Starting phenix.real_space_refine on Mon Aug 25 08:51:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jme_36417/08_2025/8jme_36417_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jme_36417/08_2025/8jme_36417.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jme_36417/08_2025/8jme_36417_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jme_36417/08_2025/8jme_36417_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jme_36417/08_2025/8jme_36417.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jme_36417/08_2025/8jme_36417.map" } resolution = 2.5 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= 0.007 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: 5 Type Number sf(0) Gaussians S 96 5.16 5 C 8824 2.51 5 N 2212 2.21 5 O 2220 1.98 5 H 13812 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27164 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 6791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 6791 Classifications: {'peptide': 407} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 390} Restraints were copied for chains: B, C, D Time building chain proxies: 6.59, per 1000 atoms: 0.24 Number of scatterers: 27164 At special positions: 0 Unit cell: (116.25, 116.25, 100.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 96 16.00 O 2220 8.00 N 2212 7.00 C 8824 6.00 H 13812 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: 2.07 Conformation dependent library (CDL) restraints added in 696.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3136 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 0 sheets defined 79.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 58 through 73 Proline residue: A 65 - end of helix removed outlier: 3.773A pdb=" N VAL A 73 " --> pdb=" O LEU A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 89 Processing helix chain 'A' and resid 95 through 123 Processing helix chain 'A' and resid 125 through 164 removed outlier: 3.998A pdb=" N VAL A 130 " --> pdb=" O ALA A 126 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N GLY A 131 " --> pdb=" O LYS A 127 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU A 132 " --> pdb=" O ASN A 128 " (cutoff:3.500A) Proline residue: A 153 - end of helix Processing helix chain 'A' and resid 165 through 168 Processing helix chain 'A' and resid 177 through 214 Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 232 through 237 removed outlier: 3.561A pdb=" N PHE A 236 " --> pdb=" O TYR A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 287 removed outlier: 4.171A pdb=" N ASP A 264 " --> pdb=" O TRP A 260 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG A 277 " --> pdb=" O GLY A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 339 removed outlier: 3.571A pdb=" N PHE A 298 " --> pdb=" O CYS A 294 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N SER A 321 " --> pdb=" O SER A 317 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N LEU A 322 " --> pdb=" O ALA A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 387 removed outlier: 3.953A pdb=" N ILE A 375 " --> pdb=" O THR A 371 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ASN A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY A 382 " --> pdb=" O GLU A 378 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LEU A 383 " --> pdb=" O SER A 379 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY A 384 " --> pdb=" O LYS A 380 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N VAL A 385 " --> pdb=" O ARG A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 408 Processing helix chain 'A' and resid 421 through 448 removed outlier: 4.243A pdb=" N GLN A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N PHE A 442 " --> pdb=" O VAL A 438 " (cutoff:3.500A) Proline residue: A 445 - end of helix Processing helix chain 'B' and resid 58 through 73 Proline residue: B 65 - end of helix removed outlier: 3.773A pdb=" N VAL B 73 " --> pdb=" O LEU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 89 Processing helix chain 'B' and resid 95 through 123 Processing helix chain 'B' and resid 125 through 164 removed outlier: 3.998A pdb=" N VAL B 130 " --> pdb=" O ALA B 126 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N GLY B 131 " --> pdb=" O LYS B 127 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU B 132 " --> pdb=" O ASN B 128 " (cutoff:3.500A) Proline residue: B 153 - end of helix Processing helix chain 'B' and resid 165 through 168 Processing helix chain 'B' and resid 177 through 214 Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'B' and resid 232 through 237 removed outlier: 3.561A pdb=" N PHE B 236 " --> pdb=" O TYR B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 287 removed outlier: 4.171A pdb=" N ASP B 264 " --> pdb=" O TRP B 260 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG B 277 " --> pdb=" O GLY B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 339 removed outlier: 3.571A pdb=" N PHE B 298 