Starting phenix.real_space_refine on Sun May 25 10:06:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jme_36417/05_2025/8jme_36417_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jme_36417/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8jme_36417/05_2025/8jme_36417.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jme_36417/05_2025/8jme_36417.map" model { file = "/net/cci-nas-00/data/ceres_data/8jme_36417/05_2025/8jme_36417_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jme_36417/05_2025/8jme_36417_neut.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: C, B, D Time building chain proxies: 16.33, per 1000 atoms: 0.60 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: 6.42 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 1.67 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: 9.33 Time building geometry restraints manager: 7.77 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 1.120 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: 0.400 Extract box with map and model: 0.920 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 56.480 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.480 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.009 0.001 TRP C 355 HIS 0.001 0.000 HIS C 118 PHE 0.007 0.001 PHE A 417 TYR 0.009 0.001 TYR C 208 ARG 0.011 0.001 ARG D 346 Details of bonding type rmsd hydrogen bonds : bond 0.08352 ( 984) hydrogen bonds : angle 4.49025 ( 2916) covalent geometry : bond 0.00261 (13688) covalent geometry : angle 0.50435 (18572) *********************** 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 : 1.839 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: 3.5302 time to fit residues: 833.4636 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 : 2.126 ------------------------------------------------------------------------------- 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 135 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 125 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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 = 0.3560 r_free = 0.3560 target = 0.141827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.110210 restraints weight = 34108.104| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.26 r_work: 0.3018 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.0910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13688 Z= 0.168 Angle : 0.522 5.254 18572 Z= 0.275 Chirality : 0.037 0.125 2140 Planarity : 0.005 0.060 2276 Dihedral : 4.001 28.263 1832 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.82 % Allowed : 13.04 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.00 (0.20), residues: 1620 helix: 2.72 (0.14), residues: 1192 sheet: None (None), residues: 0 loop : -0.21 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 355 HIS 0.002 0.001 HIS B 197 PHE 0.013 0.002 PHE C 66 TYR 0.014 0.002 TYR C 353 ARG 0.005 0.001 ARG B 423 Details of bonding type rmsd hydrogen bonds : bond 0.04911 ( 984) hydrogen bonds : angle 3.97147 ( 2916) covalent geometry : bond 0.00362 (13688) covalent geometry : angle 0.52191 (18572) *********************** 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 224 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 212 time to evaluate : 2.096 Fit side-chains revert: symmetry clash REVERT: A 415 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8277 (mttp) REVERT: B 392 ARG cc_start: 0.7498 (mpp80) cc_final: 0.6934 (mpp-170) REVERT: B 415 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8288 (mttp) REVERT: C 392 ARG cc_start: 0.7494 (mpp80) cc_final: 0.6943 (mpp-170) REVERT: C 415 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8284 (mttp) REVERT: D 415 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8270 (mttp) outliers start: 12 outliers final: 4 residues processed: 216 average time/residue: 3.5413 time to fit residues: 820.9364 Evaluate side-chains 210 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 202 time to evaluate : 2.210 ------------------------------------------------------------------------------- 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 154 optimal weight: 0.9990 chunk 119 optimal weight: 6.9990 chunk 134 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 = 0.3500 r_free = 0.3500 target = 0.137091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.104707 restraints weight = 34376.529| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 1.27 r_work: 0.2955 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 13688 Z= 0.232 Angle : 0.559 5.217 18572 Z= 0.301 Chirality : 0.039 0.119 2140 Planarity : 0.007 0.111 2276 Dihedral : 4.059 16.627 1824 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.43 % Allowed : 12.70 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.60 (0.20), residues: 1620 helix: 2.44 (0.14), residues: 1192 sheet: None (None), residues: 0 loop : -0.36 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 355 HIS 0.003 0.001 HIS A 197 PHE 0.017 0.002 PHE D 419 TYR 0.016 0.002 TYR A 353 ARG 0.009 0.001 ARG B 61 Details of bonding type rmsd hydrogen bonds : bond 0.05449 ( 984) hydrogen bonds : angle 4.08744 ( 2916) covalent geometry : bond 0.00517 (13688) covalent geometry : angle 0.55948 (18572) *********************** 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 220 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 199 time to evaluate : 2.053 Fit side-chains REVERT: A 295 GLU cc_start: 0.7589 (tt0) cc_final: 0.7208 (tt0) REVERT: A 415 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8441 (mttp) REVERT: A 423 ARG cc_start: 0.8265 (mmm160) cc_final: 0.8021 (mmm160) REVERT: B 295 GLU cc_start: 0.7565 (tt0) cc_final: 0.7188 (tt0) REVERT: B 415 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8449 (mttp) REVERT: B 423 ARG cc_start: 0.8269 (mmm160) cc_final: 0.8023 (mmm160) REVERT: C 295 GLU cc_start: 0.7571 (tt0) cc_final: 0.7189 (tt0) REVERT: C 415 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8468 (mttp) REVERT: C 423 ARG cc_start: 0.8264 (mmm160) cc_final: 0.8019 (mmm160) REVERT: D 295 GLU cc_start: 0.7574 (tt0) cc_final: 0.7199 (tt0) REVERT: D 415 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8443 (mttp) REVERT: D 423 ARG cc_start: 0.8273 (mmm160) cc_final: 0.8032 (mmm160) outliers start: 21 outliers final: 9 residues processed: 212 average time/residue: 3.7518 time to fit residues: 852.4271 Evaluate side-chains 203 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 190 time to evaluate : 2.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE 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 172 GLU Chi-restraints excluded: chain C residue 415 LYS Chi-restraints excluded: chain D residue 75 ILE 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 142 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 140 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 80 optimal weight: 8.9990 chunk 151 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 155 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 121 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.140273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.107817 restraints weight = 34225.726| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.28 r_work: 0.2967 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 13688 Z= 0.167 Angle : 0.516 5.257 18572 Z= 0.274 Chirality : 0.037 0.124 2140 Planarity : 0.006 0.090 2276 Dihedral : 3.933 16.056 1824 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.77 % Allowed : 12.23 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.62 (0.20), residues: 1620 helix: 2.48 (0.14), residues: 1192 sheet: None (None), residues: 0 loop : -0.48 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 355 HIS 0.002 0.001 HIS A 197 PHE 0.014 0.002 PHE A 66 TYR 0.015 0.002 TYR C 353 ARG 0.008 0.001 ARG D 346 Details of bonding type rmsd hydrogen bonds : bond 0.04934 ( 984) hydrogen bonds : angle 4.00625 ( 2916) covalent geometry : bond 0.00356 (13688) covalent geometry : angle 0.51615 (18572) *********************** 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 226 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 200 time to evaluate : 2.134 Fit side-chains REVERT: A 196 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7539 (tm-30) REVERT: A 295 GLU cc_start: 0.7582 (tt0) cc_final: 0.7204 (tt0) REVERT: A 415 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8429 (mttp) REVERT: B 196 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7551 (tm-30) REVERT: B 295 GLU cc_start: 0.7565 (tt0) cc_final: 0.7191 (tt0) REVERT: B 415 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8423 (mttp) REVERT: C 196 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7542 (tm-30) REVERT: C 295 GLU cc_start: 0.7568 (tt0) cc_final: 0.7196 (tt0) REVERT: C 415 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8427 (mttp) REVERT: D 196 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7550 (tm-30) REVERT: D 295 GLU cc_start: 0.7570 (tt0) cc_final: 0.7197 (tt0) REVERT: D 415 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8417 (mttp) outliers start: 26 outliers final: 6 residues processed: 213 average time/residue: 3.5752 time to fit residues: 817.8799 Evaluate side-chains 207 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 193 time to evaluate : 1.