Starting phenix.real_space_refine on Fri Jul 3 11:51:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o96_70243/07_2026/9o96_70243.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o96_70243/07_2026/9o96_70243.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9o96_70243/07_2026/9o96_70243.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o96_70243/07_2026/9o96_70243.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9o96_70243/07_2026/9o96_70243.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o96_70243/07_2026/9o96_70243.map" } resolution = 3.2 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= 0.003 sd= 0.035 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: 6 Type Number sf(0) Gaussians S 40 5.16 5 Cl 4 4.86 5 C 4380 2.51 5 N 1120 2.21 5 O 1126 1.98 5 H 6970 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13640 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 6818 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 19, 'TRANS': 424} Chain: "B" Number of atoms: 6818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 6818 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 19, 'TRANS': 424} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CL': 2} Chain breaks: 2 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CL': 2} Chain breaks: 2 Time building chain proxies: 2.29, per 1000 atoms: 0.17 Number of scatterers: 13640 At special positions: 0 Unit cell: (109.728, 111.456, 73.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 4 17.00 S 40 16.00 O 1126 8.00 N 1120 7.00 C 4380 6.00 H 6970 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 370.8 milliseconds 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1548 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 0 sheets defined 86.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 17 through 19 No H-bonds generated for 'chain 'A' and resid 17 through 19' Processing helix chain 'A' and resid 20 through 68 removed outlier: 3.618A pdb=" N GLN A 24 " --> pdb=" O GLN A 20 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ARG A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N THR A 31 " --> pdb=" O GLU A 27 " (cutoff:3.500A) Proline residue: A 32 - end of helix removed outlier: 4.016A pdb=" N ALA A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL A 41 " --> pdb=" O PHE A 37 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL A 51 " --> pdb=" O GLY A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 101 removed outlier: 3.750A pdb=" N LEU A 78 " --> pdb=" O ASN A 74 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N SER A 86 " --> pdb=" O ALA A 82 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU A 89 " --> pdb=" O CYS A 85 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE A 92 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL A 97 " --> pdb=" O GLY A 93 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG A 98 " --> pdb=" O TYR A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 105 Processing helix chain 'A' and resid 108 through 117 removed outlier: 3.525A pdb=" N GLU A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 141 Proline residue: A 129 - end of helix removed outlier: 3.675A pdb=" N GLY A 137 " --> pdb=" O PHE A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 167 removed outlier: 3.540A pdb=" N VAL A 162 " --> pdb=" O ILE A 158 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU A 163 " --> pdb=" O GLY A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 191 removed outlier: 3.658A pdb=" N LEU A 178 " --> pdb=" O ARG A 174 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA A 179 " --> pdb=" O HIS A 175 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA A 188 " --> pdb=" O ALA A 184 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA A 189 " --> pdb=" O GLY A 185 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 203 removed outlier: 3.506A pdb=" N GLY A 196 " --> pdb=" O ALA A 192 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ILE A 200 " --> pdb=" O GLY A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 232 removed outlier: 3.531A pdb=" N ILE A 215 " --> pdb=" O THR A 211 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LYS A 216 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N PHE A 232 " --> pdb=" O MET A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 251 Processing helix chain 'A' and resid 252 through 285 removed outlier: 3.891A pdb=" N LEU A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE A 257 " --> pdb=" O TRP A 253 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE A 265 " --> pdb=" O ILE A 261 " (cutoff:3.500A) Proline residue: A 267 - end of helix removed outlier: 3.850A pdb=" N GLN A 277 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASP A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU A 279 " --> pdb=" O GLY A 275 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ARG