Starting phenix.real_space_refine on Wed Aug 5 14:32:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e4d_47506/08_2026/9e4d_47506.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e4d_47506/08_2026/9e4d_47506.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e4d_47506/08_2026/9e4d_47506.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e4d_47506/08_2026/9e4d_47506.map" model { file = "/net/cci-nas-00/data/ceres_data/9e4d_47506/08_2026/9e4d_47506.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e4d_47506/08_2026/9e4d_47506.cif" } resolution = 3.19 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 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 87 5.16 5 C 6330 2.51 5 N 1632 2.21 5 O 1866 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9915 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3305 Classifications: {'peptide': 413} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 394} Chain: "B" Number of atoms: 3305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3305 Classifications: {'peptide': 413} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 394} Chain: "C" Number of atoms: 3305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3305 Classifications: {'peptide': 413} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 394} Time building chain proxies: 2.38, per 1000 atoms: 0.24 Number of scatterers: 9915 At special positions: 0 Unit cell: (92.84, 98.748, 131.664, 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 87 16.00 O 1866 8.00 N 1632 7.00 C 6330 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 93 " - pdb=" SG CYS A 194 " distance=2.03 Simple disulfide: pdb=" SG CYS A 172 " - pdb=" SG CYS A 179 " distance=2.03 Simple disulfide: pdb=" SG CYS A 290 " - pdb=" SG CYS A 367 " distance=2.03 Simple disulfide: pdb=" SG CYS A 310 " - pdb=" SG CYS A 363 " distance=2.03 Simple disulfide: pdb=" SG CYS A 314 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 323 " - pdb=" SG CYS A 345 " distance=2.03 Simple disulfide: pdb=" SG CYS A 325 " - pdb=" SG CYS A 337 " distance=2.03 Simple disulfide: pdb=" SG CYS B 93 " - pdb=" SG CYS B 194 " distance=2.02 Simple disulfide: pdb=" SG CYS B 172 " - pdb=" SG CYS B 179 " distance=2.03 Simple disulfide: pdb=" SG CYS B 290 " - pdb=" SG CYS B 367 " distance=2.03 Simple disulfide: pdb=" SG CYS B 310 " - pdb=" SG CYS B 363 " distance=2.03 Simple disulfide: pdb=" SG CYS B 314 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 323 " - pdb=" SG CYS B 345 " distance=2.03 Simple disulfide: pdb=" SG CYS B 325 " - pdb=" SG CYS B 337 " distance=2.03 Simple disulfide: pdb=" SG CYS C 93 " - pdb=" SG CYS C 194 " distance=2.02 Simple disulfide: pdb=" SG CYS C 172 " - pdb=" SG CYS C 179 " distance=2.03 Simple disulfide: pdb=" SG CYS C 290 " - pdb=" SG CYS C 367 " distance=2.03 Simple disulfide: pdb=" SG CYS C 310 " - pdb=" SG CYS C 363 " distance=2.03 Simple disulfide: pdb=" SG CYS C 314 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 323 " - pdb=" SG CYS C 345 " distance=2.03 Simple disulfide: pdb=" SG CYS C 325 " - pdb=" SG CYS C 337 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 356.6 milliseconds 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2322 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 12 sheets defined 42.1% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 40 through 70 removed outlier: 3.574A pdb=" N LEU A 45 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU A 54 " --> pdb=" O PHE A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 112 Processing helix chain 'A' and resid 131 through 143 removed outlier: 3.517A pdb=" N ASN A 143 " --> pdb=" O GLN A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 162 Processing helix chain 'A' and resid 164 through 169 Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 199 through 203 removed outlier: 4.111A pdb=" N ASP A 202 " --> pdb=" O SER A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 Processing helix chain 'A' and resid 225 through 229 Processing helix chain 'A' and resid 292 through 297 removed outlier: 3.772A pdb=" N ASP A 296 " --> pdb=" O VAL A 293 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER A 297 " --> pdb=" O THR A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 324 Processing helix chain 'A' and resid 338 through 345 Processing helix chain 'A' and resid 345 through 355 Processing helix chain 'A' and resid 386 through 394 Processing helix chain 'A' and resid 397 through 404 removed outlier: 3.500A pdb=" N GLY A 402 " --> pdb=" O GLU A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 452 removed outlier: 3.836A pdb=" N LEU A 432 " --> pdb=" O ILE A 428 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLY A 433 " --> pdb=" O ALA A 429 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP A 434 " --> pdb=" O GLY A 430 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY A 437 " --> pdb=" O GLY A 433 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN A 438 " --> pdb=" O ASP