Starting phenix.real_space_refine on Wed Sep 17 11:15:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jkq_61567/09_2025/9jkq_61567.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jkq_61567/09_2025/9jkq_61567.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jkq_61567/09_2025/9jkq_61567.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jkq_61567/09_2025/9jkq_61567.map" model { file = "/net/cci-nas-00/data/ceres_data/9jkq_61567/09_2025/9jkq_61567.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jkq_61567/09_2025/9jkq_61567.cif" } resolution = 2.66 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= -0.002 sd= 0.078 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 63 5.16 5 C 5336 2.51 5 N 1446 2.21 5 O 1541 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8386 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1947 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain breaks: 2 Chain: "B" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2606 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "C" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 442 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 2407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2407 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 11, 'TRANS': 284} Chain breaks: 1 Chain: "R" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'B40': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.90, per 1000 atoms: 0.23 Number of scatterers: 8386 At special positions: 0 Unit cell: (79.143, 102.12, 134.458, 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 63 16.00 O 1541 8.00 N 1446 7.00 C 5336 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 182 " 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: 0.51 Conformation dependent library (CDL) restraints added in 448.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB B40 R 401 " Number of C-beta restraints generated: 1986 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 10 sheets defined 41.8% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 9 through 39 removed outlier: 3.570A pdb=" N GLN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 60 removed outlier: 3.585A pdb=" N MET A 60 " --> pdb=" O ILE A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.567A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.708A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 391 removed outlier: 3.838A pdb=" N ARG A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 37 Processing helix chain 'B' and resid 40 through 46 removed outlier: 3.765A pdb=" N ILE B 44 " --> pdb=" O THR B 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 24 removed outlier: 3.665A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.566A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.550A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.959A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 19 through 51 removed outlier: 3.620A pdb=" N ASN R 41 " --> pdb=" O THR R 37 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE R 51 " --> pdb=" O SER R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 56 through 76 removed outlier: 3.531A pdb=" N LEU R 61 " --> pdb=" O PRO R 57 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL R 76 " --> pdb=" O LEU R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 76 through 87 Processing helix chain 'R' and resid 94 through 127 removed outlier: 5.947A pdb=" N THR R 100 " --> pdb=" O CYS R 96 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER R 101 " --> pdb=" O LYS R 97 " (cutoff:3.500A) Processing helix chain 'R' and resid 130 through 135 Processing helix chain 'R' and resid 136 through 160 Proline residue: R 151 - end of helix removed outlier: 3.629A pdb=" N PHE R 160 " --> pdb=" O PHE R 156 " (cutoff:3.500A) Processing helix chain 'R' and resid 169 through 179 Processing helix chain 'R' and resid 187 through 199 Processing helix chain 'R' and resid 199 through 230 removed outlier: 4.007A pdb=" N ARG R 212 " --> pdb=" O CYS R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 248 through 274 removed outlier: 3.707A pdb=" N PHE R 260 " --> pdb=" O VAL R 256 " (cutoff:3.500A) Proline residue: R 266 - end of helix removed outlier: 3.885A pdb=" N MET R 273 " --> pdb=" O ILE R 269 " (cutoff:3.500A) Processing helix chain 'R' and resid 275 through 278 removed outlier: 3.620A pdb=" N HIS R 278 " --> pdb=" O PRO R 275 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 275 through 278' Processing helix chain 'R' and resid 282 through 305 removed outlier: 3.939A pdb=" N ASN R 296 " --> pdb=" O PHE R 292 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N SER R 297 " --> pdb=" O GLY R 293 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N