Starting phenix.real_space_refine on Wed Mar 12 21:59:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jkq_61567/03_2025/9jkq_61567.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jkq_61567/03_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_61567/03_2025/9jkq_61567.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jkq_61567/03_2025/9jkq_61567.map" model { file = "/net/cci-nas-00/data/ceres_data/9jkq_61567/03_2025/9jkq_61567.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jkq_61567/03_2025/9jkq_61567.cif" } resolution = 2.66 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.35, per 1000 atoms: 0.64 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: 2.06 Conformation dependent library (CDL) restraints added in 958.2 milliseconds 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: 0.81 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: 2.27 Time building geometry restraints manager: 2.46 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: 2.070 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: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.870 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.880 ------------------------------------------------------------------------------- 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 8568 Z= 0.175 Angle : 0.529 7.149 11591 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (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 TRP 0.024 0.002 TRP R 291 HIS 0.005 0.001 HIS A 357 PHE 0.015 0.001 PHE B 162 TYR 0.012 0.001 TYR R 172 ARG 0.003 0.000 ARG N 67 *********************** 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 : 0.913 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: 1.2570 time to fit residues: 186.9779 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 : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 0.3980 chunk 77 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 26 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4061 r_free = 0.4061 target = 0.178710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.134579 restraints weight = 8696.282| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 1.86 r_work: 0.3342 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.0893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8568 Z= 0.174 Angle : 0.530 6.331 11591 Z= 0.293 Chirality : 0.042 0.143 1287 Planarity : 0.004 0.057 1472 Dihedral : 4.358 22.930 1154 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.75 % Allowed : 8.11 % Favored : 90.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.26), residues: 1039 helix: 1.89 (0.25), residues: 425 sheet: 0.77 (0.37), residues: 205 loop : -0.77 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 93 HIS 0.004 0.001 HIS A 357 PHE 0.015 0.001 PHE B 162 TYR 0.023 0.001 TYR R 90 ARG 0.005 0.000 ARG A 38 *********************** 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 131 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.981 Fit side-chains REVERT: A 60 MET cc_start: 0.5144 (mtt) cc_final: 0.4446 (ptp) REVERT: A 208 PHE cc_start: 0.7464 (m-10) cc_final: 0.7201 (m-10) REVERT: A 263 THR cc_start: 0.6164 (m) cc_final: 0.5951 (m) REVERT: N 19 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.7093 (ttt180) outliers start: 16 outliers final: 6 residues processed: 123 average time/residue: 1.3820 time to fit residues: 181.3458 Evaluate side-chains 116 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 109 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 197 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 80 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 chunk 59 optimal weight: 0.8980 chunk 23 optimal weight: 7.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 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 = 0.176581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.132306 restraints weight = 8791.688| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 1.93 r_work: 0.3304 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8568 Z= 0.242 Angle : 0.567 7.257 11591 Z= 0.312 Chirality : 0.044 0.146 1287 Planarity : 0.004 0.058 1472 Dihedral : 4.575 22.337 1154 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.41 % Allowed : 9.42 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.26), residues: 1039 helix: 1.88 (0.25), residues: 423 sheet: 0.83 (0.37), residues: 205 loop : -0.89 (0.28), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 93 HIS 0.007 0.001 HIS A 357 PHE 0.019 0.002 PHE B 162 TYR 0.035 0.002 TYR R 90 ARG 0.005 0.000 ARG A 38 *********************** 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 137 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 0.986 Fit side-chains revert: symmetry clash REVERT: A 60 MET