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N SER B 321 " --> pdb=" O SER B 317 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N LEU B 322 " --> pdb=" O ALA B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 387 removed outlier: 3.953A pdb=" N ILE B 375 " --> pdb=" O THR B 371 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ASN B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY B 382 " --> pdb=" O GLU B 378 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LEU B 383 " --> pdb=" O SER B 379 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY B 384 " --> pdb=" O LYS B 380 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N VAL B 385 " --> pdb=" O ARG B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 408 Processing helix chain 'B' and resid 421 through 448 removed outlier: 4.243A pdb=" N GLN B 441 " --> pdb=" O LEU B 437 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N PHE B 442 " --> pdb=" O VAL B 438 " (cutoff:3.500A) Proline residue: B 445 - end of helix Processing helix chain 'C' and resid 58 through 73 Proline residue: C 65 - end of helix removed outlier: 3.773A pdb=" N VAL C 73 " --> pdb=" O LEU C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 89 Processing helix chain 'C' and resid 95 through 123 Processing helix chain 'C' and resid 125 through 164 removed outlier: 3.997A pdb=" N VAL C 130 " --> pdb=" O ALA C 126 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N GLY C 131 " --> pdb=" O LYS C 127 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU C 132 " --> pdb=" O ASN C 128 " (cutoff:3.500A) Proline residue: C 153 - end of helix Processing helix chain 'C' and resid 165 through 168 Processing helix chain 'C' and resid 177 through 214 Processing helix chain 'C' and resid 223 through 232 Processing helix chain 'C' and resid 232 through 237 removed outlier: 3.561A pdb=" N PHE C 236 " --> pdb=" O TYR C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 287 removed outlier: 4.171A pdb=" N ASP C 264 " --> pdb=" O TRP C 260 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG C 277 " --> pdb=" O GLY C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 339 removed outlier: 3.571A pdb=" N PHE C 298 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N SER C 321 " --> pdb=" O SER C 317 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N LEU C 322 " --> pdb=" O ALA C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 387 removed outlier: 3.954A pdb=" N ILE C 375 " --> pdb=" O THR C 371 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ASN C 376 " --> pdb=" O ALA C 372 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY C 382 " --> pdb=" O GLU C 378 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LEU C 383 " --> pdb=" O SER C 379 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLY C 384 " --> pdb=" O LYS C 380 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N VAL C 385 " --> pdb=" O ARG C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 408 Processing helix chain 'C' and resid 421 through 448 removed outlier: 4.242A pdb=" N GLN C 441 " --> pdb=" O LEU C 437 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N PHE C 442 " --> pdb=" O VAL C 438 " (cutoff:3.500A) Proline residue: C 445 - end of helix Processing helix chain 'D' and resid 58 through 73 Proline residue: D 65 - end of helix removed outlier: 3.772A pdb=" N VAL D 73 " --> pdb=" O LEU D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 89 Processing helix chain 'D' and resid 95 through 123 Processing helix chain 'D' and resid 125 through 164 removed outlier: 3.997A pdb=" N VAL D 130 " --> pdb=" O ALA D 126 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N GLY D 131 " --> pdb=" O LYS D 127 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU D 132 " --> pdb=" O ASN D 128 " (cutoff:3.500A) Proline residue: D 153 - end of helix Processing helix chain 'D' and resid 165 through 168 Processing helix chain 'D' and resid 177 through 214 Processing helix chain 'D' and resid 223 through 232 Processing helix chain 'D' and resid 232 through 237 removed outlier: 3.561A pdb=" N PHE D 236 " --> pdb=" O TYR D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 287 removed outlier: 4.172A pdb=" N ASP D 264 " --> pdb=" O TRP D 260 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG D 277 " --> pdb=" O GLY D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 339 removed outlier: 3.571A pdb=" N PHE D 298 " --> pdb=" O CYS D 294 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N SER D 321 " --> pdb=" O SER D 317 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N LEU D 322 " --> pdb=" O ALA D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 387 removed outlier: 3.953A pdb=" N ILE D 375 " --> pdb=" O THR D 371 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ASN D 376 " --> pdb=" O ALA D 372 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY D 382 " --> pdb=" O GLU D 378 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LEU D 383 " --> pdb=" O SER D 379 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY D 384 " --> pdb=" O LYS D 380 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N VAL D 385 " --> pdb=" O ARG D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 408 Processing helix chain 'D' and resid 421 through 448 removed outlier: 4.242A pdb=" N GLN D 441 " --> pdb=" O LEU D 437 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE D 442 " --> pdb=" O VAL D 438 " (cutoff:3.500A) Proline residue: D 445 - end of helix 984 hydrogen bonds defined for protein. 