THR R 298 " --> pdb=" O TYR R 294 " (cutoff:3.500A) Proline residue: R 301 - end of helix Processing helix chain 'R' and resid 308 through 322 removed outlier: 3.613A pdb=" N ARG R 312 " --> pdb=" O TYR R 308 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.269A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 9.770A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.723A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 57 through 62 removed outlier: 3.648A pdb=" N ARG B 57 " --> pdb=" O ASN B 351 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE B 349 " --> pdb=" O ARG B 59 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N THR B 61 " --> pdb=" O LEU B 347 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LEU B 347 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N CYS B 328 " --> pdb=" O GLY B 341 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 69 through 74 removed outlier: 4.059A pdb=" N ALA B 71 " --> pdb=" O ALA B 84 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LYS B 89 " --> pdb=" O SER B 85 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ASP B 94 " --> pdb=" O LYS B 100 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N LYS B 100 " --> pdb=" O ASP B 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 111 through 116 removed outlier: 6.866A pdb=" N GLY B 126 " --> pdb=" O MET B 112 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N CYS B 114 " --> pdb=" O ALA B 124 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ALA B 124 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N TYR B 116 " --> pdb=" O TYR B 122 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N TYR B 122 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLY B 127 " --> pdb=" O ILE B 131 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N ILE B 131 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG B 148 " --> pdb=" O ILE B 134 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ASN B 136 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N VAL B 146 " --> pdb=" O ASN B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 157 through 162 removed outlier: 3.666A pdb=" N CYS B 159 " --> pdb=" O SER B 171 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE B 168 " --> pdb=" O TRP B 180 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR B 189 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ASP B 181 " --> pdb=" O GLN B 187 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N GLN B 187 " --> pdb=" O ASP B 181 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 198 through 203 removed outlier: 6.859A pdb=" N GLY B 213 " --> pdb=" O MET B 199 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LEU B 201 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL B 211 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N LEU B 203 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N LEU B 209 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLN B 231 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ASP B 223 " --> pdb=" O CYS B 229 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N CYS B 229 " --> pdb=" O ASP B 223 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 240 through 245 removed outlier: 6.504A pdb=" N GLY B 255 " --> pdb=" O ASN B 241 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ILE B 243 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ALA B 253 " --> pdb=" O ILE B 243 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N PHE B 245 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ALA B 251 " --> pdb=" O PHE B 245 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N MET B 273 " --> pdb=" O LEU B 263 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ASP B 265 " --> pdb=" O GLU B 271 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N GLU B 271 " --> pdb=" O ASP B 265 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 284 through 289 removed outlier: 3.513A pdb=" N SER B 286 " --> pdb=" O GLY B 299 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N CYS B 305 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N VAL B 318 " --> pdb=" O CYS B 305 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL B 307 " --> pdb=" O ALA B 316 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.558A pdb=" N SER N 71 " --> pdb=" O TYR N 80 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.490A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 410 hydrogen bonds defined for protein. 