A 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 71 removed outlier: 3.715A pdb=" N CYS B 59 " --> pdb=" O ALA B 55 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL B 60 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR B 71 " --> pdb=" O TYR B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 112 Processing helix chain 'B' and resid 126 through 130 removed outlier: 3.521A pdb=" N ALA B 130 " --> pdb=" O THR B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 142 Processing helix chain 'B' and resid 153 through 162 Processing helix chain 'B' and resid 164 through 168 Processing helix chain 'B' and resid 180 through 182 No H-bonds generated for 'chain 'B' and resid 180 through 182' Processing helix chain 'B' and resid 199 through 203 removed outlier: 3.815A pdb=" N ASP B 202 " --> pdb=" O SER B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 229 Processing helix chain 'B' and resid 257 through 262 Processing helix chain 'B' and resid 292 through 297 removed outlier: 3.575A pdb=" N ASP B 296 " --> pdb=" O VAL B 293 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER B 297 " --> pdb=" O THR B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 324 Processing helix chain 'B' and resid 338 through 345 removed outlier: 3.533A pdb=" N LYS B 343 " --> pdb=" O PRO B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 355 Processing helix chain 'B' and resid 386 through 394 Processing helix chain 'B' and resid 397 through 404 removed outlier: 3.601A pdb=" N GLY B 402 " --> pdb=" O GLU B 398 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU B 403 " --> pdb=" O GLN B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 452 removed outlier: 3.504A pdb=" N LEU B 432 " --> pdb=" O ILE B 428 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY B 433 " --> pdb=" O ALA B 429 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY B 437 " --> pdb=" O GLY B 433 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLN B 438 " --> pdb=" O ASP B 434 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLU B 452 " --> pdb=" O LEU B 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 70 removed outlier: 3.948A pdb=" N VAL C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 112 Processing helix chain 'C' and resid 126 through 130 removed outlier: 4.063A pdb=" N ALA C 130 " --> pdb=" O THR C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 142 Processing helix chain 'C' and resid 153 through 162 Processing helix chain 'C' and resid 164 through 168 Processing helix chain 'C' and resid 180 through 182 No H-bonds generated for 'chain 'C' and resid 180 through 182' Processing helix chain 'C' and resid 199 through 203 removed outlier: 4.127A pdb=" N ASP C 202 " --> pdb=" O SER C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 229 Processing helix chain 'C' and resid 257 through 262 removed outlier: 3.617A pdb=" N GLY C 262 " --> pdb=" O ILE C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 324 Processing helix chain 'C' and resid 338 through 345 removed outlier: 3.596A pdb=" N LYS C 343 " --> pdb=" O PRO C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 355 Processing helix chain 'C' and resid 386 through 394 Processing helix chain 'C' and resid 397 through 403 removed outlier: 3.619A pdb=" N GLY C 402 " --> pdb=" O GLU C 398 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU C 403 " --> pdb=" O GLN C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 452 removed outlier: 3.666A pdb=" N LEU C 441 " --> pdb=" O GLY C 437 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 80 removed outlier: 3.625A pdb=" N GLU A 421 " --> pdb=" O LYS A 76 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 177 through 178 removed outlier: 4.208A pdb=" N PHE A 269 " --> pdb=" O ILE A 405 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL A 407 " --> pdb=" O PHE A 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 86 Processing sheet with id=AA4, first strand: chain 'A' and resid 184 through 189 removed outlier: 6.668A pdb=" N LYS A 193 " --> pdb=" O ASN A 94 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ASN A 94 " --> pdb=" O LYS A 193 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 73 through 80 removed outlier: 3.533A pdb=" N GLU B 421 " --> pdb=" O LYS B 76 " (cutoff:3.500A) removed outlier: 9.412A pdb=" N GLU B 418 " --> pdb=" O CYS B 275 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLU B 277 " --> pdb=" O GLU B 418 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N ILE B 420 " --> pdb=" O GLU B 277 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ARG B 279 " --> pdb=" O ILE B 420 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N GLN B 422 " --> pdb=" O ARG B 279 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE B 281 " --> pdb=" O GLN B 422 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N LYS B 424 " --> pdb=" O ILE B 281 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 169 through 174 removed outlier: 5.745A