2916 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: 5.32 Time building geometry restraints manager: 2.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 13772 1.03 - 1.23: 40 1.23 - 1.42: 5775 1.42 - 1.62: 7761 1.62 - 1.81: 152 Bond restraints: 27500 Sorted by residual: bond pdb=" C VAL B 438 " pdb=" N LEU B 439 " ideal model delta sigma weight residual 1.333 1.424 -0.091 1.50e-02 4.44e+03 3.69e+01 bond pdb=" C VAL C 438 " pdb=" N LEU C 439 " ideal model delta sigma weight residual 1.333 1.411 -0.079 1.50e-02 4.44e+03 2.77e+01 bond pdb=" C LEU C 437 " pdb=" N VAL C 438 " ideal model delta sigma weight residual 1.335 1.396 -0.061 1.20e-02 6.94e+03 2.62e+01 bond pdb=" C LEU A 437 " pdb=" N VAL A 438 " ideal model delta sigma weight residual 1.334 1.390 -0.055 1.26e-02 6.30e+03 1.93e+01 bond pdb=" C LEU B 437 " pdb=" N VAL B 438 " ideal model delta sigma weight residual 1.335 1.383 -0.048 1.20e-02 6.94e+03 1.59e+01 ... (remaining 27495 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.07: 46509 1.07 - 2.14: 2948 2.14 - 3.20: 159 3.20 - 4.27: 60 4.27 - 5.34: 20 Bond angle restraints: 49696 Sorted by residual: angle pdb=" O VAL C 438 " pdb=" C VAL C 438 " pdb=" N LEU C 439 " ideal model delta sigma weight residual 121.80 116.46 5.34 1.13e+00 7.83e-01 2.23e+01 angle pdb=" CA VAL C 438 " pdb=" C VAL C 438 " pdb=" N LEU C 439 " ideal model delta sigma weight residual 117.69 122.59 -4.90 1.27e+00 6.20e-01 1.49e+01 angle pdb=" O VAL B 438 " pdb=" C VAL B 438 " pdb=" N LEU B 439 " ideal model delta sigma weight residual 121.80 117.57 4.23 1.13e+00 7.83e-01 1.40e+01 angle pdb=" CA VAL B 438 " pdb=" C VAL B 438 " pdb=" N LEU B 439 " ideal model delta sigma weight residual 117.69 121.49 -3.80 1.27e+00 6.20e-01 8.94e+00 angle pdb=" O LEU C 437 " pdb=" C LEU C 437 " pdb=" N VAL C 438 " ideal model delta sigma weight residual 122.07 124.81 -2.74 1.03e+00 9.43e-01 7.07e+00 ... (remaining 49691 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 11433 17.34 - 34.68: 1055 34.68 - 52.02: 332 52.02 - 69.36: 76 69.36 - 86.69: 20 Dihedral angle restraints: 12916 sinusoidal: 6912 harmonic: 6004 Sorted by residual: dihedral pdb=" CB GLU C 83 " pdb=" CG GLU C 83 " pdb=" CD GLU C 83 " pdb=" OE1 GLU C 83 " ideal model delta sinusoidal sigma weight residual 0.00 -83.94 83.94 1 3.00e+01 1.11e-03 9.54e+00 dihedral pdb=" CB GLU D 83 " pdb=" CG GLU D 83 " pdb=" CD GLU D 83 " pdb=" OE1 GLU D 83 " ideal model delta sinusoidal sigma weight residual 0.00 -83.92 83.92 1 3.00e+01 1.11e-03 9.54e+00 dihedral pdb=" CB GLU A 83 " pdb=" CG GLU A 83 " pdb=" CD GLU A 83 " pdb=" OE1 GLU A 83 " ideal model delta sinusoidal sigma weight residual 0.00 -83.89 83.89 1 3.00e+01 1.11e-03 9.53e+00 ... (remaining 12913 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1480 0.026 - 0.052: 355 0.052 - 0.078: 189 0.078 - 0.104: 95 0.104 - 0.130: 21 Chirality restraints: 2140 Sorted by residual: chirality pdb=" CA ILE C 173 " pdb=" N ILE C 173 " pdb=" C ILE C 173 " pdb=" CB ILE C 173 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.21e-01 chirality pdb=" CA ILE D 173 " pdb=" N ILE D 173 " pdb=" C ILE D 173 " pdb=" CB ILE D 173 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.21e-01 chirality pdb=" CA ILE B 173 " pdb=" N ILE B 173 " pdb=" C ILE B 173 " pdb=" CB ILE B 173 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.19e-01 ... (remaining 2137 not shown) Planarity restraints: 3836 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 346 " 0.154 9.50e-02 1.11e+02 5.15e-02 3.29e+00 pdb=" NE ARG B 346 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG B 346 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG B 346 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG B 346 " -0.000 2.00e-02 2.50e+03 pdb="HH11 ARG B 346 " -0.004 2.00e-02 2.50e+03 pdb="HH12 ARG B 346 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG B 346 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG B 346 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 346 " 0.153 9.50e-02 1.11e+02 5.14e-02 3.28e+00 pdb=" NE ARG D 346 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG D 346 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG D 346 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG D 346 " -0.000 2.00e-02 2.50e+03 pdb="HH11 ARG D 346 " -0.004 2.00e-02 2.50e+03 