1191 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: 1.35 Time building geometry restraints manager: 0.74 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: 2713 1.34 - 1.46: 1934 1.46 - 1.58: 3829 1.58 - 1.70: 0 1.70 - 1.81: 92 Bond restraints: 8568 Sorted by residual: bond pdb=" CB B40 R 401 " pdb=" CG B40 R 401 " ideal model delta sigma weight residual 1.501 1.521 -0.020 2.00e-02 2.50e+03 1.00e+00 bond pdb=" SD MET R 30 " pdb=" CE MET R 30 " ideal model delta sigma weight residual 1.791 1.767 0.024 2.50e-02 1.60e+03 9.35e-01 bond pdb=" CA THR B 207 " pdb=" C THR B 207 " ideal model delta sigma weight residual 1.524 1.538 -0.014 1.57e-02 4.06e+03 7.84e-01 bond pdb=" CG1 ILE A 348 " pdb=" CD1 ILE A 348 " ideal model delta sigma weight residual 1.513 1.484 0.029 3.90e-02 6.57e+02 5.60e-01 bond pdb=" CG1 ILE R 290 " pdb=" CD1 ILE R 290 " ideal model delta sigma weight residual 1.513 1.484 0.029 3.90e-02 6.57e+02 5.41e-01 ... (remaining 8563 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 11307 1.43 - 2.86: 240 2.86 - 4.29: 30 4.29 - 5.72: 13 5.72 - 7.15: 1 Bond angle restraints: 11591 Sorted by residual: angle pdb=" CA TYR R 90 " pdb=" CB TYR R 90 " pdb=" CG TYR R 90 " ideal model delta sigma weight residual 113.90 118.62 -4.72 1.80e+00 3.09e-01 6.89e+00 angle pdb=" N CYS R 96 " pdb=" CA CYS R 96 " pdb=" C CYS R 96 " ideal model delta sigma weight residual 113.20 109.87 3.33 1.36e+00 5.41e-01 5.98e+00 angle pdb=" N LYS R 97 " pdb=" CA LYS R 97 " pdb=" C LYS R 97 " ideal model delta sigma weight residual 114.62 111.84 2.78 1.14e+00 7.69e-01 5.94e+00 angle pdb=" CA TRP R 291 " pdb=" CB TRP R 291 " pdb=" CG TRP R 291 " ideal model delta sigma weight residual 113.60 109.05 4.55 1.90e+00 2.77e-01 5.72e+00 angle pdb=" CA TRP R 89 " pdb=" C TRP R 89 " pdb=" N TYR R 90 " ideal model delta sigma weight residual 114.17 117.22 -3.05 1.45e+00 4.76e-01 4.42e+00 ... (remaining 11586 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 4659 17.79 - 35.57: 363 35.57 - 53.36: 58 53.36 - 71.15: 7 71.15 - 88.93: 10 Dihedral angle restraints: 5097 sinusoidal: 2024 harmonic: 3073 Sorted by residual: dihedral pdb=" CB CYS R 96 " pdb=" SG CYS R 96 " pdb=" SG CYS R 182 " pdb=" CB CYS R 182 " ideal model delta sinusoidal sigma weight residual 93.00 168.91 -75.91 1 1.00e+01 1.00e-02 7.26e+01 dihedral pdb=" CA CYS R 96 " pdb=" C CYS R 96 " pdb=" N LYS R 97 " pdb=" CA LYS R 97 " ideal model delta harmonic sigma weight residual 180.00 155.24 24.76 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA TRP B 93 " pdb=" C TRP B 93 " pdb=" N ASP B 94 " pdb=" CA ASP B 94 " ideal model delta harmonic sigma weight residual 180.00 160.98 19.02 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 5094 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 867 0.038 - 0.076: 313 0.076 - 0.114: 91 0.114 - 0.152: 15 0.152 - 0.191: 1 Chirality restraints: 1287 Sorted by residual: chirality pdb=" CA B40 R 401 " pdb=" N B40 R 401 " pdb=" C B40 R 401 " pdb=" CB B40 R 401 " both_signs ideal model delta sigma weight residual False -2.42 -2.61 0.19 2.00e-01 2.50e+01 9.08e-01 chirality pdb=" CA MET R 77 " pdb=" N MET R 77 " pdb=" C MET R 77 " pdb=" CB MET R 77 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.16e-01 chirality pdb=" CA VAL N 37 " pdb=" N VAL N 37 " pdb=" C VAL N 37 " pdb=" CB VAL N 37 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.94e-01 ... (remaining 1284 not shown) Planarity restraints: 1472 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 246 " 0.038 5.00e-02 4.00e+02 5.75e-02 5.28e+00 pdb=" N PRO B 247 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO B 247 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 247 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 54 " -0.028 5.00e-02 4.00e+02 4.29e-02 2.94e+00 pdb=" N PRO C 55 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO C 55 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 55 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR R 56 " -0.026 5.00e-02 4.00e+02 3.89e-02 2.42e+00 pdb=" N PRO R 57 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO R 57 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO R 57 " -0.022 5.00e-02 4.00e+02 ... (remaining 1469 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 86 2.66 - 3.22: 7499 3.22 - 3.78: 12627 3.78 - 4.34: 17986 4.34 - 4.90: 29772 Nonbonded interactions: 67970 Sorted by model distance: nonbonded pdb=" OG SER B 256 " pdb=" OD1 ASP B 258 " model vdw 2.097 3.040 nonbonded pdb=" O ARG N 98 " pdb=" OH TYR N 115 " model vdw 2.220 3.040 nonbonded pdb=" OG SER B 292 " pdb=" OD2 ASP C 48 " model vdw 2.255 3.040 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.270 3.040 nonbonded pdb=" O ASP A 368 " pdb=" OG1 THR A 369 " model vdw 2.275 3.040 ... (remaining 67965 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.690 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: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.070 Find NCS groups from input model: 0.030 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:7.