A 282 " --> pdb=" O ASP A 278 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N VAL A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N HIS A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 309 removed outlier: 3.550A pdb=" N CYS A 302 " --> pdb=" O ILE A 298 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE A 307 " --> pdb=" O GLY A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 313 Processing helix chain 'A' and resid 315 through 318 removed outlier: 3.634A pdb=" N ASN A 318 " --> pdb=" O GLY A 315 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 315 through 318' Processing helix chain 'A' and resid 319 through 325 Processing helix chain 'A' and resid 329 through 350 removed outlier: 3.945A pdb=" N VAL A 334 " --> pdb=" O MET A 330 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE A 335 " --> pdb=" O GLY A 331 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A 345 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A 346 " --> pdb=" O ILE A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 379 removed outlier: 3.850A pdb=" N VAL A 374 " --> pdb=" O ALA A 370 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU A 377 " --> pdb=" O MET A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 383 removed outlier: 3.746A pdb=" N HIS A 383 " --> pdb=" O PRO A 380 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 380 through 383' Processing helix chain 'A' and resid 386 through 393 removed outlier: 3.516A pdb=" N ALA A 390 " --> pdb=" O ALA A 386 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA A 392 " --> pdb=" O THR A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 402 Processing helix chain 'A' and resid 404 through 417 Processing helix chain 'A' and resid 418 through 420 No H-bonds generated for 'chain 'A' and resid 418 through 420' Processing helix chain 'A' and resid 421 through 439 removed outlier: 3.694A pdb=" N THR A 433 " --> pdb=" O GLY A 429 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN A 437 " --> pdb=" O THR A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 457 removed outlier: 3.966A pdb=" N LYS A 455 " --> pdb=" O ARG A 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 19 No H-bonds generated for 'chain 'B' and resid 17 through 19' Processing helix chain 'B' and resid 20 through 68 removed outlier: 3.719A pdb=" N GLN B 24 " --> pdb=" O GLN B 20 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ARG B 28 " --> pdb=" O GLN B 24 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N THR B 31 " --> pdb=" O GLU B 27 " (cutoff:3.500A) Proline residue: B 32 - end of helix removed outlier: 4.068A pdb=" N ALA B 40 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL B 41 " --> pdb=" O PHE B 37 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL B 51 " --> pdb=" O GLY B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 101 removed outlier: 3.822A pdb=" N LEU B 78 " --> pdb=" O ASN B 74 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N SER B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LEU B 89 " --> pdb=" O CYS B 85 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE B 92 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY B 93 " --> pdb=" O LEU B 89 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL B 97 " --> pdb=" O GLY B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 105 Processing helix chain 'B' and resid 108 through 117 Processing helix chain 'B' and resid 123 through 141 Proline residue: B 129 - end of helix removed outlier: 3.532A pdb=" N GLY B 137 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR B 138 " --> pdb=" O GLY B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 167 removed outlier: 3.538A pdb=" N VAL B 162 " --> pdb=" O ILE B 158 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU B 163 " --> pdb=" O GLY B 159 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP B 164 " --> pdb=" O ARG B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 191 removed outlier: 3.658A pdb=" N LEU B 178 " --> pdb=" O ARG B 174 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA B 179 " --> pdb=" O HIS B 175 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA B 188 " --> pdb=" O ALA B 184 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA B 189 " --> pdb=" O GLY B 185 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 203 removed outlier: 4.190A pdb=" N ILE B 200 " --> pdb=" O GLY B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 232 removed outlier: 4.077A pdb=" N PHE B 232 " --> pdb=" O MET B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 251 Processing helix chain 'B' and resid 252 through 285 removed outlier: 3.898A pdb=" N LEU B 256 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE B 257 " --> pdb=" O TRP B 253 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE B 265 " --> pdb=" O ILE B 261 " (cutoff:3.500A) Proline residue: B 267 - end of