cc_start: 0.5211 (mtt) cc_final: 0.4408 (ptp) REVERT: A 208 PHE cc_start: 0.7552 (m-10) cc_final: 0.7298 (m-10) REVERT: A 209 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7399 (tm-30) REVERT: A 263 THR cc_start: 0.6294 (m) cc_final: 0.6078 (m) REVERT: A 364 THR cc_start: 0.8034 (OUTLIER) cc_final: 0.7655 (p) REVERT: B 228 MET cc_start: 0.8283 (OUTLIER) cc_final: 0.7924 (ptt) REVERT: B 347 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8437 (mt) REVERT: N 19 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.7100 (ttt180) outliers start: 22 outliers final: 11 residues processed: 126 average time/residue: 1.4007 time to fit residues: 187.7439 Evaluate side-chains 125 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 209 GLU 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 19 ARG Chi-restraints excluded: chain N residue 114 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 197 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 12 optimal weight: 0.0170 chunk 101 optimal weight: 1.9990 chunk 25 optimal weight: 8.9990 chunk 5 optimal weight: 4.9990 overall best weight: 1.5624 ------------------------------------------------------------------------------- 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 86 GLN B 186 GLN N 3 GLN N 31 ASN N 77 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.175773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.131420 restraints weight = 8715.844| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.02 r_work: 0.3292 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8568 Z= 0.280 Angle : 0.592 6.950 11591 Z= 0.325 Chirality : 0.045 0.149 1287 Planarity : 0.005 0.058 1472 Dihedral : 4.718 22.513 1154 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.30 % Allowed : 13.03 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.26), residues: 1039 helix: 1.80 (0.26), residues: 423 sheet: 0.88 (0.36), residues: 205 loop : -0.92 (0.28), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 93 HIS 0.007 0.001 HIS A 357 PHE 0.022 0.002 PHE B 162 TYR 0.023 0.002 TYR R 172 ARG 0.004 0.000 ARG R 121 *********************** 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 135 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.976 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.6639 (pp20) cc_final: 0.6369 (pp20) REVERT: A 60 MET cc_start: 0.5350 (mtt) cc_final: 0.4367 (ptp) REVERT: A 209 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7260 (tm-30) REVERT: A 263 THR cc_start: 0.6258 (m) cc_final: 0.6036 (m) REVERT: A 364 THR cc_start: 0.8070 (OUTLIER) cc_final: 0.7707 (p) REVERT: B 228 MET cc_start: 0.8296 (OUTLIER) cc_final: 0.7938 (ptt) REVERT: B 347 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8413 (mt) REVERT: N 19 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.7138 (ttt180) outliers start: 21 outliers final: 11 residues processed: 125 average time/residue: 1.3049 time to fit residues: 173.7386 Evaluate side-chains 127 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 209 GLU 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 19 ARG Chi-restraints excluded: chain N residue 114 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 197 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 49 optimal weight: 0.0040 chunk 92 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 17 optimal weight: 0.0470 chunk 15 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 overall best weight: 0.5692 ------------------------------------------------------------------------------- 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 86 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 = 0.4061 r_free = 0.4061 target = 0.178786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.134941 restraints weight = 8625.445| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 1.83 r_work: 0.3343 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8568 Z= 0.154 Angle : 0.494 5.249 11591 Z= 0.274 Chirality : 0.042 0.139 1287 Planarity : 0.004 0.058 1472 Dihedral : 4.310 22.625 1154 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.19 % Allowed : 14.13 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.26), residues: 1039 helix: 2.01 (0.26), residues: 425 sheet: 1.01 (0.37), residues: 204 loop : -0.79 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 93 HIS 0.003 0.001 HIS A 357 PHE 0.015 0.001 PHE A 222 TYR 0.029 0.001 TYR R 90 ARG 0.003 0.000 ARG R 121 *********************** 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 141 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.6548 (OUTLIER) cc_final: 0.6312 (pp20) REVERT: A 60 MET cc_start: 0.5243 (mtt) cc_final: 0.4260 (ptp) REVERT: A 364 THR cc_start: 0.7938 (OUTLIER) cc_final: 0.7544 (p) REVERT: B 54 ILE cc_start: 0.8423 (mm) cc_final: 0.8195 (mp) REVERT: B 228 MET cc_start: 0.8293 (OUTLIER) cc_final: 0.7806 (pp-130) REVERT: B 347 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8435 (mt) REVERT: R 222 ARG cc_start: 0.7888 (tmm160) cc_final: 0.7497 (ttt180) outliers start: 20 outliers final: 10 residues processed: 129 average time/residue: 1.2205 time to fit residues: 167.9447 Evaluate side-chains 129 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU 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 61 THR Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 47 SER 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 65 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 4 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 chunk 29 optimal weight: 0.0470 chunk 36 optimal weight: 0.1980 chunk 14 optimal weight: 0.3980 chunk 42 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 61 optimal weight: 0.4980 overall best weight: 0.3878 ------------------------------------------------------------------------------- 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 R 296 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.179123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.135631 restraints weight = 8631.187| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 1.99 r_work: 0.3352 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8568 Z= 0.140 Angle : 0.478 6.063 11591 Z= 0.264 Chirality : 0.041 0.143 1287 Planarity : 0.004 0.057 1472 Dihedral : 4.089 22.602 1154 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.52 % Allowed : 14.13 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.26), residues: 1039 helix: 2.15 (0.26), residues: 425 sheet: 1.18 (0.37), residues: 202 loop : -0.79 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 93 HIS 0.002 0.000 HIS A 357 PHE 0.012 0.001 PHE A 222 TYR 0.024 0.001 TYR R 90 ARG 0.004 0.000 ARG R 121 *********************** 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 142 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 1.005 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.6401 (OUTLIER) cc_final: 0.6126 (pp20) REVERT: A 60 MET cc_start: 0.4996 (mtt) cc_final: 0.4134 (ptp) REVERT: A 364 THR cc_start: 0.7826 (OUTLIER) cc_final: 0.7409 (p) REVERT: B 54 ILE cc_start: 0.8323 (mm) cc_final: 0.8105 (mp) REVERT: B 228 MET cc_start: 0.8218 (OUTLIER) cc_final: 0.7861 (pp-130) REVERT: B 347 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8465 (mt) REVERT: C 21 MET cc_start: 0.6165 (OUTLIER) cc_final: 0.5298 (ttp) REVERT: C 46 LYS cc_start: 0.8557 (mmmt) cc_final: 0.8164 (ttmm) REVERT: N 46 GLU cc_start: 0.8238 (pm20) cc_final: 0.7885 (pp20) REVERT: R 212 ARG cc_start: 0.7871 (ttt-90) cc_final: 0.7643 (ttt-90) outliers start: 23 outliers final: 9 residues processed: 131 average time/residue: 1.7504 time to fit residues: 245.6631 Evaluate side-chains 130 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 0.952 ------------------------------------------------------------------------------- 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 364 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 228 MET Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain C residue 21 MET 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 47 SER Chi-restraints excluded: chain R residue 90 TYR Chi-restraints excluded: chain R residue 183 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 20.0000 chunk 36 optimal weight: 0.0050 chunk 5 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 60 optimal weight: 0.0170 chunk 88 optimal weight: 0.0970 chunk 55 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.6032 ------------------------------------------------------------------------------- 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 R 228 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.180015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.129116 restraints weight = 8990.070| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.00 r_work: 0.3343 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8568 Z= 0.156 Angle : 0.494 5.374 11591 Z= 0.272 Chirality : 0.042 0.139 1287 Planarity : 0.004 0.056 1472 Dihedral : 4.134 22.422 1154 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.41 % Allowed : 15.44 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.26), residues: 1039 helix: 2.19 (0.26), residues: 425 sheet: 1.14 (0.38), residues: 204 loop : -0.78 (0.28), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 93 HIS 0.004 0.001 HIS R 55 PHE 0.018 0.001 PHE A 208 TYR 0.023 0.001 TYR R 90 ARG 0.004 0.000 ARG R 121 *********************** 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 142 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 0.876 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.6425 (OUTLIER) cc_final: 0.6153 (pp20) REVERT: A 60 MET cc_start: 0.4924 (mtt) cc_final: 0.4099 (ptp) REVERT: A 263 THR cc_start: 0.5942 (OUTLIER) cc_final: 0.5726 (m) REVERT: A 308 ILE cc_start: 0.6514 (OUTLIER) cc_final: 0.6161 (mp) REVERT: A 364 THR cc_start: 0.7827 (OUTLIER) cc_final: 0.7440 (p) REVERT: B 54 ILE cc_start: 0.8355 (mm) cc_final: 0.8144 (mp) REVERT: B 228 MET cc_start: 0.8216 (OUTLIER) cc_final: 0.7832 (pp-130) REVERT: B 347 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8465 (mt) REVERT: C 46 LYS cc_start: 0.8564 (mmmt) cc_final: 0.8231 (ttmm) REVERT: N 5 GLN cc_start: 0.7090 (tp-100) cc_final: 0.6825 (mt0) REVERT: R 212 ARG cc_start: 0.7886 (ttt-90) cc_final: 0.7645 (ttt-90) outliers start: 22 outliers final: 12 residues processed: 133 average time/residue: 1.2077 time to fit residues: 171.2201 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 : 0.916 ------------------------------------------------------------------------------- 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 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 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 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 287 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 32 optimal weight: 0.4980 chunk 64 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 72 optimal weight: 0.0980 chunk 22 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.180045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.137596 restraints weight = 9064.283| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.14 r_work: 0.3382 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8568 Z= 0.159 Angle : 0.496 5.580 11591 Z= 0.273 Chirality : 0.042 0.138 1287 Planarity : 0.004 0.056 1472 Dihedral : 4.140 22.349 1154 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.26), residues: 1039 helix: 2.18 (0.26), residues: 425 sheet: 1.16 (0.37), residues: 204 loop : -0.77 (0.28), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 93 HIS 0.004 0.001 HIS R 55 PHE 0.017 0.001 PHE A 222 TYR 0.022 0.001 TYR R 90 ARG 0.003 0.000 ARG R 121 *********************** 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 138 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 0.899 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.6404 (OUTLIER) cc_final: 0.6143 (pp20) REVERT: A 60 MET cc_start: 0.4907 (mtt) cc_final: 0.4040 (ptp) REVERT: A 263 THR cc_start: 0.5952 (OUTLIER) cc_final: 0.5750 (m) REVERT: A 308 ILE cc_start: 0.6531 (OUTLIER) cc_final: 0.6179 (mp) REVERT: A 364 THR cc_start: 0.7735 (OUTLIER) cc_final: 0.7364 (p) REVERT: B 228 MET cc_start: 0.8197 (OUTLIER) cc_final: 0.7821 (pp-130) REVERT: B 347 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8472 (mt) REVERT: C 46 LYS cc_start: 0.8559 (mmmt) cc_final: 0.8237 (ttmm) REVERT: N 5 GLN cc_start: 0.7095 (tp-100) cc_final: 0.6836 (mt0) REVERT: R 212 ARG cc_start: 0.7868 (ttt-90) cc_final: 0.7624 (ttt-90) outliers start: 21 outliers final: 11 residues processed: 129 average time/residue: 1.1611 time to fit residues: 160.0315 Evaluate side-chains 133 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.903 ------------------------------------------------------------------------------- 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 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 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 29 LEU Chi-restraints excluded: chain R residue 47 SER Chi-restraints excluded: chain R residue 196 MET 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 53 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 71 optimal weight: 0.3980 chunk 12 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 R 228 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.177842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.126356 restraints weight = 9091.270| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.01 r_work: 0.3314 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8568 Z= 0.234 Angle : 0.557 6.121 11591 Z= 0.305 Chirality : 0.044 0.149 1287 Planarity : 0.004 0.055 1472 Dihedral : 4.422 22.156 1154 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.52 % Allowed : 16.