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8570 Z= 0.124 Angle : 0.529 7.149 11595 Z= 0.289 Chirality : 0.042 0.191 1287 Planarity : 0.004 0.057 1472 Dihedral : 13.250 88.932 3105 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.26), residues: 1039 helix: 1.81 (0.26), residues: 421 sheet: 0.61 (0.38), residues: 204 loop : -0.77 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 67 TYR 0.012 0.001 TYR R 172 PHE 0.015 0.001 PHE B 162 TRP 0.024 0.002 TRP R 291 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 8568) covalent geometry : angle 0.52921 (11591) SS BOND : bond 0.00397 ( 2) SS BOND : angle 0.66840 ( 4) hydrogen bonds : bond 0.15647 ( 410) hydrogen bonds : angle 5.99310 ( 1191) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: A 60 MET cc_start: 0.5059 (mtt) cc_final: 0.4565 (ptp) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.6270 time to fit residues: 93.0113 Evaluate side-chains 117 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 292 ASN B 186 GLN N 3 GLN N 31 ASN N 77 ASN R 228 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.176631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.132346 restraints weight = 8764.997| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.03 r_work: 0.3311 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.0903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8570 Z= 0.160 Angle : 0.577 7.103 11595 Z= 0.319 Chirality : 0.044 0.151 1287 Planarity : 0.005 0.057 1472 Dihedral : 4.567 22.800 1154 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.97 % Allowed : 8.21 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.26), residues: 1039 helix: 1.80 (0.25), residues: 423 sheet: 0.73 (0.37), residues: 206 loop : -0.87 (0.28), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 38 TYR 0.023 0.002 TYR R 90 PHE 0.020 0.002 PHE B 162 TRP 0.023 0.002 TRP B 93 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 8568) covalent geometry : angle 0.57741 (11591) SS BOND : bond 0.00372 ( 2) SS BOND : angle 0.54251 ( 4) hydrogen bonds : bond 0.05447 ( 410) hydrogen bonds : angle 4.80024 ( 1191) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: A 60 MET cc_start: 0.5126 (mtt) cc_final: 0.4355 (ptp) REVERT: A 208 PHE cc_start: 0.7571 (OUTLIER) cc_final: 0.7277 (m-10) REVERT: A 263 THR cc_start: 0.6232 (m) cc_final: 0.6029 (m) REVERT: N 19 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.7113 (ttt180) outliers start: 18 outliers final: 7 residues processed: 125 average time/residue: 0.6011 time to fit residues: 79.8369 Evaluate side-chains 121 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 112 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 26 LEU Chi-restraints excluded: chain R residue 47 SER Chi-restraints excluded: chain R residue 197 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 100 optimal weight: 0.3980 chunk 42 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 38 optimal weight: 0.0970 chunk 81 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 88 optimal weight: 7.9990 chunk 99 optimal weight: 0.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 264 ASN A 292 ASN B 186 GLN N 3 GLN N 31 ASN N 77 ASN R 228 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.178538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.134221 restraints weight = 8668.058| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.88 r_work: 0.3341 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8570 Z= 0.116 Angle : 0.511 5.911 11595 Z= 0.283 Chirality : 0.042 0.141 1287 Planarity : 0.004 0.057 1472 Dihedral : 4.354 22.554 1154 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.19 % Allowed : 10.19 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.26), residues: 1039 helix: 1.93 (0.26), residues: 425 sheet: 0.90 (0.37), residues: 204 loop : -0.81 (0.28), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 38 TYR 0.036 0.002 TYR R 90 PHE 0.015 0.001 PHE B 162 TRP 0.023 0.002 TRP B 93 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 8568) covalent geometry : angle 0.51134 (11591) SS BOND : bond 0.00357 ( 2) SS BOND : angle 0.52585 ( 4) hydrogen bonds : bond 0.04501 ( 410) hydrogen bonds : angle 4.44696 ( 1191) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 0.281 Fit side-chains REVERT: A 21 GLU cc_start: 0.6556 (pp20) cc_final: 0.6290 (pp20) REVERT: A 60 MET cc_start: 0.5150 (mtt) cc_final: 0.4389 (ptp) REVERT: A 208 PHE cc_start: 0.7445 (m-10) cc_final: 0.7224 (m-10) REVERT: A 263 THR cc_start: 0.6205 (m) cc_final: 0.5975 (m) REVERT: A 364 THR cc_start: 0.8012 (OUTLIER) cc_final: 0.7592 (p) REVERT: B 228 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.7768 (pp-130) REVERT: B 347 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8471 (mt) outliers start: 20 outliers final: 9 residues processed: 124 average time/residue: 0.5607 time to fit residues: 73.9317 Evaluate side-chains 122 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 228 MET Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 26 LEU Chi-restraints excluded: chain R residue 29 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 21 optimal weight: 0.2980 chunk 20 optimal weight: 0.0020 overall best weight: 0.