pdb="HH12 ARG D 346 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG D 346 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG D 346 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 346 " 0.154 9.50e-02 1.11e+02 5.16e-02 3.27e+00 pdb=" NE ARG C 346 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG C 346 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG C 346 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG C 346 " -0.000 2.00e-02 2.50e+03 pdb="HH11 ARG C 346 " -0.004 2.00e-02 2.50e+03 pdb="HH12 ARG C 346 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG C 346 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG C 346 " 0.000 2.00e-02 2.50e+03 ... (remaining 3833 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.19: 1357 2.19 - 2.79: 55465 2.79 - 3.39: 81476 3.39 - 4.00: 103775 4.00 - 4.60: 161669 Nonbonded interactions: 403742 Sorted by model distance: nonbonded pdb=" OD2 ASP A 316 " pdb=" HG SER A 413 " model vdw 1.584 2.450 nonbonded pdb=" OD2 ASP D 316 " pdb=" HG SER D 413 " model vdw 1.584 2.450 nonbonded pdb=" OD2 ASP B 316 " pdb=" HG SER B 413 " model vdw 1.585 2.450 nonbonded pdb=" OD2 ASP C 316 " pdb=" HG SER C 413 " model vdw 1.585 2.450 nonbonded pdb="HE22 GLN C 441 " pdb=" OE1 GLN D 441 " model vdw 1.624 2.450 ... (remaining 403737 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 1.080 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: 0.130 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 24.740 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 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 0.091 13688 Z= 0.153 Angle : 0.504 5.341 18572 Z= 0.272 Chirality : 0.034 0.130 2140 Planarity : 0.005 0.068 2276 Dihedral : 16.254 86.694 4996 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.27 % Allowed : 14.95 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.95 (0.21), residues: 1620 helix: 2.65 (0.14), residues: 1184 sheet: None (None), residues: 0 loop : -0.04 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 346 TYR 0.009 0.001 TYR C 208 PHE 0.007 0.001 PHE A 417 TRP 0.009 0.001 TRP C 355 HIS 0.001 0.000 HIS C 118 Details of bonding type rmsd covalent geometry : bond 0.00261 (13688) covalent geometry : angle 0.50435 (18572) hydrogen bonds : bond 0.08352 ( 984) hydrogen bonds : angle 4.49025 ( 2916) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 216 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 220 average time/residue: 1.5910 time to fit residues: 374.9548 Evaluate side-chains 211 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 207 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain D residue 75 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.145273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.113393 restraints weight = 34133.911| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.29 r_work: 0.3053 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.0681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13688 Z= 0.130 Angle : 0.487 5.220 18572 Z= 0.254 Chirality : 0.035 0.131 2140 Planarity : 0.005 0.060 2276 Dihedral : 3.827 27.236 1832 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.82 % Allowed : 12.77 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.14 (0.21), residues: 1620 helix: 2.85 (0.14), residues: 1188 sheet: None (None), residues: 0 loop : -0.19 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 423 TYR 0.011 0.001 TYR C 208 PHE 0.010 0.001 PHE C 66 TRP 0.010 0.001 TRP B 355 HIS 0.002 0.001 HIS B 118 Details of bonding type rmsd covalent geometry : bond 0.00265 (13688) covalent geometry : angle 0.48663 (18572) hydrogen bonds : bond 0.04557 ( 984) hydrogen bonds : angle 3.91821 ( 2916) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 209 time to evaluate : 0.735 Fit side-chains revert: symmetry clash REVERT: A 441 GLN cc_start: 0.7408 (mt0) cc_final: 0.7197 (mt0) REVERT: B 392 ARG cc_start: 0.7471 (mpp80) cc_final: 0.6916 (mpp-170) REVERT: B 441 GLN cc_start: 0.7383 (mt0) cc_final: 0.7173 (mt0) REVERT: C 392 ARG cc_start: 0.7456 (mpp80) cc_final: 0.6913 (mpp-170) outliers start: 12 outliers final: 4 residues processed: 213 average time/residue: 1.6595 time to fit residues: 378.7354 Evaluate side-chains 207 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 203 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain D residue 172 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 101 optimal weight: 3.9990 chunk 83 optimal weight: 0.4980 chunk 127 optimal weight: 5.9990 chunk 158 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 GLN B 441 GLN C 441 GLN D 441 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.139088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.106361 restraints weight = 34364.277| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 1.30 r_work: 0.2980 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 13688 Z= 0.192 Angle : 0.529 5.225 18572 Z= 