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.26), residues: 1039 helix: 2.03 (0.26), residues: 424 sheet: 1.20 (0.37), residues: 203 loop : -0.85 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 93 HIS 0.006 0.001 HIS A 357 PHE 0.022 0.002 PHE A 222 TYR 0.014 0.002 TYR N 95 ARG 0.004 0.000 ARG N 67 *********************** 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 135 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.6497 (OUTLIER) cc_final: 0.6208 (pp20) REVERT: A 60 MET cc_start: 0.4855 (mtt) cc_final: 0.3999 (ptp) REVERT: A 263 THR cc_start: 0.5995 (OUTLIER) cc_final: 0.5786 (m) REVERT: A 308 ILE cc_start: 0.6542 (OUTLIER) cc_final: 0.6186 (mp) REVERT: A 364 THR cc_start: 0.7833 (OUTLIER) cc_final: 0.7461 (p) REVERT: A 386 MET cc_start: 0.7829 (mtm) cc_final: 0.7556 (mtm) REVERT: B 228 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.7775 (pp-130) REVERT: B 347 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8413 (mt) REVERT: C 46 LYS cc_start: 0.8595 (mmmt) cc_final: 0.8244 (ttmm) REVERT: N 5 GLN cc_start: 0.7106 (tp-100) cc_final: 0.6826 (mt0) REVERT: R 212 ARG cc_start: 0.7947 (ttt-90) cc_final: 0.7705 (ttt-90) outliers start: 23 outliers final: 13 residues processed: 127 average time/residue: 1.1713 time to fit residues: 158.7999 Evaluate side-chains 128 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.948 ------------------------------------------------------------------------------- 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 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 334 ASP 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 47 SER Chi-restraints excluded: chain R residue 183 SER Chi-restraints excluded: chain R residue 196 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 94 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 96 optimal weight: 0.6980 chunk 56 optimal weight: 10.0000 chunk 69 optimal weight: 0.7980 chunk 4 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4064 r_free = 0.4064 target = 0.178854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.127904 restraints weight = 8873.450| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 1.97 r_work: 0.3352 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8568 Z= 0.189 Angle : 0.525 6.071 11591 Z= 0.288 Chirality : 0.043 0.146 1287 Planarity : 0.004 0.056 1472 Dihedral : 4.337 22.344 1154 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.19 % Allowed : 16.87 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.26), residues: 1039 helix: 2.05 (0.26), residues: 424 sheet: 1.20 (0.37), residues: 203 loop : -0.84 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 93 HIS 0.004 0.001 HIS A 357 PHE 0.023 0.001 PHE A 222 TYR 0.022 0.001 TYR R 90 ARG 0.004 0.000 ARG N 67 ********************** 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 132 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.986 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.6453 (OUTLIER) cc_final: 0.6200 (pp20) REVERT: A 60 MET cc_start: 0.4822 (mtt) cc_final: 0.3968 (ptp) REVERT: A 308 ILE cc_start: 0.6543 (OUTLIER) cc_final: 0.6182 (mp) REVERT: A 364 THR cc_start: 0.7787 (OUTLIER) cc_final: 0.7423 (p) REVERT: A 386 MET cc_start: 0.7847 (mtm) cc_final: 0.7568 (mtm) REVERT: B 228 MET cc_start: 0.8238 (OUTLIER) cc_final: 0.7816 (pp-130) REVERT: B 347 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8447 (mt) REVERT: C 46 LYS cc_start: 0.8590 (mmmt) cc_final: 0.8241 (ttmm) REVERT: N 5 GLN cc_start: 0.7108 (tp-100) cc_final: 0.6847 (mt0) REVERT: R 212 ARG cc_start: 0.7912 (ttt-90) cc_final: 0.7668 (ttt-90) outliers start: 20 outliers final: 12 residues processed: 124 average time/residue: 1.1732 time to fit residues: 155.4011 Evaluate side-chains 128 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.889 ------------------------------------------------------------------------------- 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 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 47 SER Chi-restraints excluded: chain R residue 183 SER Chi-restraints excluded: chain R residue 196 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 28 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 68 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 101 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 55 optimal weight: 0.0980 chunk 86 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.4069 r_free = 0.4069 target = 0.179345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.135987 restraints weight = 8953.598| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.03 r_work: 0.3359 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8568 Z= 0.171 Angle : 0.510 5.847 11591 Z= 0.280 Chirality : 0.042 0.146 1287 Planarity : 0.004 0.056 1472 Dihedral : 4.256 22.193 1154 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.08 % Allowed : 16.87 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.26), residues: 1039 helix: 2.09 (0.26), residues: 424 sheet: 1.25 (0.38), residues: 203 loop : -0.80 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 93 HIS 0.004 0.001 HIS R 55 PHE 0.022 0.001 PHE A 208 TYR 0.013 0.001 TYR R 90 ARG 0.004 0.000 ARG N 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7964.94 seconds wall clock time: 139 minutes 24.46 seconds (8364.46 seconds total)