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 292 ASN B 186 GLN B 270 GLN N 3 GLN N 31 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.177674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.132587 restraints weight = 8802.191| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 1.89 r_work: 0.3311 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8570 Z= 0.121 Angle : 0.513 5.337 11595 Z= 0.283 Chirality : 0.042 0.142 1287 Planarity : 0.004 0.057 1472 Dihedral : 4.328 22.451 1154 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.86 % Allowed : 12.92 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.26), residues: 1039 helix: 2.01 (0.26), residues: 425 sheet: 1.00 (0.37), residues: 204 loop : -0.79 (0.28), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 38 TYR 0.024 0.001 TYR R 172 PHE 0.016 0.001 PHE B 162 TRP 0.021 0.002 TRP B 93 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 8568) covalent geometry : angle 0.51259 (11591) SS BOND : bond 0.00356 ( 2) SS BOND : angle 0.54037 ( 4) hydrogen bonds : bond 0.04487 ( 410) hydrogen bonds : angle 4.38120 ( 1191) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.6450 (pp20) cc_final: 0.6174 (pp20) REVERT: A 60 MET cc_start: 0.5136 (mtt) cc_final: 0.4281 (ptp) REVERT: A 208 PHE cc_start: 0.7304 (m-10) cc_final: 0.7098 (m-10) REVERT: A 263 THR cc_start: 0.5884 (m) cc_final: 0.5658 (m) REVERT: A 364 THR cc_start: 0.7918 (OUTLIER) cc_final: 0.7493 (p) REVERT: B 54 ILE cc_start: 0.8302 (mm) cc_final: 0.8083 (mp) REVERT: B 228 MET cc_start: 0.8249 (OUTLIER) cc_final: 0.7693 (pp-130) REVERT: B 336 MET cc_start: 0.8465 (mtp) cc_final: 0.8173 (mtp) REVERT: B 347 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8458 (mt) outliers start: 17 outliers final: 10 residues processed: 127 average time/residue: 0.5668 time to fit residues: 76.7138 Evaluate side-chains 125 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 228 MET Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 26 LEU Chi-restraints excluded: chain R residue 47 SER Chi-restraints excluded: chain R residue 197 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 37 optimal weight: 2.9990 chunk 31 optimal weight: 0.0770 chunk 82 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 chunk 69 optimal weight: 0.0980 chunk 47 optimal weight: 0.7980 chunk 97 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 292 ASN B 86 GLN B 186 GLN N 3 GLN N 31 ASN R 296 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.179824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.136075 restraints weight = 8766.919| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.89 r_work: 0.3359 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8570 Z= 0.105 Angle : 0.487 5.786 11595 Z= 0.268 Chirality : 0.041 0.139 1287 Planarity : 0.004 0.057 1472 Dihedral : 4.165 22.484 1154 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.08 % Allowed : 13.47 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.26), residues: 1039 helix: 2.13 (0.26), residues: 425 sheet: 1.10 (0.37), residues: 204 loop : -0.76 (0.28), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 121 TYR 0.030 0.001 TYR R 90 PHE 0.012 0.001 PHE B 162 TRP 0.020 0.001 TRP B 93 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 8568) covalent geometry : angle 0.48720 (11591) SS BOND : bond 0.00349 ( 2) SS BOND : angle 0.48565 ( 4) hydrogen bonds : bond 0.04038 ( 410) hydrogen bonds : angle 4.24379 ( 1191) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: A 60 MET cc_start: 0.5112 (mtt) cc_final: 0.4332 (ptp) REVERT: A 364 THR cc_start: 0.7916 (OUTLIER) cc_final: 0.7497 (p) REVERT: B 54 ILE cc_start: 0.8401 (mm) cc_final: 0.8176 (mp) REVERT: B 228 MET cc_start: 0.8296 (OUTLIER) cc_final: 0.7868 (pp-130) REVERT: B 347 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8450 (mt) REVERT: C 46 LYS cc_start: 0.8601 (mmmt) cc_final: 0.8322 (mttp) REVERT: R 222 ARG cc_start: 0.7890 (tmm160) cc_final: 0.7502 (ttt180) outliers start: 19 outliers final: 10 residues processed: 124 average time/residue: 0.5827 time to fit residues: 76.9536 Evaluate side-chains 124 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 