0.283 Chirality : 0.037 0.123 2140 Planarity : 0.007 0.117 2276 Dihedral : 3.870 15.189 1824 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.15 % Allowed : 13.04 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.88 (0.20), residues: 1620 helix: 2.65 (0.14), residues: 1192 sheet: None (None), residues: 0 loop : -0.28 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 346 TYR 0.015 0.002 TYR D 353 PHE 0.017 0.002 PHE C 419 TRP 0.013 0.002 TRP B 355 HIS 0.003 0.001 HIS B 197 Details of bonding type rmsd covalent geometry : bond 0.00424 (13688) covalent geometry : angle 0.52861 (18572) hydrogen bonds : bond 0.05188 ( 984) hydrogen bonds : angle 3.99497 ( 2916) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 208 time to evaluate : 0.745 Fit side-chains REVERT: A 392 ARG cc_start: 0.7500 (mpp80) cc_final: 0.6981 (mpp-170) REVERT: A 415 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8495 (mttp) REVERT: B 415 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8487 (mttp) REVERT: C 415 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8359 (mttp) REVERT: D 392 ARG cc_start: 0.7495 (mpp80) cc_final: 0.6971 (mpp-170) REVERT: D 415 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8496 (mttp) outliers start: 17 outliers final: 5 residues processed: 217 average time/residue: 1.9045 time to fit residues: 441.4358 Evaluate side-chains 204 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 195 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 415 LYS Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 415 LYS Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 415 LYS Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 415 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 101 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 146 optimal weight: 2.9990 chunk 127 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.137550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.104778 restraints weight = 34470.052| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.28 r_work: 0.2953 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 13688 Z= 0.194 Angle : 0.525 5.324 18572 Z= 0.280 Chirality : 0.037 0.121 2140 Planarity : 0.006 0.093 2276 Dihedral : 3.926 16.813 1824 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.29 % Allowed : 13.32 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.65 (0.20), residues: 1620 helix: 2.51 (0.14), residues: 1192 sheet: None (None), residues: 0 loop : -0.45 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 61 TYR 0.016 0.002 TYR D 353 PHE 0.014 0.002 PHE B 66 TRP 0.012 0.002 TRP C 355 HIS 0.003 0.001 HIS B 197 Details of bonding type rmsd covalent geometry : bond 0.00421 (13688) covalent geometry : angle 0.52492 (18572) hydrogen bonds : bond 0.05083 ( 984) hydrogen bonds : angle 4.01468 ( 2916) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 204 time to evaluate : 0.759 Fit side-chains REVERT: A 415 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8428 (mttp) REVERT: B 196 GLU cc_start: 0.7880 (tt0) cc_final: 0.7575 (tm-30) REVERT: B 415 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8386 (mttp) REVERT: C 196 GLU cc_start: 0.7879 (tt0) cc_final: 0.7574 (tm-30) REVERT: C 415 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8391 (mttp) REVERT: D 196 GLU cc_start: 0.7884 (tt0) cc_final: 0.7581 (tm-30) REVERT: D 415 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8418 (mttp) outliers start: 19 outliers final: 12 residues processed: 217 average time/residue: 1.7043 time to fit residues: 396.2767 Evaluate side-chains 206 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 190 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 415 LYS Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 415 LYS Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 415 LYS Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 415 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 62 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 116 optimal weight: 4.9990 chunk 156 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 GLN B 441 GLN C 441 GLN D 441 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.136448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.103752 restraints weight = 34380.846| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.28 r_work: 0.2929 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 13688 Z= 0.244 Angle : 0.564 5.136 18572 Z= 0.305 Chirality : 0.039 0.118 2140 Planarity : 0.007 0.096 2276 Dihedral : 4.141 18.230 1824 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.70 % Allowed : 13.25 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.35 (0.20), residues: 1620 helix: 2.27 (0.14), residues: 1192 sheet: None (None), residues: 0 loop : -0.51 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 346 TYR 0.017 0.002 TYR C 353 PHE 0.018 0.002 PHE D 419 TRP 0.014 0.002 TRP B 355 HIS 0.003 