pdb=" N LEU B 169 " --> pdb=" O ASP B 223 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ASP B 223 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N PHE B 269 " --> pdb=" O ILE B 405 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL B 407 " --> pdb=" O PHE B 269 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 85 through 86 Processing sheet with id=AA8, first strand: chain 'B' and resid 184 through 189 removed outlier: 6.926A pdb=" N LYS B 193 " --> pdb=" O ASN B 94 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N ASN B 94 " --> pdb=" O LYS B 193 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 73 through 80 removed outlier: 3.559A pdb=" N GLU C 421 " --> pdb=" O LYS C 76 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 169 through 174 removed outlier: 5.689A pdb=" N LEU C 169 " --> pdb=" O ASP C 223 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ASP C 223 " --> pdb=" O LEU C 169 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N PHE C 269 " --> pdb=" O ILE C 405 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 85 through 86 Processing sheet with id=AB3, first strand: chain 'C' and resid 184 through 189 removed outlier: 6.773A pdb=" N LYS C 193 " --> pdb=" O ASN C 94 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ASN C 94 " --> pdb=" O LYS C 193 " (cutoff:3.500A) 479 hydrogen bonds defined for protein. 1326 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: 1.55 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3237 1.34 - 1.46: 2358 1.46 - 1.58: 4428 1.58 - 1.70: 0 1.70 - 1.82: 120 Bond restraints: 10143 Sorted by residual: bond pdb=" CG1 ILE A 258 " pdb=" CD1 ILE A 258 " ideal model delta sigma weight residual 1.513 1.473 0.040 3.90e-02 6.57e+02 1.07e+00 bond pdb=" CA VAL C 178 " pdb=" CB VAL C 178 " ideal model delta sigma weight residual 1.527 1.537 -0.011 1.31e-02 5.83e+03 6.44e-01 bond pdb=" CA VAL A 186 " pdb=" CB VAL A 186 " ideal model delta sigma weight residual 1.540 1.530 0.010 1.36e-02 5.41e+03 5.21e-01 bond pdb=" CB CYS C 314 " pdb=" SG CYS C 314 " ideal model delta sigma weight residual 1.808 1.784 0.024 3.30e-02 9.18e+02 5.10e-01 bond pdb=" CB CYS C 93 " pdb=" SG CYS C 93 " ideal model delta sigma weight residual 1.808 1.785 0.023 3.30e-02 9.18e+02 4.95e-01 ... (remaining 10138 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 13426 1.21 - 2.42: 214 2.42 - 3.63: 60 3.63 - 4.84: 8 4.84 - 6.06: 5 Bond angle restraints: 13713 Sorted by residual: angle pdb=" N VAL C 178 " pdb=" CA VAL C 178 " pdb=" C VAL C 178 " ideal model delta sigma weight residual 106.55 109.89 -3.34 1.45e+00 4.76e-01 5.29e+00 angle pdb=" N LEU C 169 " pdb=" CA LEU C 169 " pdb=" C LEU C 169 " ideal model delta sigma weight residual 108.17 111.29 -3.12 1.85e+00 2.92e-01 2.85e+00 angle pdb=" CA LEU C 369 " pdb=" CB LEU C 369 " pdb=" CG LEU C 369 " ideal model delta sigma weight residual 116.30 121.86 -5.56 3.50e+00 8.16e-02 2.53e+00 angle pdb=" C PHE A 257 " pdb=" N ILE A 258 " pdb=" CA ILE A 258 " ideal model delta sigma weight residual 121.97 124.81 -2.84 1.80e+00 3.09e-01 2.48e+00 angle pdb=" N ILE A 124 " pdb=" CA ILE A 124 " pdb=" CB ILE A 124 " ideal model delta sigma weight residual 110.08 111.50 -1.42 9.30e-01 1.16e+00 2.34e+00 ... (remaining 13708 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.49: 5393 16.49 - 32.99: 610 32.99 - 49.48: 113 49.48 - 65.98: 29 65.98 - 82.47: 8 Dihedral angle restraints: 6153 sinusoidal: 2535 harmonic: 3618 Sorted by residual: dihedral pdb=" CB CYS A 172 " pdb=" SG CYS A 172 " pdb=" SG CYS A 179 " pdb=" CB CYS A 179 " ideal model delta sinusoidal sigma weight residual -86.00 -37.37 -48.63 1 1.00e+01 1.00e-02 3.26e+01 dihedral pdb=" CB CYS B 310 " pdb=" SG CYS B 310 " pdb=" SG CYS B 363 " pdb=" CB CYS B 363 " ideal model delta sinusoidal sigma weight residual -86.00 -131.39 45.39 1 1.00e+01 1.00e-02 2.86e+01 dihedral pdb=" CB CYS B 314 " pdb=" SG CYS B 314 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual 93.00 50.15 42.85 1 1.00e+01 1.00e-02 2.56e+01 ... (remaining 6150 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 890 0.029 - 0.058: 411 0.058 - 0.086: 105 0.086 - 0.115: 66 0.115 - 0.144: 4 Chirality restraints: 1476 Sorted by residual: chirality pdb=" CA ILE A 410 " pdb=" N ILE A 410 " pdb=" C ILE A 410 " pdb=" CB ILE A 410 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.19e-01 chirality pdb=" CA ILE B 410 " pdb=" N ILE B 410 " pdb=" C ILE B 410 " pdb=" CB ILE B 410 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.82e-01 chirality pdb=" CA ILE C 410 " pdb=" N ILE C 410 " pdb=" C ILE C 410 " pdb=" CB ILE C 410 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.59e-01 ... (remaining 1473 not shown) Planarity restraints: 1788 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 342 " 0.009 2.00e-02 2.50e+03 7.21e-03 1.04e+00 pdb=" CG TYR C 342 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 TYR C 342 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR C 342 