228 MET Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 26 LEU Chi-restraints excluded: chain R residue 90 TYR Chi-restraints excluded: chain R residue 183 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 15 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 73 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 292 ASN B 86 GLN B 186 GLN N 3 GLN N 31 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.177351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.132904 restraints weight = 8629.772| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.99 r_work: 0.3319 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8570 Z= 0.122 Angle : 0.508 5.669 11595 Z= 0.280 Chirality : 0.042 0.138 1287 Planarity : 0.004 0.056 1472 Dihedral : 4.253 22.306 1154 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.41 % Allowed : 14.35 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.26), residues: 1039 helix: 2.15 (0.26), residues: 425 sheet: 1.13 (0.37), residues: 204 loop : -0.77 (0.28), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 121 TYR 0.024 0.001 TYR R 90 PHE 0.015 0.001 PHE B 162 TRP 0.019 0.002 TRP B 93 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 8568) covalent geometry : angle 0.50797 (11591) SS BOND : bond 0.00354 ( 2) SS BOND : angle 0.49805 ( 4) hydrogen bonds : bond 0.04320 ( 410) hydrogen bonds : angle 4.29119 ( 1191) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.6422 (OUTLIER) cc_final: 0.6145 (pp20) REVERT: A 60 MET cc_start: 0.5074 (mtt) cc_final: 0.4221 (ptp) REVERT: A 209 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7002 (tm-30) REVERT: A 263 THR cc_start: 0.5957 (OUTLIER) cc_final: 0.5734 (m) REVERT: A 364 THR cc_start: 0.7853 (OUTLIER) cc_final: 0.7441 (p) REVERT: B 54 ILE cc_start: 0.8310 (mm) cc_final: 0.8087 (mp) REVERT: B 228 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.7757 (pp-130) REVERT: B 347 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8428 (mt) REVERT: C 46 LYS cc_start: 0.8607 (mmmt) cc_final: 0.8296 (mttp) REVERT: N 46 GLU cc_start: 0.8258 (pm20) cc_final: 0.7923 (pp20) REVERT: R 222 ARG cc_start: 0.7820 (tmm160) cc_final: 0.7405 (ttt180) outliers start: 22 outliers final: 12 residues processed: 130 average time/residue: 0.6070 time to fit residues: 83.7680 Evaluate side-chains 132 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 228 MET Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 26 LEU Chi-restraints excluded: chain R residue 47 SER Chi-restraints excluded: chain R residue 90 TYR Chi-restraints excluded: chain R residue 183 SER Chi-restraints excluded: chain R residue 196 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 71 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 35 optimal weight: 0.4980 chunk 6 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 292 ASN B 86 GLN B 186 GLN N 3 GLN N 31 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.178033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.133631 restraints weight = 8747.740| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.00 r_work: 0.3331 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8570 Z= 0.136 Angle : 0.530 5.483 11595 Z= 0.292 Chirality : 0.043 0.145 1287 Planarity : 0.004 0.056 1472 Dihedral : 4.352 22.286 1154 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.85 % Allowed : 14.35 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.26), residues: 1039 helix: 2.09 (0.26), residues: 425 sheet: 1.21 (0.37), residues: 203 loop : -0.85 (0.28), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 121 TYR 0.024 0.002 TYR R 90 PHE 0.017 0.001 PHE B 162 TRP 0.019 0.002 TRP B 93 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 8568) covalent geometry : angle 0.53040 (11591) SS BOND : bond 0.00362 ( 2) SS BOND : angle 0.53883 ( 4) hydrogen bonds : bond 0.04582 ( 410) hydrogen bonds : angle 4.36886 ( 1191) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 115 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.6533 (OUTLIER) cc_final: 0.6288 (pp20) REVERT: A 60 MET cc_start: 0.4959 (mtt) cc_final: 0.4161 (ptp) REVERT: A 263 THR cc_start: 0.6147 (OUTLIER) cc_final: 0.5916 (m) REVERT: A 308 ILE cc_start: 0.6607 (OUTLIER) cc_final: 0.6208 (mp) REVERT: A 364 THR cc_start: 0.7905 (OUTLIER) cc_final: 0.7506 (p) REVERT: B 54 ILE cc_start: 0.8406 (mm) cc_final: 0.8182 (mp) REVERT: B 228 MET cc_start: 0.8321 (OUTLIER) cc_final: 0.7858 (pp-130) REVERT: B 347 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8413 (mt) REVERT: C 46 LYS cc_start: 0.8622 (mmmt) cc_final: 0.8357 (mttp) outliers start: 26 outliers final: 16 residues processed: 130 average time/residue: 0.5522 time to fit residues: 76.6884 Evaluate side-chains 