helix removed outlier: 3.915A pdb=" N GLN B 277 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP B 278 " --> pdb=" O LEU B 274 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU B 279 " --> pdb=" O GLY B 275 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N ARG B 282 " --> pdb=" O ASP B 278 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N VAL B 283 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N HIS B 284 " --> pdb=" O LEU B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 309 removed outlier: 3.536A pdb=" N CYS B 302 " --> pdb=" O ILE B 298 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY B 306 " --> pdb=" O CYS B 302 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N PHE B 307 " --> pdb=" O GLY B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 313 Processing helix chain 'B' and resid 315 through 318 removed outlier: 3.665A pdb=" N ASN B 318 " --> pdb=" O GLY B 315 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 315 through 318' Processing helix chain 'B' and resid 319 through 325 Processing helix chain 'B' and resid 329 through 350 removed outlier: 3.932A pdb=" N VAL B 334 " --> pdb=" O MET B 330 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE B 335 " --> pdb=" O GLY B 331 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU B 346 " --> pdb=" O ILE B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 379 removed outlier: 3.797A pdb=" N VAL B 374 " --> pdb=" O ALA B 370 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU B 377 " --> pdb=" O MET B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 383 removed outlier: 3.772A pdb=" N HIS B 383 " --> pdb=" O PRO B 380 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 380 through 383' Processing helix chain 'B' and resid 386 through 393 removed outlier: 3.550A pdb=" N ALA B 390 " --> pdb=" O ALA B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 402 Processing helix chain 'B' and resid 404 through 417 Processing helix chain 'B' and resid 418 through 420 No H-bonds generated for 'chain 'B' and resid 418 through 420' Processing helix chain 'B' and resid 421 through 439 removed outlier: 3.681A pdb=" N THR B 433 " --> pdb=" O GLY B 429 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU B 435 " --> pdb=" O GLY B 431 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN B 437 " --> pdb=" O THR B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 457 removed outlier: 3.911A pdb=" N LYS B 455 " --> pdb=" O ARG B 451 " (cutoff:3.500A) 459 hydrogen bonds defined for protein. 1359 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: 1.87 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.13: 6964 1.13 - 1.30: 1086 1.30 - 1.47: 2394 1.47 - 1.65: 3262 1.65 - 1.82: 74 Bond restraints: 13780 Sorted by residual: bond pdb=" N LEU B 33 " pdb=" H LEU B 33 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" CE2 TYR A 255 " pdb=" HE2 TYR A 255 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" N ILE A 391 " pdb=" H ILE A 391 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" N PHE A 166 " pdb=" H PHE A 166 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" NH2 ARG B 451 " pdb="HH22 ARG B 451 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.65e+01 ... (remaining 13775 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 20456 2.39 - 4.78: 3635 4.78 - 7.17: 805 7.17 - 9.56: 126 9.56 - 11.95: 6 Bond angle restraints: 25028 Sorted by residual: angle pdb=" CA PHE A 357 " pdb=" CB PHE A 357 " pdb=" CG PHE A 357 " ideal model delta sigma weight residual 113.80 121.09 -7.29 1.00e+00 1.00e+00 5.32e+01 angle pdb=" CA PHE B 357 " pdb=" CB PHE B 357 " pdb=" CG PHE B 357 " ideal model delta sigma weight residual 113.80 120.45 -6.65 1.00e+00 1.00e+00 4.42e+01 angle pdb=" C LEU B 319 " pdb=" N ILE B 320 " pdb=" CA ILE B 320 " ideal model delta sigma weight residual 120.33 124.27 -3.94 8.00e-01 1.56e+00 2.42e+01 angle pdb=" C ARG A 209 " pdb=" N TYR A 210 " pdb=" CA TYR A 210 " ideal model delta sigma weight residual 120.71 127.52 -6.81 1.42e+00 4.96e-01 2.30e+01 angle pdb=" C ARG B 209 " pdb=" N TYR B 210 " pdb=" CA TYR B 210 " ideal model delta sigma weight residual 120.71 127.48 -6.77 1.42e+00 4.96e-01 2.27e+01 ... (remaining 25023 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.70: 5818 16.70 - 33.40: 253 33.40 - 50.10: 141 50.10 - 66.80: 182 66.80 - 83.49: 6 Dihedral angle restraints: 6400 sinusoidal: 3498 harmonic: 2902 Sorted by residual: dihedral pdb=" C GLU B 459 " pdb=" N GLU B 459 " pdb=" CA GLU B 459 " pdb=" CB GLU B 459 " ideal model delta harmonic sigma weight residual -122.60 -134.99 12.39 0 2.50e+00 1.60e-01 2.46e+01 dihedral pdb=" C GLU A 459 " pdb=" N GLU A 459 " pdb=" CA GLU A 459 " pdb=" CB GLU A 459 " ideal model delta harmonic sigma weight residual -122.60 -134.72 12.12 0 2.50e+00 1.60e-01 2.35e+01 dihedral pdb=" CA GLN A 207 " pdb=" C GLN A 207 " pdb=" N PHE A 