a residue 300 THR Chi-restraints excluded: chain b residue 26 HIS Chi-restraints excluded: chain b residue 171 LEU Chi-restraints excluded: chain b residue 212 ILE Chi-restraints excluded: chain b residue 312 CYS Chi-restraints excluded: chain b residue 351 THR Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 241 MET Chi-restraints excluded: chain B residue 329 CYS Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 212 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 112 optimal weight: 0.4980 chunk 122 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 114 optimal weight: 0.3980 chunk 104 optimal weight: 1.9990 chunk 79 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 134 optimal weight: 0.8980 chunk 36 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 253 GLN ** A 35 GLN ** 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 = 0.4374 r_free = 0.4374 target = 0.146144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.115851 restraints weight = 24013.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.119560 restraints weight = 26945.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.119972 restraints weight = 16859.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.120938 restraints weight = 11890.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.122162 restraints weight = 10185.128| |-----------------------------------------------------------------------------| r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 11293 Z= 0.103 Angle : 0.586 13.260 15328 Z= 0.291 Chirality : 0.042 0.178 1646 Planarity : 0.003 0.032 1944 Dihedral : 5.376 77.469 1474 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 2.24 % Allowed : 17.47 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.22), residues: 1368 helix: 1.70 (0.45), residues: 156 sheet: -2.21 (0.35), residues: 216 loop : -1.63 (0.18), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 322 TYR 0.014 0.001 TYR b 260 PHE 0.020 0.001 PHE a 34 TRP 0.027 0.001 TRP a 225 HIS 0.004 0.001 HIS B 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.10 (11272) covalent geometry : angle 0.58640 / 0.29 (15286) SS BOND : bond 0.00165 / 0.11 ( 21) SS BOND : angle 0.61065 / 0.39 ( 42) hydrogen bonds : bond 0.03171 / 2.12 ( 232) hydrogen bonds : angle 4.98662 / 3.51 ( 654) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1894.67 seconds wall clock time: 33 minutes 30.71 seconds (2010.71 seconds total)