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR C 342 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR C 342 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR C 342 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 342 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 342 " 0.007 2.00e-02 2.50e+03 6.77e-03 9.17e-01 pdb=" CG TYR B 342 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR B 342 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR B 342 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR B 342 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 342 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 342 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 342 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 338 " -0.016 5.00e-02 4.00e+02 2.39e-02 9.17e-01 pdb=" N PRO A 339 " 0.041 5.00e-02 4.00e+02 pdb=" CA PRO A 339 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 339 " -0.013 5.00e-02 4.00e+02 ... (remaining 1785 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 460 2.73 - 3.27: 10096 3.27 - 3.81: 16672 3.81 - 4.36: 20424 4.36 - 4.90: 35162 Nonbonded interactions: 82814 Sorted by model distance: nonbonded pdb=" OH TYR C 426 " pdb=" OD2 ASP C 434 " model vdw 2.181 3.040 nonbonded pdb=" O PHE C 87 " pdb=" ND2 ASN C 198 " model vdw 2.246 3.120 nonbonded pdb=" O LEU A 77 " pdb=" OG1 THR C 75 " model vdw 2.271 3.040 nonbonded pdb=" NH1 ARG A 326 " pdb=" O MET A 330 " model vdw 2.276 3.120 nonbonded pdb=" OD2 ASP A 313 " pdb=" NH2 ARG A 317 " model vdw 2.307 3.120 ... (remaining 82809 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' selection = chain 'C' } 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: 4.540 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.450 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 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 0.040 10164 Z= 0.142 Angle : 0.448 6.055 13755 Z= 0.228 Chirality : 0.038 0.144 1476 Planarity : 0.002 0.024 1788 Dihedral : 14.131 82.475 3768 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.83 (0.25), residues: 1233 helix: 1.49 (0.27), residues: 385 sheet: -0.46 (0.31), residues: 286 loop : 0.65 (0.27), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 43 TYR 0.017 0.001 TYR C 342 PHE 0.010 0.001 PHE C 257 TRP 0.005 0.001 TRP B 46 HIS 0.002 0.000 HIS A 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (10143) covalent geometry : angle 0.44355 / 0.23 (13713) SS BOND : bond 0.00310 / 0.22 ( 21) SS BOND : angle 1.23177 / 0.82 ( 42) hydrogen bonds : bond 0.21454 / 14.43 ( 479) hydrogen bonds : angle 8.78813 / 6.21 ( 1326) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ARG cc_start: 0.8298 (mmt180) cc_final: 0.8088 (mmm160) REVERT: A 426 TYR cc_start: 0.7451 (t80) cc_final: 0.7160 (t80) REVERT: B 64 ARG cc_start: 0.8176 (mmp-170) cc_final: 0.7751 (mmt-90) REVERT: B 66 GLN cc_start: 0.8914 (tp40) cc_final: 0.8341 (tm-30) REVERT: B 68 TYR cc_start: 0.9257 (t80) cc_final: 0.8941 (t80) REVERT: B 73 HIS cc_start: 0.9023 (p90) cc_final: 0.8589 (p-80) REVERT: C 70 HIS cc_start: 0.9204 (m90) cc_final: 0.8523 (m-70) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.1364 time to fit residues: 22.9832 Evaluate side-chains 68 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.5980 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 65 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 70.6328 > 50:) chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 117 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 HIS B 139 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.104510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.078621 restraints weight = 20416.866| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.74 r_work: 0.3163 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10164 Z= 0.166 Angle : 0.591 12.976 13755 Z= 0.301 Chirality : 0.042 0.178 1476 Planarity : 0.003 0.026 1788 Dihedral : 4.074 20.286 1350 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.28 % Allowed : 5.91 % Favored : 93.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.91 (0.25), residues: 1233 helix: 1.59 (0.25), residues: 427 sheet: -0.57 (0.31), residues: 280 loop : 0.66 (0.29), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 201 TYR 0.016 0.001 TYR C 342 PHE 0.011 0.001 PHE C 442 TRP 0.017 0.001 TRP C 287 HIS 0.007 0.001 HIS C 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 (10143) covalent geometry : angle 0.58446 / 0.30 (13713) SS BOND : bond 0.00506 / 0.35 ( 21) SS BOND : angle 1.74646 / 1.01 ( 42) hydrogen bonds : bond 0.04904 / 3.29 ( 479) hydrogen bonds : angle 6.36195 / 4.57 ( 1326) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 83 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8244 (mm-30) REVERT: A 418 GLU cc_start: 0.8077 (pt0) cc_final: 0.7718 (pm20) REVERT: B 64 ARG cc_start: 0.8221 (mmp-170) cc_final: 0.7759 (mmt-90) REVERT: B 66 GLN cc_start: 0.9002 (tp40) cc_final: 0.8399 (tm-30) REVERT: B 68 TYR