208 " pdb=" CA PHE A 208 " ideal model delta harmonic sigma weight residual -180.00 -156.22 -23.78 0 5.00e+00 4.00e-02 2.26e+01 ... (remaining 6397 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 715 0.082 - 0.164: 309 0.164 - 0.245: 48 0.245 - 0.327: 12 0.327 - 0.409: 2 Chirality restraints: 1086 Sorted by residual: chirality pdb=" CA GLU B 459 " pdb=" N GLU B 459 " pdb=" C GLU B 459 " pdb=" CB GLU B 459 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.17e+00 chirality pdb=" CA GLU A 459 " pdb=" N GLU A 459 " pdb=" C GLU A 459 " pdb=" CB GLU A 459 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.89e+00 chirality pdb=" CA LYS A 455 " pdb=" N LYS A 455 " pdb=" C LYS A 455 " pdb=" CB LYS A 455 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.25e+00 ... (remaining 1083 not shown) Planarity restraints: 2008 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 125 " -0.115 2.00e-02 2.50e+03 4.95e-02 9.80e+01 pdb=" CG TRP B 125 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP B 125 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP B 125 " -0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP B 125 " 0.033 2.00e-02 2.50e+03 pdb=" CE2 TRP B 125 " -0.014 2.00e-02 2.50e+03 pdb=" CE3 TRP B 125 " 0.024 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 125 " -0.038 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 125 " 0.014 2.00e-02 2.50e+03 pdb=" CH2 TRP B 125 " -0.034 2.00e-02 2.50e+03 pdb=" HD1 TRP B 125 " 0.019 2.00e-02 2.50e+03 pdb=" HE1 TRP B 125 " 0.087 2.00e-02 2.50e+03 pdb=" HE3 TRP B 125 " 0.082 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 125 " -0.043 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 125 " 0.045 2.00e-02 2.50e+03 pdb=" HH2 TRP B 125 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 147 " -0.355 9.50e-02 1.11e+02 1.32e-01 8.86e+01 pdb=" NE ARG B 147 " -0.036 2.00e-02 2.50e+03 pdb=" CZ ARG B 147 " -0.021 2.00e-02 2.50e+03 pdb=" NH1 ARG B 147 " -0.070 2.00e-02 2.50e+03 pdb=" NH2 ARG B 147 " 0.039 2.00e-02 2.50e+03 pdb="HH11 ARG B 147 " 0.081 2.00e-02 2.50e+03 pdb="HH12 ARG B 147 " 0.033 2.00e-02 2.50e+03 pdb="HH21 ARG B 147 " 0.078 2.00e-02 2.50e+03 pdb="HH22 ARG B 147 " -0.090 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 147 " -0.349 9.50e-02 1.11e+02 1.28e-01 7.83e+01 pdb=" NE ARG A 147 " -0.031 2.00e-02 2.50e+03 pdb=" CZ ARG A 147 " -0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG A 147 " -0.062 2.00e-02 2.50e+03 pdb=" NH2 ARG A 147 " 0.039 2.00e-02 2.50e+03 pdb="HH11 ARG A 147 " 0.066 2.00e-02 2.50e+03 pdb="HH12 ARG A 147 " 0.038 2.00e-02 2.50e+03 pdb="HH21 ARG A 147 " 0.072 2.00e-02 2.50e+03 pdb="HH22 ARG A 147 " -0.091 2.00e-02 2.50e+03 ... (remaining 2005 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.22: 661 2.22 - 2.82: 24748 2.82 - 3.41: 36293 3.41 - 4.01: 47122 4.01 - 4.60: 69085 Nonbonded interactions: 177909 Sorted by model distance: nonbonded pdb=" OE1 GLU B 202 " pdb=" HG1 THR B 407 " model vdw 1.630 2.450 nonbonded pdb=" OE1 GLU A 202 " pdb=" HG1 THR A 407 " model vdw 1.645 2.450 nonbonded pdb=" HG SER B 86 " pdb=" O GLY B 141 " model vdw 1.704 2.450 nonbonded pdb=" HG SER A 86 " pdb=" O GLY A 141 " model vdw 1.715 2.450 nonbonded pdb=" O VAL A 412 " pdb=" HG1 THR A 416 " model vdw 1.715 2.450 ... (remaining 177904 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.590 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: 0.070 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.890 Find NCS groups from input model: 0.060 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:0.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 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 : 0.013 0.036 6810 Z= 0.830 Angle : 1.796 7.292 9242 Z= 1.253 Chirality : 0.090 0.409 1086 Planarity : 0.012 0.104 1160 Dihedral : 10.815 83.495 2404 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.81 % Favored : 97.96 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.26 % 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 are not related in a simple way. whole: -2.24 (0.25), residues: 884 helix: -1.58 (0.16), residues: 656 sheet: None (None), residues: 0 loop : -0.47 (0.45), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 205 TYR 0.089 0.018 TYR A 75 PHE 0.047 0.009 PHE A 199 TRP 0.065 0.013 TRP B 125 HIS 0.009 0.003 HIS A 284 Details of bonding type rmsd/Z covalent geometry : bond 0.01316 / 0.83 ( 6810) covalent geometry : angle 1.79588 / 1.25 ( 9242) hydrogen bonds : bond 0.29076 / 19.90 ( 459) hydrogen bonds : angle 7.71060 / 5.44 ( 1359) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 167 ARG cc_start: 0.8307 (mtp180) cc_final: 0.7643 (tpt170) REVERT: A 172 GLU cc_start: 0.8664 (pm20) cc_final: 0.8295 (tm-30) REVERT: A 228 MET cc_start: 0.8767 (mmp) cc_final: 0.8225 (mmt) REVERT: A 373 MET cc_start: 0.8447 (mtt) cc_final: 0.8212 (mtp) REVERT: B 164 ASP cc_start: 0.8290 (m-30) cc_final: 