134 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 228 MET Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 26 LEU Chi-restraints excluded: chain R residue 47 SER Chi-restraints excluded: chain R residue 90 TYR Chi-restraints excluded: chain R residue 183 SER Chi-restraints excluded: chain R residue 196 MET Chi-restraints excluded: chain R residue 197 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 35 optimal weight: 0.0970 chunk 46 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 61 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 71 optimal weight: 0.0070 chunk 70 optimal weight: 2.9990 chunk 56 optimal weight: 9.9990 chunk 89 optimal weight: 20.0000 chunk 30 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 292 ASN B 186 GLN N 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.179168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.134662 restraints weight = 8732.722| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.01 r_work: 0.3356 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8570 Z= 0.104 Angle : 0.489 5.772 11595 Z= 0.270 Chirality : 0.041 0.141 1287 Planarity : 0.004 0.056 1472 Dihedral : 4.156 22.417 1154 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.30 % Allowed : 15.44 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.26), residues: 1039 helix: 2.18 (0.26), residues: 425 sheet: 1.25 (0.37), residues: 203 loop : -0.82 (0.28), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 356 TYR 0.023 0.001 TYR R 90 PHE 0.020 0.001 PHE A 208 TRP 0.020 0.002 TRP B 93 HIS 0.005 0.001 HIS R 55 Details of bonding type rmsd covalent geometry : bond 0.00222 ( 8568) covalent geometry : angle 0.48923 (11591) SS BOND : bond 0.00328 ( 2) SS BOND : angle 0.49033 ( 4) hydrogen bonds : bond 0.03976 ( 410) hydrogen bonds : angle 4.21604 ( 1191) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 119 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: A 60 MET cc_start: 0.4942 (mtt) cc_final: 0.4111 (ptp) REVERT: A 263 THR cc_start: 0.5967 (OUTLIER) cc_final: 0.5750 (m) REVERT: A 308 ILE cc_start: 0.6526 (OUTLIER) cc_final: 0.6158 (mp) REVERT: A 364 THR cc_start: 0.7771 (OUTLIER) cc_final: 0.7379 (p) REVERT: A 386 MET cc_start: 0.7911 (mtp) cc_final: 0.7645 (mtm) REVERT: B 54 ILE cc_start: 0.8389 (mm) cc_final: 0.8163 (mp) REVERT: B 228 MET cc_start: 0.8224 (OUTLIER) cc_final: 0.7849 (pp-130) REVERT: B 347 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8457 (mt) REVERT: C 46 LYS cc_start: 0.8587 (mmmt) cc_final: 0.8289 (ttmm) REVERT: N 5 GLN cc_start: 0.7067 (tp40) cc_final: 0.6850 (mt0) outliers start: 21 outliers final: 12 residues processed: 132 average time/residue: 0.5617 time to fit residues: 79.0408 Evaluate side-chains 136 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 228 MET Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 26 LEU Chi-restraints excluded: chain R residue 29 LEU Chi-restraints excluded: chain R residue 47 SER Chi-restraints excluded: chain R residue 287 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 54 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 15 optimal weight: 0.3980 chunk 5 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 292 ASN B 186 GLN N 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.177341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.134650 restraints weight = 9036.005| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.16 r_work: 0.3315 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8570 Z= 0.171 Angle : 0.572 6.702 11595 Z= 0.314 Chirality : 0.044 0.145 1287 Planarity : 0.005 0.056 1472 Dihedral : 4.507 22.021 1154 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.74 % Allowed : 15.99 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.26), residues: 1039 helix: 2.04 (0.26), residues: 423 sheet: 1.16 (0.37), residues: 203 loop : -0.92 (0.28), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 356 TYR 0.015 0.002 TYR N 95 PHE 0.021 0.002 PHE A 222 TRP 0.018 0.002 TRP B 93 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 8568) covalent geometry : angle 0.57219 (11591) SS BOND : bond 0.00373 ( 2) SS BOND : angle 0.60556 ( 4) hydrogen bonds : bond 0.05032 ( 410) hydrogen bonds : angle 4.47852 ( 1191) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 116 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.6445 (pp20) cc_final: 0.6191 (pp20) REVERT: A 60 MET cc_start: 0.4923 (mtt) cc_final: 0.4011 (ptp) REVERT: A 263 THR cc_start: 0.6109 (OUTLIER) cc_final: 0.5902 (m) REVERT: A 308 ILE cc_start: 0.6572 (OUTLIER) cc_final: 0.6209 (mp) REVERT: A 364 THR cc_start: 0.7884 (OUTLIER) cc_final: 0.7525 (p) REVERT: A 386 MET cc_start: 0.7947 (mtp) cc_final: 0.7637 (mtm) REVERT: B 54 ILE