cc_start: 0.9311 (t80) cc_final: 0.9005 (t80) REVERT: B 73 HIS cc_start: 0.8921 (p90) cc_final: 0.8506 (p-80) REVERT: C 70 HIS cc_start: 0.9388 (m90) cc_final: 0.9000 (m170) REVERT: C 356 LYS cc_start: 0.9004 (OUTLIER) cc_final: 0.8591 (mtmm) outliers start: 3 outliers final: 1 residues processed: 84 average time/residue: 0.1033 time to fit residues: 12.0619 Evaluate side-chains 69 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 67 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain C residue 356 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 5.9990 chunk 109 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 97 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 94 optimal weight: 0.6980 chunk 90 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 329 HIS ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.104752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.078771 restraints weight = 20387.553| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.74 r_work: 0.3132 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10164 Z= 0.142 Angle : 0.539 12.468 13755 Z= 0.271 Chirality : 0.040 0.213 1476 Planarity : 0.003 0.027 1788 Dihedral : 4.170 27.753 1350 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.55 % Allowed : 7.85 % Favored : 91.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.94 (0.25), residues: 1233 helix: 1.67 (0.25), residues: 429 sheet: -0.55 (0.31), residues: 278 loop : 0.60 (0.29), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 145 TYR 0.011 0.001 TYR C 342 PHE 0.008 0.001 PHE A 442 TRP 0.020 0.001 TRP C 287 HIS 0.002 0.001 HIS C 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (10143) covalent geometry : angle 0.53179 / 0.27 (13713) SS BOND : bond 0.00481 / 0.32 ( 21) SS BOND : angle 1.68611 / 0.96 ( 42) hydrogen bonds : bond 0.04073 / 2.77 ( 479) hydrogen bonds : angle 5.93957 / 4.29 ( 1326) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8267 (mm-30) REVERT: A 418 GLU cc_start: 0.7988 (pt0) cc_final: 0.7512 (pm20) REVERT: B 64 ARG cc_start: 0.8232 (mmp-170) cc_final: 0.7814 (mpt180) REVERT: B 66 GLN cc_start: 0.8955 (tp40) cc_final: 0.8370 (tm-30) REVERT: B 68 TYR cc_start: 0.9309 (t80) cc_final: 0.9000 (t80) REVERT: B 73 HIS cc_start: 0.8947 (p90) cc_final: 0.8518 (p-80) REVERT: B 210 MET cc_start: 0.8567 (mmt) cc_final: 0.8334 (mmt) REVERT: C 70 HIS cc_start: 0.9355 (m90) cc_final: 0.8985 (m90) REVERT: C 330 MET cc_start: 0.9085 (mtt) cc_final: 0.8698 (mtt) REVERT: C 356 LYS cc_start: 0.9062 (OUTLIER) cc_final: 0.8652 (mtmm) outliers start: 6 outliers final: 2 residues processed: 77 average time/residue: 0.1029 time to fit residues: 11.2814 Evaluate side-chains 66 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain C residue 356 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 22 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 103 optimal weight: 0.0040 chunk 1 optimal weight: 0.9990 chunk 90 optimal weight: 0.5980 chunk 78 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 70 HIS ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.104311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.077977 restraints weight = 20334.592| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.74 r_work: 0.3122 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10164 Z= 0.126 Angle : 0.514 12.517 13755 Z= 0.257 Chirality : 0.040 0.178 1476 Planarity : 0.003 0.031 1788 Dihedral : 4.086 24.568 1350 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.65 % Allowed : 9.79 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.01 (0.25), residues: 1233 helix: 1.81 (0.25), residues: 429 sheet: -0.57 (0.31), residues: 274 loop : 0.59 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 201 TYR 0.012 0.001 TYR C 68 PHE 0.008 0.001 PHE C 263 TRP 0.026 0.001 TRP C 287 HIS 0.003 0.001 HIS A 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (10143) covalent geometry : angle 0.50908 / 0.25 (13713) SS BOND : bond 0.00390 / 0.27 ( 21) SS BOND : angle 1.36440 / 0.81 ( 42) hydrogen bonds : bond 0.03494 / 2.40 ( 479) hydrogen bonds : angle 5.69129 / 4.12 ( 1326) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8130 (mm-30) REVERT: A 418 GLU cc_start: 0.7920 (pt0) cc_final: 0.7556 (pm20) REVERT: B 64 ARG cc_start: 0.8268 (mmp-170) cc_final: 0.7845 (mpt180) REVERT: B 66 GLN cc_start: 0.9017 (tp40) cc_final: 0.8384 (tm-30) REVERT: B 68 TYR cc_start: 0.9288 (t80) cc_final: 0.8964 (t80) REVERT: B 73 HIS cc_start: 0.8982 (p90) cc_final: 0.8541 (p-80) REVERT: C 70 HIS cc_start: 0.9348 (m90) cc_final: 0.8949 (m90) REVERT: C 330 MET cc_start: 0.9120 (mtt) cc_final: 0.8692 (mtt) REVERT: C 356 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8684 (mtmm) outliers start: 7 outliers final: 3 residues processed: 82 average time/residue: 0.0762 time to fit residues: 9.2521 Evaluate side-chains 70 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 66 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 356 