0.7818 (m-30) REVERT: B 172 GLU cc_start: 0.8458 (pm20) cc_final: 0.8140 (tm-30) REVERT: B 373 MET cc_start: 0.8457 (mtt) cc_final: 0.8240 (mtp) REVERT: B 425 MET cc_start: 0.8469 (mtt) cc_final: 0.8211 (mtm) REVERT: B 433 THR cc_start: 0.8721 (m) cc_final: 0.8500 (p) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.1574 time to fit residues: 21.7227 Evaluate side-chains 84 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 327 ASN B 327 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.150699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.118772 restraints weight = 22597.880| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.95 r_work: 0.3174 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6810 Z= 0.200 Angle : 0.645 5.432 9242 Z= 0.365 Chirality : 0.043 0.128 1086 Planarity : 0.006 0.035 1160 Dihedral : 4.993 23.628 946 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 0.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.28), residues: 884 helix: 0.66 (0.20), residues: 656 sheet: None (None), residues: 0 loop : -1.13 (0.42), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 174 TYR 0.015 0.002 TYR B 75 PHE 0.020 0.002 PHE A 92 TRP 0.011 0.002 TRP B 253 HIS 0.006 0.002 HIS B 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.20 ( 6810) covalent geometry : angle 0.64498 / 0.37 ( 9242) hydrogen bonds : bond 0.09188 / 6.19 ( 459) hydrogen bonds : angle 4.99003 / 3.55 ( 1359) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: A 38 MET cc_start: 0.7485 (mmt) cc_final: 0.6798 (mmt) REVERT: A 167 ARG cc_start: 0.7489 (mtp180) cc_final: 0.7260 (mtt180) REVERT: A 172 GLU cc_start: 0.7354 (pm20) cc_final: 0.6758 (tt0) REVERT: A 228 MET cc_start: 0.8606 (mmp) cc_final: 0.8260 (mmm) REVERT: A 290 LYS cc_start: 0.7029 (mttt) cc_final: 0.6776 (mttp) REVERT: A 373 MET cc_start: 0.8223 (mtt) cc_final: 0.7937 (mtp) REVERT: B 118 ASP cc_start: 0.7133 (m-30) cc_final: 0.6800 (t0) REVERT: B 172 GLU cc_start: 0.7291 (pm20) cc_final: 0.6767 (tt0) REVERT: B 228 MET cc_start: 0.8694 (mmt) cc_final: 0.8370 (mmm) REVERT: B 373 MET cc_start: 0.8156 (mtt) cc_final: 0.7937 (mtp) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1738 time to fit residues: 18.9595 Evaluate side-chains 76 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 69 optimal weight: 0.9990 chunk 38 optimal weight: 0.3980 chunk 29 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 21 optimal weight: 0.4980 chunk 63 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.151192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.120862 restraints weight = 22709.342| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.80 r_work: 0.3215 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6810 Z= 0.143 Angle : 0.509 4.448 9242 Z= 0.281 Chirality : 0.038 0.112 1086 Planarity : 0.005 0.037 1160 Dihedral : 4.402 19.429 946 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 1.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.15 % Allowed : 4.18 % Favored : 95.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.29), residues: 884 helix: 1.27 (0.21), residues: 658 sheet: None (None), residues: 0 loop : -1.25 (0.39), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 174 TYR 0.015 0.002 TYR B 419 PHE 0.011 0.001 PHE A 92 TRP 0.008 0.001 TRP B 253 HIS 0.003 0.001 HIS B 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.14 ( 6810) covalent geometry : angle 0.50899 / 0.28 ( 9242) hydrogen bonds : bond 0.07195 / 4.87 ( 459) hydrogen bonds : angle 4.41233 / 3.13 ( 1359) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 73 time to evaluate : 0.251 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7460 (tm-30) cc_final: 0.7238 (tp30) REVERT: A 172 GLU cc_start: 0.7295 (pm20) cc_final: 0.6678 (tt0) REVERT: A 228 MET cc_start: 0.8579 (mmp) cc_final: 0.8252 (mmt) REVERT: A 373 MET cc_start: 0.8219 (mtt) cc_final: 0.7977 (mtp) REVERT: B 27 GLU cc_start: 0.7480 (tm-30) cc_final: 0.7263 (tp30) REVERT: B 172 GLU cc_start: 0.7191 (pm20) cc_final: 0.6622 (tt0) REVERT: B 228 MET cc_start: 0.8643 (mmt) cc_final: 0.8307 (mmm) outliers start: 1 outliers final: 1 residues processed: 74 average time/residue: 0.1586 time to fit residues: 15.8593 Evaluate side-chains 65 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 64 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 80 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.148159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.117734 restraints weight = 22696.976| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.81 r_work: 0.3158 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6810 Z= 0.182 Angle : 0.541 4.368 9242 Z= 0.298 Chirality : 0.039 0.126 1086 Planarity : 0.006 0.043 1160 Dihedral : 4.316 19.116 946 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 1.