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00549 (13688) covalent geometry : angle 0.56389 (18572) hydrogen bonds : bond 0.05428 ( 984) hydrogen bonds : angle 4.11111 ( 2916) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 191 time to evaluate : 0.580 Fit side-chains REVERT: A 415 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8497 (mttp) REVERT: B 415 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.8596 (mttp) REVERT: C 415 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8600 (mttp) REVERT: D 415 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8598 (mttp) outliers start: 25 outliers final: 21 residues processed: 211 average time/residue: 1.6762 time to fit residues: 379.0781 Evaluate side-chains 211 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 186 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 415 LYS Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 415 LYS Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 415 LYS Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 329 ASN Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 415 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 chunk 122 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 441 GLN C 441 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.139727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.107694 restraints weight = 34054.945| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 1.26 r_work: 0.2955 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 13688 Z= 0.163 Angle : 0.513 5.449 18572 Z= 0.273 Chirality : 0.036 0.123 2140 Planarity : 0.006 0.097 2276 Dihedral : 3.995 17.082 1824 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.43 % Allowed : 13.52 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.58 (0.20), residues: 1620 helix: 2.45 (0.14), residues: 1192 sheet: None (None), residues: 0 loop : -0.47 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 346 TYR 0.015 0.002 TYR D 353 PHE 0.013 0.002 PHE D 66 TRP 0.012 0.002 TRP D 355 HIS 0.002 0.001 HIS B 197 Details of bonding type rmsd covalent geometry : bond 0.00348 (13688) covalent geometry : angle 0.51341 (18572) hydrogen bonds : bond 0.04913 ( 984) hydrogen bonds : angle 4.01865 ( 2916) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 205 time to evaluate : 0.730 Fit side-chains REVERT: A 94 LYS cc_start: 0.6837 (OUTLIER) cc_final: 0.5815 (tmtt) REVERT: A 295 GLU cc_start: 0.7511 (tt0) cc_final: 0.7175 (tt0) REVERT: A 415 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8449 (mttp) REVERT: B 415 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8407 (mttp) REVERT: C 295 GLU cc_start: 0.7526 (tt0) cc_final: 0.7186 (tt0) REVERT: C 415 LYS cc_start: 0.8814 (OUTLIER) cc_final: 0.8412 (mttp) REVERT: D 295 GLU cc_start: 0.7532 (tt0) cc_final: 0.7188 (tt0) REVERT: D 415 LYS cc_start: 0.8814 (OUTLIER) cc_final: 0.8410 (mttp) outliers start: 21 outliers final: 16 residues processed: 222 average time/residue: 1.7824 time to fit residues: 424.0126 Evaluate side-chains 217 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 196 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 415 LYS Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 415 LYS Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 415 LYS Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 329 ASN Chi-restraints excluded: chain D residue 415 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 15 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 42 optimal weight: 0.3980 chunk 98 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 96 optimal weight: 0.0870 chunk 148 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 92 optimal weight: 0.0870 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.140594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.107622 restraints weight = 36139.356| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 1.37 r_work: 0.2945 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 13688 Z= 0.110 Angle : 0.471 5.761 18572 Z= 0.248 Chirality : 0.035 0.134 2140 Planarity : 0.006 0.116 2276 Dihedral : 3.769 16.048 1824 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.15 % Allowed : 13.59 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.99 (0.20), residues: 1620 helix: 2.77 (0.14), residues: 1192 sheet: None (None), residues: 0 loop : -0.38 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 346 TYR 0.010 0.001 TYR A 353 PHE 0.010 0.001 PHE B 66 TRP 0.010 0.001 TRP B 355 HIS 0.002 0.001 HIS C 118 Details of bonding type rmsd covalent geometry : bond 0.00212 (13688) covalent geometry : angle 0.47104 (18572) hydrogen bonds : bond 0.04367 ( 984) hydrogen bonds : angle 3.86757 ( 2916) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 207 time to evaluate : 0.776 Fit side-chains REVERT: A 258 PHE cc_start: 0.8460 (t80) cc_final: 0.8133 (t80) REVERT: A 295 GLU cc_start: 0.7495 (tt0) cc_final: 0.7134 (tt0) REVERT: B 94 LYS