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 41 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 107 optimal weight: 8.9990 chunk 11 optimal weight: 0.7980 chunk 108 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 73 optimal weight: 0.0020 chunk 106 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 70 HIS ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.106011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.080986 restraints weight = 20707.220| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.70 r_work: 0.3130 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10164 Z= 0.134 Angle : 0.532 10.034 13755 Z= 0.268 Chirality : 0.041 0.180 1476 Planarity : 0.003 0.037 1788 Dihedral : 4.195 25.955 1350 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.74 % Allowed : 10.80 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.95 (0.25), residues: 1233 helix: 1.74 (0.25), residues: 430 sheet: -0.53 (0.31), residues: 270 loop : 0.53 (0.28), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 201 TYR 0.009 0.001 TYR A 417 PHE 0.007 0.001 PHE C 263 TRP 0.025 0.001 TRP C 287 HIS 0.002 0.001 HIS A 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (10143) covalent geometry : angle 0.52327 / 0.26 (13713) SS BOND : bond 0.00534 / 0.30 ( 21) SS BOND : angle 1.79516 / 1.24 ( 42) hydrogen bonds : bond 0.03459 / 2.42 ( 479) hydrogen bonds : angle 5.47323 / 3.95 ( 1326) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8538 (mm-30) cc_final: 0.8153 (mm-30) REVERT: A 418 GLU cc_start: 0.7911 (pt0) cc_final: 0.7527 (pm20) REVERT: B 64 ARG cc_start: 0.8322 (mmp-170) cc_final: 0.7870 (mmt-90) REVERT: B 66 GLN cc_start: 0.9029 (tp40) cc_final: 0.8383 (tm-30) REVERT: B 68 TYR cc_start: 0.9275 (t80) cc_final: 0.8949 (t80) REVERT: B 73 HIS cc_start: 0.9003 (p90) cc_final: 0.8610 (p-80) REVERT: B 210 MET cc_start: 0.8603 (mmt) cc_final: 0.8384 (mmt) REVERT: C 70 HIS cc_start: 0.9373 (m90) cc_final: 0.8932 (m90) REVERT: C 330 MET cc_start: 0.9150 (mtt) cc_final: 0.8668 (mtt) REVERT: C 356 LYS cc_start: 0.9086 (OUTLIER) cc_final: 0.8695 (mtmm) outliers start: 8 outliers final: 3 residues processed: 75 average time/residue: 0.0867 time to fit residues: 9.4923 Evaluate side-chains 66 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 356 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 113 optimal weight: 0.0980 chunk 107 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 92 optimal weight: 0.0970 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 70 HIS ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 GLN B 128 GLN ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.104475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.078237 restraints weight = 20576.175| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.78 r_work: 0.3129 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10164 Z= 0.125 Angle : 0.550 12.583 13755 Z= 0.275 Chirality : 0.040 0.200 1476 Planarity : 0.003 0.031 1788 Dihedral : 4.181 28.016 1350 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.92 % Allowed : 11.27 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.96 (0.25), residues: 1233 helix: 1.80 (0.25), residues: 428 sheet: -0.53 (0.32), residues: 270 loop : 0.48 (0.28), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 201 TYR 0.009 0.001 TYR A 417 PHE 0.021 0.001 PHE C 442 TRP 0.026 0.001 TRP C 287 HIS 0.002 0.001 HIS B 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 (10143) covalent geometry : angle 0.53779 / 0.27 (13713) SS BOND : bond 0.00408 / 0.27 ( 21) SS BOND : angle 2.16338 / 1.73 ( 42) hydrogen bonds : bond 0.03284 / 2.29 ( 479) hydrogen bonds : angle 5.32737 / 3.84 ( 1326) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8139 (mm-30) REVERT: A 418 GLU cc_start: 0.7864 (pt0) cc_final: 0.7477 (pm20) REVERT: B 64 ARG cc_start: 0.8341 (mmp-170) cc_final: 0.7942 (mpt180) REVERT: B 66 GLN cc_start: 0.9011 (tp40) cc_final: 0.8340 (tm-30) REVERT: B 68 TYR cc_start: 0.9276 (t80) cc_final: 0.8936 (t80) REVERT: B 73 HIS cc_start: 0.8993 (p90) cc_final: 0.8578 (p-80) REVERT: C 70 HIS cc_start: 0.9357 (m90) cc_final: 0.8900 (m90) REVERT: C 330 MET cc_start: 0.9186 (OUTLIER) cc_final: 0.8745 (mtt) REVERT: C 356 LYS cc_start: 0.9092 (OUTLIER) cc_final: 0.8703 (mtmm) outliers start: 10 outliers final: 5 residues processed: 74 average time/residue: 0.0876 time to fit residues: 9.4098 Evaluate side-chains 70 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain C residue 356 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 26 optimal weight: 4.9990 chunk 73 optimal weight: 0.0070 chunk 63 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 80 optimal weight: 9.9990 chunk 30 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 94 optimal weight: 0.0870 chunk 102 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 0 optimal weight: 40.0000 overall best weight: 0.5576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 70 HIS ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.104923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.078784 restraints weight = 20630.186| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.80 r_work: 0.3142 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10164 Z= 0.117 Angle : 0.544 11.440 13755 Z= 0.272 Chirality : 0.040 0.159 1476 Planarity : 0.003 0.029 1788 Dihedral : 4.185 29.235 1350 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.92 % Allowed : 11.63 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.03 (0.25), residues: 1233 helix: 1.87 (0.25), residues: 428 sheet: -0.48 (0.31), residues: 268 loop : 0.51 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 201 TYR 0.010 0.001 TYR C 426 PHE 0.015 0.001 PHE C 442 TRP 0.024 0.001 TRP C 287 HIS 0.003 0.001 HIS B 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (10143) covalent geometry : angle 0.53233 / 0.27 (13713) SS BOND : bond 0.00405 / 0.26 ( 21) SS BOND : angle 2.07614 / 1.64 ( 42) hydrogen bonds : bond 0.03139 / 2.19 ( 479) hydrogen bonds : angle 5.26174 / 3.78 ( 1326) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8518 (mm-30) cc_final: 0.8140 (mm-30) REVERT: A 418 GLU cc_start: 0.7865 (pt0) cc_final: 0.7460 (pm20) REVERT: B 64 ARG cc_start: 0.8357 (mmp-170) cc_final: 0.7963 (mpt180) REVERT: B 66 GLN cc_start: 0.9012 (tp40) cc_final: 0.8343 (tm-30) REVERT: B 68 TYR cc_start: 0.9284 (t80) cc_final: 0.8955 (t80) REVERT: B 73 HIS cc_start: 0.9004 (p90) cc_final: 0.8599 (p-80) REVERT: C 70 HIS cc_start: 0.9328 (m90) cc_final: 0.8873 (m90) REVERT: C 330 MET cc_start: 0.9191 (OUTLIER) cc_final: 0.8687 (mtt) REVERT: C 356 LYS cc_start: 0.9096 (OUTLIER) cc_final: 0.8710 (mtmm) outliers start: 10 outliers final: 4 residues processed: 74 average time/residue: 0.0838 time to fit residues: 9.3092 Evaluate side-chains 71 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain C residue 356 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 34 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 98 optimal weight: 0.0170 chunk 86 optimal weight: 0.3980 chunk 14 optimal weight: 2.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 70 HIS ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.101215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.074171 restraints weight = 20604.730| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 2.86 r_work: 0.3001 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10164 Z= 0.113 Angle : 0.525 10.257 13755 Z= 0.263 Chirality : 0.039 0.150 1476 Planarity : 0.003 0.026 1788 Dihedral : 4.107 28.705 1350 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.55 % Allowed : 12.00 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.09 (0.25), residues: 1233 helix: 1.87 (0.26), residues: 430 sheet: -0.43 (0.31), residues: 268 loop : 0.56 (0.28), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 201 TYR 0.010 0.001 TYR C 426 PHE 0.009 0.001 PHE C 442 TRP 0.027 0.001 TRP C 287 HIS 0.002 0.001 HIS B 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (10143) covalent geometry : angle 0.51558 / 0.26 (13713) SS BOND : bond 0.00381 / 0.25 ( 21) SS BOND : angle 1.84799 / 1.45 ( 42) hydrogen bonds : bond 0.03041 / 2.13 ( 479) hydrogen bonds : angle 5.19299 / 3.73 ( 1326) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8600 (mm-30) cc_final: 0.8177 (mm-30) REVERT: A 418 GLU cc_start: 0.7852 (pt0) cc_final: 0.7364 (pm20) REVERT: B 64 ARG cc_start: 0.8385 (mmp-170) cc_final: 0.7988 (mpt180) REVERT: B 66 GLN cc_start: 0.9063 (tp40) cc_final: 0.8387 (tm-30) REVERT: B 68 TYR cc_start: 0.9273 (t80) cc_final: 0.8937 (t80) REVERT: B 73 HIS cc_start: 0.9047 (p90) cc_final: 0.8610 (p-80) REVERT: C 70 HIS cc_start: 0.9370 (m90) cc_final: 0.8880 (m90) REVERT: C 201 ARG cc_start: 0.8743 (mmm160) cc_final: 0.8384 (mtt180) REVERT: C 330 MET cc_start: 0.9275 (OUTLIER) cc_final: 0.8800 (mtt) REVERT: C 356 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8685 (mtmm) outliers start: 6 outliers final: 3 residues processed: 73 average time/residue: 0.1011 time to fit residues: 10.6115 Evaluate side-chains 68 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain C residue 356 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 39 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 70 HIS ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.099573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.072366 restraints weight = 20751.076| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.86 r_work: 0.2963 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10164 Z= 0.176 Angle : 0.565 11.654 13755 Z= 0.280 Chirality : 0.041 0.176 1476 Planarity : 0.003 0.027 1788 Dihedral : 4.206 27.986 1350 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.65 % Allowed : 12.56 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.03 (0.25), residues: 1233 helix: 1.94 (0.26), residues: 425 sheet: -0.49 (0.31), residues: 268 loop : 0.45 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 145 TYR 0.010 0.001 TYR C 342 PHE 