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.45 % Allowed : 4.93 % Favored : 94.63 % 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 are not related in a simple way. whole: 0.81 (0.28), residues: 884 helix: 1.30 (0.21), residues: 652 sheet: None (None), residues: 0 loop : -1.65 (0.38), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 174 TYR 0.010 0.002 TYR A 419 PHE 0.018 0.002 PHE A 92 TRP 0.008 0.001 TRP B 253 HIS 0.003 0.001 HIS A 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.18 ( 6810) covalent geometry : angle 0.54051 / 0.30 ( 9242) hydrogen bonds : bond 0.08001 / 5.41 ( 459) hydrogen bonds : angle 4.39516 / 3.10 ( 1359) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 0.218 Fit side-chains revert: symmetry clash REVERT: A 172 GLU cc_start: 0.7280 (pm20) cc_final: 0.6635 (tt0) REVERT: A 228 MET cc_start: 0.8708 (mmp) cc_final: 0.8369 (mmm) REVERT: A 373 MET cc_start: 0.8292 (mtt) cc_final: 0.8049 (mtp) REVERT: B 172 GLU cc_start: 0.7294 (pm20) cc_final: 0.6634 (tt0) REVERT: B 228 MET cc_start: 0.8766 (mmt) cc_final: 0.8439 (mmm) outliers start: 3 outliers final: 2 residues processed: 64 average time/residue: 0.1434 time to fit residues: 12.7954 Evaluate side-chains 63 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 61 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 136 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 45 optimal weight: 0.8980 chunk 44 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.140750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.106853 restraints weight = 22440.790| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.05 r_work: 0.3017 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6810 Z= 0.145 Angle : 0.497 4.294 9242 Z= 0.271 Chirality : 0.038 0.117 1086 Planarity : 0.005 0.042 1160 Dihedral : 4.175 18.192 946 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 1.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.30 % Allowed : 5.97 % Favored : 93.73 % 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 are not related in a simple way. whole: 1.02 (0.29), residues: 884 helix: 1.41 (0.21), residues: 658 sheet: None (None), residues: 0 loop : -1.50 (0.39), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 174 TYR 0.018 0.002 TYR B 419 PHE 0.015 0.001 PHE A 92 TRP 0.005 0.001 TRP B 125 HIS 0.002 0.001 HIS B 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 ( 6810) covalent geometry : angle 0.49730 / 0.27 ( 9242) hydrogen bonds : bond 0.06981 / 4.72 ( 459) hydrogen bonds : angle 4.22219 / 2.99 ( 1359) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 64 time to evaluate : 0.241 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7354 (tm-30) cc_final: 0.7152 (tp30) REVERT: A 172 GLU cc_start: 0.6996 (pm20) cc_final: 0.6260 (tt0) REVERT: A 210 TYR cc_start: 0.7787 (t80) cc_final: 0.7412 (t80) REVERT: A 228 MET cc_start: 0.8554 (mmp) cc_final: 0.8209 (mmm) REVERT: A 373 MET cc_start: 0.8051 (mtt) cc_final: 0.7776 (mtp) REVERT: B 172 GLU cc_start: 0.7065 (pm20) cc_final: 0.6350 (tt0) REVERT: B 228 MET cc_start: 0.8578 (mmt) cc_final: 0.8236 (mmm) outliers start: 2 outliers final: 2 residues processed: 66 average time/residue: 0.1454 time to fit residues: 13.2157 Evaluate side-chains 65 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 63 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain B residue 136 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 56 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 44 optimal weight: 9.9990 chunk 29 optimal weight: 0.2980 chunk 23 optimal weight: 0.0370 overall best weight: 0.8062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.156147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.126013 restraints weight = 22437.820| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.78 r_work: 0.3291 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6810 Z= 0.121 Angle : 0.461 4.339 9242 Z= 0.249 Chirality : 0.037 0.110 1086 Planarity : 0.005 0.040 1160 Dihedral : 3.963 16.315 946 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 1.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.45 % Allowed : 5.97 % Favored : 93.58 % 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 are not related in a simple way. whole: 1.36 (0.29), residues: 884 helix: 1.66 (0.21), residues: 668 sheet: None (None), residues: 0 loop : -1.50 (0.41), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 174 TYR 0.017 0.001 TYR B 419 PHE 0.011 0.001 PHE A 92 TRP 0.005 0.001 TRP A 125 HIS 0.002 0.001 HIS A 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 ( 6810) covalent geometry : angle 0.46097 / 0.25 ( 9242) hydrogen bonds : bond 0.06046 / 4.10 ( 459) hydrogen bonds : angle 4.03609 / 2.85 ( 1359) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 0.266 Fit side-chains REVERT: A 172 GLU cc_start: 0.7359 (pm20) cc_final: 0.6723 (tt0) REVERT: A 210 TYR cc_start: 0.7990 (t80) cc_final: 0.7693 (t80) REVERT: A 228 MET cc_start: 0.8710 (mmp) cc_final: 0.8323 (mmt) REVERT: B 172 GLU cc_start: 0.7359 (pm20) cc_final: 0.6725 (tt0) REVERT: B 228 MET cc_start: 0.8737 (mmt) cc_final: 0.8411 (mmm) outliers start: 3 outliers final: 3 residues processed: 65 average time/residue: 0.1450 time to fit residues: 13.1343 Evaluate side-chains 66 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 136 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 37 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.156238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.126195 restraints weight = 22197.753| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.77 r_work: 0.3312 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6810 Z= 0.119 Angle : 0.457 4.320 9242 Z= 0.246 Chirality : 0.036 0.110 1086 Planarity : 0.005 0.039 1160 Dihedral : 3.886 16.484 946 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 1.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.45 % Allowed : 6.42 % Favored : 93.13 % 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 are not related in a simple way. whole: 1.49 (0.29), residues: 884 helix: 1.74 (0.21), residues: 672 sheet: None (None), residues: 0 loop : -1.51 (0.41), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 174 TYR 0.029 0.002 TYR B 419 PHE 0.011 0.001 PHE A 92 TRP 0.004 0.001 TRP A 125 HIS 0.002 0.001 HIS B 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 ( 6810) covalent geometry : angle 0.45704 / 0.25 ( 9242) hydrogen bonds : bond 0.05931 / 4.02 ( 459) hydrogen bonds : angle 3.97996 / 2.82 ( 1359) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 64 time to evaluate : 0.274 Fit side-chains REVERT: A 27 GLU cc_start: 0.7534 (tp30) cc_final: 0.7219 (tm-30) REVERT: A 172 GLU cc_start: 0.7187 (pm20) cc_final: 0.6521 (tt0) REVERT: A 210 TYR cc_start: 0.7846 (t80) cc_final: 0.7576 (t80) REVERT: A 228 MET cc_start: 0.8668 (mmp) cc_final: 0.8091 (mmt) REVERT: A 419 TYR cc_start: 0.8463 (m-80) cc_final: 0.6703 (p90) REVERT: B 172 GLU cc_start: 0.7204 (pm20) cc_final: 0.6514 (tt0) REVERT: B 228 MET cc_start: 0.8685 (mmt) cc_final: 0.8353 (mmm) outliers start: 3 outliers final: 3 residues processed: 66 average time/residue: 0.1512 time to fit residues: 13.8186 Evaluate side-chains 65 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 136 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 13 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 45 optimal weight: 0.0770 chunk 36 optimal weight: 0.0470 chunk 11 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 1 optimal weight: 0.2980 chunk 79 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.160572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.130617 restraints weight = 22070.704| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 1.77 r_work: 0.3330 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6810 Z= 0.096 Angle : 0.429 5.226 9242 Z= 0.227 Chirality : 0.036 0.108 1086 Planarity : 0.005 0.037 1160 Dihedral : 3.658 15.806 946 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 1.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.60 % Allowed : 6.42 % Favored : 92.99 % 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 are not related in a simple way. whole: 2.05 (0.30), residues: 884 helix: 2.19 (0.21), residues: 672 sheet: None (None), residues: 0 loop : -1.48 (0.42), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 174 TYR 0.019 0.001 TYR B 419 PHE 0.007 0.001 PHE A 92 TRP 0.005 0.001 TRP A 125 HIS 0.001 0.001 HIS A 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00190 / 0.10 ( 6810) covalent geometry : angle 0.42890 / 0.23 ( 9242) hydrogen bonds : bond 0.04715 / 3.20 ( 459) hydrogen bonds : angle 3.77917 / 2.68 ( 1359) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.296 Fit side-chains REVERT: A 172 GLU cc_start: 0.7227 (pm20) cc_final: 0.6567 (tt0) REVERT: A 210 TYR cc_start: 0.7902 (t80) cc_final: 0.7696 (t80) REVERT: A 228 MET cc_start: 0.8627 (mmp) cc_final: 0.8276 (mmt) REVERT: A 419 TYR cc_start: 0.8378 (m-80) cc_final: 0.6695 (p90) REVERT: B 172 GLU cc_start: 0.7278 (pm20) cc_final: 0.6624 (tt0) REVERT: B 228 MET cc_start: 0.8660 (mmt) cc_final: 0.8281 (mmt) outliers start: 4 outliers final: 3 residues processed: 67 average time/residue: 0.1594 time to fit residues: 14.6466 Evaluate side-chains 65 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 415 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 71 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.157089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.126449 restraints weight = 22315.459| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.83 r_work: 0.3293 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.4097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6810 Z= 0.117 Angle : 0.451 5.098 9242 Z= 0.239 Chirality : 0.036 0.113 1086 Planarity : 0.005 0.038 1160 Dihedral : 3.685 15.975 946 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 1.