cc_start: 0.8358 (mm) cc_final: 0.8125 (mp) REVERT: B 228 MET cc_start: 0.8260 (OUTLIER) cc_final: 0.7715 (pp-130) REVERT: B 347 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8408 (mt) REVERT: C 46 LYS cc_start: 0.8637 (mmmt) cc_final: 0.8334 (mttp) REVERT: R 212 ARG cc_start: 0.7911 (ttt-90) cc_final: 0.7675 (ttt-90) outliers start: 25 outliers final: 15 residues processed: 131 average time/residue: 0.5409 time to fit residues: 75.6199 Evaluate side-chains 132 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 228 MET Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 26 LEU Chi-restraints excluded: chain R residue 47 SER Chi-restraints excluded: chain R residue 105 MET Chi-restraints excluded: chain R residue 183 SER Chi-restraints excluded: chain R residue 196 MET Chi-restraints excluded: chain R residue 273 MET Chi-restraints excluded: chain R residue 287 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 56 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 chunk 81 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 84 optimal weight: 0.0020 chunk 79 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 292 ASN B 186 GLN N 3 GLN R 228 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.178129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.133480 restraints weight = 8703.947| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.00 r_work: 0.3334 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8570 Z= 0.119 Angle : 0.510 5.348 11595 Z= 0.282 Chirality : 0.042 0.150 1287 Planarity : 0.004 0.056 1472 Dihedral : 4.296 22.515 1154 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.30 % Allowed : 16.32 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.26), residues: 1039 helix: 2.10 (0.26), residues: 425 sheet: 1.21 (0.37), residues: 203 loop : -0.87 (0.28), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 67 TYR 0.022 0.001 TYR R 90 PHE 0.021 0.001 PHE A 222 TRP 0.020 0.002 TRP B 93 HIS 0.004 0.001 HIS R 55 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 8568) covalent geometry : angle 0.51021 (11591) SS BOND : bond 0.00328 ( 2) SS BOND : angle 0.51346 ( 4) hydrogen bonds : bond 0.04309 ( 410) hydrogen bonds : angle 4.30447 ( 1191) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.6507 (OUTLIER) cc_final: 0.6255 (pp20) REVERT: A 60 MET cc_start: 0.4966 (mtt) cc_final: 0.4051 (ptp) REVERT: A 308 ILE cc_start: 0.6529 (OUTLIER) cc_final: 0.6149 (mp) REVERT: A 364 THR cc_start: 0.7789 (OUTLIER) cc_final: 0.7406 (p) REVERT: A 386 MET cc_start: 0.7965 (mtp) cc_final: 0.7702 (mtm) REVERT: B 54 ILE cc_start: 0.8374 (mm) cc_final: 0.8156 (mp) REVERT: B 228 MET cc_start: 0.8251 (OUTLIER) cc_final: 0.7861 (pp-130) REVERT: B 347 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8441 (mt) REVERT: C 46 LYS cc_start: 0.8620 (mmmt) cc_final: 0.8374 (mttp) REVERT: N 5 GLN cc_start: 0.7149 (tp40) cc_final: 0.6903 (mt0) REVERT: R 212 ARG cc_start: 0.7905 (ttt-90) cc_final: 0.7678 (ttt-90) outliers start: 21 outliers final: 12 residues processed: 126 average time/residue: 0.5937 time to fit residues: 79.6418 Evaluate side-chains 130 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 228 MET Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 26 LEU Chi-restraints excluded: chain R residue 47 SER Chi-restraints excluded: chain R residue 183 SER Chi-restraints excluded: chain R residue 287 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 92 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 67 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 292 ASN B 186 GLN N 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.176433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.132565 restraints weight = 8701.426| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.91 r_work: 0.3314 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8570 Z= 0.165 Angle : 0.564 6.140 11595 Z= 0.310 Chirality : 0.044 0.149 1287 Planarity : 0.004 0.056 1472 Dihedral : 4.489 21.928 1154 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.41 % Allowed : 16.65 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.26), residues: 1039 helix: 2.03 (0.26), residues: 423 sheet: 1.13 (0.37), residues: 203 loop : -0.94 (0.28), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 121 TYR 0.014 0.002 TYR N 95 PHE 0.024 0.002 PHE A 222 TRP 0.018 0.002 TRP B 93 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 8568) covalent geometry : angle 0.56388 (11591) SS BOND : bond 0.00378 ( 2) SS BOND : angle 0.57143 ( 4) hydrogen bonds : bond 0.04949 ( 410) hydrogen bonds : angle 4.43789 ( 1191) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3656.92 seconds wall clock time: 62 minutes 54.49 seconds (3774.49 seconds total)