cc_start: 0.6821 (OUTLIER) cc_final: 0.5809 (tmtt) REVERT: B 258 PHE cc_start: 0.8456 (t80) cc_final: 0.8078 (t80) REVERT: B 295 GLU cc_start: 0.7489 (tt0) cc_final: 0.7124 (tt0) REVERT: C 258 PHE cc_start: 0.8465 (t80) cc_final: 0.8135 (t80) REVERT: D 94 LYS cc_start: 0.6808 (OUTLIER) cc_final: 0.5791 (tmtt) REVERT: D 258 PHE cc_start: 0.8450 (t80) cc_final: 0.8075 (t80) outliers start: 17 outliers final: 11 residues processed: 219 average time/residue: 1.9169 time to fit residues: 449.9756 Evaluate side-chains 212 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 199 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 329 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 30 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 47 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.137934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.105767 restraints weight = 33960.965| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 1.26 r_work: 0.2936 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 13688 Z= 0.241 Angle : 0.564 5.390 18572 Z= 0.303 Chirality : 0.039 0.120 2140 Planarity : 0.007 0.098 2276 Dihedral : 4.098 17.726 1824 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.56 % Allowed : 13.86 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.55 (0.20), residues: 1620 helix: 2.42 (0.14), residues: 1192 sheet: None (None), residues: 0 loop : -0.43 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 61 TYR 0.018 0.002 TYR D 353 PHE 0.018 0.002 PHE A 419 TRP 0.013 0.003 TRP D 355 HIS 0.003 0.001 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00544 (13688) covalent geometry : angle 0.56352 (18572) hydrogen bonds : bond 0.05339 ( 984) hydrogen bonds : angle 4.04578 ( 2916) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 209 time to evaluate : 0.719 Fit side-chains REVERT: A 258 PHE cc_start: 0.8507 (t80) cc_final: 0.8190 (t80) REVERT: A 295 GLU cc_start: 0.7572 (tt0) cc_final: 0.7207 (tt0) REVERT: A 344 LYS cc_start: 0.7402 (tppt) cc_final: 0.6347 (tmtt) REVERT: A 415 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8438 (mttp) REVERT: B 94 LYS cc_start: 0.6927 (OUTLIER) cc_final: 0.5891 (tmtt) REVERT: B 258 PHE cc_start: 0.8513 (t80) cc_final: 0.8197 (t80) REVERT: B 295 GLU cc_start: 0.7556 (tt0) cc_final: 0.7193 (tt0) REVERT: B 344 LYS cc_start: 0.7408 (tppt) cc_final: 0.6349 (tmtt) REVERT: B 415 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8428 (mttp) REVERT: C 94 LYS cc_start: 0.6944 (OUTLIER) cc_final: 0.5903 (tmtt) REVERT: C 258 PHE cc_start: 0.8503 (t80) cc_final: 0.8180 (t80) REVERT: C 295 GLU cc_start: 0.7559 (tt0) cc_final: 0.7201 (tt0) REVERT: C 344 LYS cc_start: 0.7393 (tppt) cc_final: 0.6323 (tmtt) REVERT: C 415 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8401 (mttp) REVERT: D 94 LYS cc_start: 0.6925 (OUTLIER) cc_final: 0.5886 (tmtt) REVERT: D 258 PHE cc_start: 0.8503 (t80) cc_final: 0.8185 (t80) REVERT: D 295 GLU cc_start: 0.7568 (tt0) cc_final: 0.7196 (tt0) REVERT: D 344 LYS cc_start: 0.7402 (tppt) cc_final: 0.6345 (tmtt) REVERT: D 415 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8398 (mttp) outliers start: 23 outliers final: 12 residues processed: 226 average time/residue: 1.9258 time to fit residues: 465.8401 Evaluate side-chains 224 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 205 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 415 LYS Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 415 LYS Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 94 LYS Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 415 LYS Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 329 ASN Chi-restraints excluded: chain D residue 415 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 7 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 136 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 137 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.137864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.104429 restraints weight = 36217.607| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.38 r_work: 0.2902 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 13688 Z= 0.149 Angle : 0.509 5.362 18572 Z= 0.269 Chirality : 0.036 0.127 2140 Planarity : 0.006 0.103 2276 Dihedral : 3.992 16.590 1824 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.36 % Allowed : 14.67 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.70 (0.20), residues: 1620 helix: 2.54 (0.14), residues: 1192 sheet: None (None), residues: 0 loop : -0.43 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 346 TYR 0.013 0.002 TYR D 353 PHE 0.012 0.001 PHE A 66 TRP 0.012 0.001 TRP C 355 HIS 0.002 0.001 HIS D 197 Details of bonding type rmsd covalent geometry : bond 0.00316 (13688) covalent geometry : angle 0.50851 (18572) hydrogen bonds : bond 0.04771 ( 984) hydrogen bonds : angle 3.96004 ( 2916) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 207 time to evaluate : 0.762 Fit side-chains REVERT: A 94 LYS cc_start: 0.6892 (OUTLIER) cc_final: 0.5858 (tmtt) REVERT: A 258 PHE cc_start: 0.8466 (t80) cc_final: 0.8151 (t80) REVERT: A 295 GLU cc_start: 0.7522 (tt0) cc_final: 0.7163 (tt0) REVERT: A 344 LYS cc_start: 0.7380 (tppt) cc_final: 0.6301 (tmtt) REVERT: B 94 LYS cc_start: 0.6887 (OUTLIER) cc_final: 0.5844 (tmtt) REVERT: B 258 PHE cc_start: 0.8465 (t80) cc_final: 0.8107 (t80) REVERT: B 295 GLU cc_start: 0.7519 (tt0) cc_final: 0.7155 (tt0) REVERT: C 94 LYS cc_start: 0.6897 (OUTLIER) cc_final: 0.5848 (tmtt) REVERT: C 258 PHE cc_start: 0.8462 (t80) cc_final: 0.8145 (t80) REVERT: C 295 GLU cc_start: 0.7519 (tt0) cc_final: 0.7148 (tt0) REVERT: D 94 LYS cc_start: 0.6894 (OUTLIER) cc_final: 0.5850 (tmtt) REVERT: D 258 PHE cc_start: 0.8456 (t80) cc_final: 0.8096 (t80) REVERT: D 295 GLU cc_start: 0.7513 (tt0) cc_final: 0.7150 (tt0) outliers start: 20 outliers final: 12 residues processed: 219 average time/residue: 1.9597 time to fit residues: 459.5993 Evaluate side-chains 214 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 198 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 94 LYS Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 329 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 33 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 78 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.139799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.106657 restraints weight = 36249.603| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 1.37 r_work: 0.2933 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 13688 Z= 0.120 Angle : 0.488 5.337 18572 Z= 0.257 Chirality : 0.035 0.131 2140 Planarity : 0.006 0.103 2276 Dihedral : 3.846 15.152 1824 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.09 % Allowed : 14.74 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.93 (0.20), residues: 1620 helix: 2.72 (0.14), residues: 1192 sheet: None (None), residues: 0 loop : -0.38 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 61 TYR 0.011 0.001 TYR D 353 PHE 0.011 0.001 PHE D 66 TRP 0.011 0.001 TRP B 355 HIS 0.002 0.001 HIS C 118 Details of bonding type rmsd covalent geometry : bond 0.00243 (13688) covalent geometry : angle 0.48831 (18572) hydrogen bonds : bond 0.04496 ( 984) hydrogen bonds : angle 3.87625 ( 2916) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 203 time to evaluate : 0.903 Fit side-chains REVERT: A 94 LYS cc_start: 0.6859 (OUTLIER) cc_final: 0.5838 (tmtt) REVERT: A 258 PHE cc_start: 0.8484 (t80) cc_final: 0.8134 (t80) REVERT: A 344 LYS cc_start: 0.7406 (tppt) cc_final: 0.6334 (tmtt) REVERT: B 94 LYS cc_start: 0.6865 (OUTLIER) cc_final: 0.5839 (tmtt) REVERT: B 258 PHE cc_start: 0.8487 (t80) cc_final: 0.8138 (t80) REVERT: B 295 GLU cc_start: 0.7499 (tt0) cc_final: 0.7132 (tt0) REVERT: C 94 LYS cc_start: 0.6872 (OUTLIER) cc_final: 0.5849 (tmtt) REVERT: C 258 PHE cc_start: 0.8486 (t80) cc_final: 0.8133 (t80) REVERT: D 94 LYS cc_start: 0.6850 (OUTLIER) cc_final: 0.5819 (tmtt) REVERT: D 258 PHE cc_start: 0.8480 (t80) cc_final: 0.8131 (t80) REVERT: D 295 GLU cc_start: 0.7499 (tt0) cc_final: 0.7138 (tt0) outliers start: 16 outliers final: 12 residues processed: 211 average time/residue: 1.8796 time to fit residues: 425.3919 Evaluate side-chains 214 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 198 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 94 LYS Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 329 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 104 optimal weight: 4.9990 chunk 109 optimal weight: 0.3980 chunk 111 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 146 optimal weight: 0.6980 chunk 95 optimal weight: 4.9990 chunk 126 optimal weight: 0.9990 chunk 123 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 107 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.140418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.107508 restraints weight = 36051.214| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.36 r_work: 0.2966 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 13688 Z= 0.113 Angle : 0.476 5.385 18572 Z= 0.249 Chirality : 0.035 0.134 2140 Planarity : 0.006 0.099 2276 Dihedral : 3.767 14.355 1824 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.29 % Allowed : 14.20 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.06 (0.20), residues: 1620 helix: 2.82 (0.14), residues: 1188 sheet: None (None), residues: 0 loop : -0.31 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 346 TYR 0.010 0.001 TYR D 353 PHE 0.011 0.001 PHE C 66 TRP 0.011 0.001 TRP C 355 HIS 0.002 0.001 HIS D 118 Details of bonding type rmsd covalent geometry : bond 0.00227 (13688) covalent geometry : angle 0.47627 (18572) hydrogen bonds : bond 0.04386 ( 984) hydrogen bonds : angle 3.80864 ( 2916) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10388.15 seconds wall clock time: 176 minutes 17.74 seconds (10577.74 seconds total)