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.30 % Allowed : 7.01 % Favored : 92.69 % 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 are not related in a simple way. whole: 1.96 (0.30), residues: 884 helix: 2.13 (0.21), residues: 672 sheet: None (None), residues: 0 loop : -1.51 (0.42), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 123 TYR 0.020 0.001 TYR B 419 PHE 0.011 0.001 PHE B 92 TRP 0.004 0.001 TRP A 124 HIS 0.002 0.001 HIS A 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 ( 6810) covalent geometry : angle 0.45080 / 0.24 ( 9242) hydrogen bonds : bond 0.05620 / 3.81 ( 459) hydrogen bonds : angle 3.85325 / 2.72 ( 1359) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 63 time to evaluate : 0.279 Fit side-chains REVERT: A 172 GLU cc_start: 0.7194 (pm20) cc_final: 0.6499 (tt0) REVERT: A 210 TYR cc_start: 0.7794 (t80) cc_final: 0.7554 (t80) REVERT: A 228 MET cc_start: 0.8610 (mmp) cc_final: 0.8080 (mmp) REVERT: A 419 TYR cc_start: 0.8436 (m-80) cc_final: 0.8198 (m-10) REVERT: B 172 GLU cc_start: 0.7244 (pm20) cc_final: 0.6554 (tt0) REVERT: B 228 MET cc_start: 0.8687 (mmt) cc_final: 0.8348 (mmm) outliers start: 2 outliers final: 2 residues processed: 65 average time/residue: 0.1344 time to fit residues: 12.3511 Evaluate side-chains 64 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain B residue 136 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 1 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 78 optimal weight: 0.4980 chunk 87 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.150686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.119642 restraints weight = 22307.678| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.83 r_work: 0.3198 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.4167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6810 Z= 0.107 Angle : 0.439 5.238 9242 Z= 0.232 Chirality : 0.036 0.108 1086 Planarity : 0.005 0.037 1160 Dihedral : 3.651 15.902 946 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.45 % Allowed : 6.87 % Favored : 92.69 % 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 are not related in a simple way. whole: 2.08 (0.30), residues: 884 helix: 2.21 (0.21), residues: 672 sheet: None (None), residues: 0 loop : -1.48 (0.42), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 174 TYR 0.017 0.001 TYR B 419 PHE 0.010 0.001 PHE A 92 TRP 0.004 0.001 TRP A 125 HIS 0.002 0.001 HIS B 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 ( 6810) covalent geometry : angle 0.43935 / 0.23 ( 9242) hydrogen bonds : bond 0.05332 / 3.62 ( 459) hydrogen bonds : angle 3.80323 / 2.69 ( 1359) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 60 time to evaluate : 0.290 Fit side-chains REVERT: A 172 GLU cc_start: 0.7190 (pm20) cc_final: 0.6509 (tt0) REVERT: A 210 TYR cc_start: 0.7837 (t80) cc_final: 0.7597 (t80) REVERT: A 228 MET cc_start: 0.8543 (mmp) cc_final: 0.7987 (mmt) REVERT: A 419 TYR cc_start: 0.8390 (m-80) cc_final: 0.8179 (m-10) REVERT: B 172 GLU cc_start: 0.7260 (pm20) cc_final: 0.6584 (tt0) REVERT: B 228 MET cc_start: 0.8625 (mmt) cc_final: 0.8301 (mmm) outliers start: 3 outliers final: 3 residues processed: 62 average time/residue: 0.1378 time to fit residues: 11.8981 Evaluate side-chains 62 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 59 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 415 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 67 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 5 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 71 optimal weight: 0.0050 chunk 29 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.150386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.119371 restraints weight = 22400.474| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.82 r_work: 0.3194 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.4207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6810 Z= 0.109 Angle : 0.442 5.433 9242 Z= 0.234 Chirality : 0.036 0.109 1086 Planarity : 0.005 0.037 1160 Dihedral : 3.625 16.080 946 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 1.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.45 % Allowed : 7.01 % Favored : 92.54 % 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 are not related in a simple way. whole: 2.12 (0.30), residues: 884 helix: 2.23 (0.21), residues: 674 sheet: None (None), residues: 0 loop : -1.44 (0.43), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 174 TYR 0.018 0.001 TYR B 419 PHE 0.010 0.001 PHE A 92 TRP 0.003 0.001 TRP A 124 HIS 0.002 0.001 HIS A 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 ( 6810) covalent geometry : angle 0.44215 / 0.23 ( 9242) hydrogen bonds : bond 0.05372 / 3.65 ( 459) hydrogen bonds : angle 3.79372 / 2.68 ( 1359) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2758.33 seconds wall clock time: 47 minutes 20.18 seconds (2840.18 seconds total)