0.013 0.001 PHE C 301 TRP 0.023 0.001 TRP C 287 HIS 0.002 0.001 HIS B 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 (10143) covalent geometry : angle 0.55495 / 0.28 (13713) SS BOND : bond 0.00495 / 0.34 ( 21) SS BOND : angle 1.96543 / 1.53 ( 42) hydrogen bonds : bond 0.03145 / 2.19 ( 479) hydrogen bonds : angle 5.18667 / 3.72 ( 1326) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.410 Fit side-chains revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8203 (mm-30) REVERT: A 314 CYS cc_start: 0.7911 (OUTLIER) cc_final: 0.7585 (t) REVERT: A 418 GLU cc_start: 0.7872 (pt0) cc_final: 0.7416 (pm20) REVERT: B 64 ARG cc_start: 0.8407 (mmp-170) cc_final: 0.8040 (mpt180) REVERT: B 66 GLN cc_start: 0.9062 (tp40) cc_final: 0.8399 (tm-30) REVERT: B 68 TYR cc_start: 0.9280 (t80) cc_final: 0.8936 (t80) REVERT: C 70 HIS cc_start: 0.9369 (m90) cc_final: 0.8875 (m90) REVERT: C 201 ARG cc_start: 0.8746 (mmm160) cc_final: 0.8407 (mtt180) REVERT: C 330 MET cc_start: 0.9279 (OUTLIER) cc_final: 0.8822 (mtt) REVERT: C 356 LYS cc_start: 0.9109 (OUTLIER) cc_final: 0.8730 (mtmm) outliers start: 7 outliers final: 3 residues processed: 69 average time/residue: 0.0959 time to fit residues: 9.7214 Evaluate side-chains 66 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain C residue 356 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 32 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 94 optimal weight: 0.8980 chunk 85 optimal weight: 0.6980 chunk 81 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 70 HIS ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.099960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.072902 restraints weight = 20592.828| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.81 r_work: 0.2973 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10164 Z= 0.148 Angle : 0.557 10.650 13755 Z= 0.276 Chirality : 0.040 0.174 1476 Planarity : 0.003 0.027 1788 Dihedral : 4.231 27.695 1350 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.55 % Allowed : 12.83 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.04 (0.25), residues: 1233 helix: 1.90 (0.25), residues: 427 sheet: -0.44 (0.31), residues: 268 loop : 0.47 (0.28), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 201 TYR 0.010 0.001 TYR C 342 PHE 0.014 0.001 PHE C 301 TRP 0.027 0.001 TRP C 287 HIS 0.002 0.001 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (10143) covalent geometry : angle 0.54620 / 0.27 (13713) SS BOND : bond 0.00431 / 0.29 ( 21) SS BOND : angle 2.07350 / 1.53 ( 42) hydrogen bonds : bond 0.03078 / 2.16 ( 479) hydrogen bonds : angle 5.19241 / 3.73 ( 1326) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8183 (mm-30) REVERT: A 314 CYS cc_start: 0.7873 (OUTLIER) cc_final: 0.7597 (t) REVERT: A 418 GLU cc_start: 0.7856 (pt0) cc_final: 0.7436 (pm20) REVERT: A 439 MET cc_start: 0.8673 (mpp) cc_final: 0.8236 (pmm) REVERT: B 64 ARG cc_start: 0.8414 (mmp-170) cc_final: 0.8040 (mpt180) REVERT: B 66 GLN cc_start: 0.9028 (tp40) cc_final: 0.8370 (tm-30) REVERT: B 68 TYR cc_start: 0.9269 (t80) cc_final: 0.8938 (t80) REVERT: C 70 HIS cc_start: 0.9360 (m90) cc_final: 0.8878 (m90) REVERT: C 201 ARG cc_start: 0.8687 (mmm160) cc_final: 0.8394 (mtt180) REVERT: C 330 MET cc_start: 0.9248 (OUTLIER) cc_final: 0.8824 (mtt) REVERT: C 356 LYS cc_start: 0.9107 (OUTLIER) cc_final: 0.8728 (mtmm) outliers start: 6 outliers final: 3 residues processed: 69 average time/residue: 0.0880 time to fit residues: 9.0849 Evaluate side-chains 65 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain C residue 356 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 47 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 73 optimal weight: 0.3980 chunk 51 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 70 HIS ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.100145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.073233 restraints weight = 20686.223| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.85 r_work: 0.2982 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10164 Z= 0.135 Angle : 0.546 10.656 13755 Z= 0.270 Chirality : 0.040 0.171 1476 Planarity : 0.003 0.026 1788 Dihedral : 4.176 27.292 1350 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.83 % Allowed : 12.65 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.05 (0.25), residues: 1233 helix: 1.93 (0.25), residues: 425 sheet: -0.42 (0.31), residues: 268 loop : 0.45 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 201 TYR 0.009 0.001 TYR A 417 PHE 0.015 0.001 PHE C 301 TRP 0.025 0.001 TRP C 287 HIS 0.006 0.001 HIS B 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (10143) covalent geometry : angle 0.53597 / 0.27 (13713) SS BOND : bond 0.00413 / 0.28 ( 21) SS BOND : angle 1.97607 / 1.45 ( 42) hydrogen bonds : bond 0.02993 / 2.10 ( 479) hydrogen bonds : angle 5.13370 / 3.69 ( 1326) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2077.39 seconds wall clock time: 36 minutes 22.28 seconds (2182.28 seconds total)