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 196 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 196 GLU Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 415 LYS Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 415 LYS Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 196 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 109 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 133 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 120 optimal weight: 8.9990 chunk 12 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 = 0.3486 r_free = 0.3486 target = 0.135801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.103381 restraints weight = 34335.854| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 1.27 r_work: 0.2930 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 13688 Z= 0.279 Angle : 0.590 5.135 18572 Z= 0.319 Chirality : 0.041 0.123 2140 Planarity : 0.006 0.091 2276 Dihedral : 4.227 17.864 1824 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.11 % Allowed : 12.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.19), residues: 1620 helix: 2.05 (0.14), residues: 1208 sheet: None (None), residues: 0 loop : -0.78 (0.26), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP C 355 HIS 0.004 0.001 HIS D 197 PHE 0.021 0.002 PHE D 419 TYR 0.017 0.002 TYR D 353 ARG 0.009 0.001 ARG C 346 Details of bonding type rmsd hydrogen bonds : bond 0.05656 ( 984) hydrogen bonds : angle 4.16331 ( 2916) covalent geometry : bond 0.00633 (13688) covalent geometry : angle 0.59038 (18572) *********************** 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 228 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 197 time to evaluate : 1.992 Fit side-chains REVERT: A 196 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7488 (tm-30) REVERT: A 295 GLU cc_start: 0.7585 (tt0) cc_final: 0.7187 (tt0) REVERT: A 415 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8491 (mttp) REVERT: B 196 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7490 (tm-30) REVERT: B 295 GLU cc_start: 0.7575 (tt0) cc_final: 0.7206 (tt0) REVERT: B 415 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8490 (mttp) REVERT: C 196 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7487 (tm-30) REVERT: C 295 GLU cc_start: 0.7560 (tt0) cc_final: 0.7205 (tt0) REVERT: C 415 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8491 (mttp) REVERT: D 196 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7487 (tm-30) REVERT: D 295 GLU cc_start: 0.7584 (tt0) cc_final: 0.7185 (tt0) REVERT: D 415 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8490 (mttp) outliers start: 31 outliers final: 13 residues processed: 218 average time/residue: 3.4901 time to fit residues: 818.7715 Evaluate side-chains 213 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 192 time to evaluate : 2.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 196 GLU 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 196 GLU 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 172 GLU Chi-restraints excluded: chain C residue 196 GLU 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 172 GLU Chi-restraints excluded: chain D residue 196 GLU 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 147 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 7 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 329 ASN D 329 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.138686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.106125 restraints weight = 34276.679| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.29 r_work: 0.2963 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 13688 Z= 0.144 Angle : 0.509 5.320 18572 Z= 0.270 Chirality : 0.036 0.126 2140 Planarity : 0.006 0.095 2276 Dihedral : 3.998 16.675 1824 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.49 % Allowed : 13.32 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.20), residues: 1620 helix: 2.44 (0.14), residues: 1192 sheet: None (None), residues: 0 loop : -0.51 (0.27), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 355 HIS 0.002 0.001 HIS A 197 PHE 0.012 0.001 PHE A 66 TYR 0.013 0.002 TYR D 353 ARG 0.009 0.000 ARG A 346 Details of bonding type rmsd hydrogen bonds : bond 0.04816 ( 984) hydrogen bonds : angle 4.00601 ( 2916) covalent geometry : bond 0.00299 (13688) covalent geometry : angle 0.50940 (18572) *********************** 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 229 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 207 time to evaluate : 2.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 LYS cc_start: 0.6871 (OUTLIER) cc_final: 0.5846 (tmtt) REVERT: A 295 GLU cc_start: 0.7533 (tt0) cc_final: 0.7171 (tt0) REVERT: A 415 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8445 (mttp) REVERT: B 94 LYS cc_start: 0.6873 (OUTLIER) cc_final: 0.5849 (tmtt) REVERT: B 295 GLU cc_start: 0.7522 (tt0) cc_final: 0.7158 (tt0) REVERT: B 415 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8496 (mttp) REVERT: C 94 LYS cc_start: 0.6859 (OUTLIER) cc_final: 0.5840 (tmtt) REVERT: C 196 GLU cc_start: 0.7844 (tt0) cc_final: 0.7562 (tm-30) REVERT: C 415 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8445 (mttp) REVERT: D 94 LYS cc_start: 0.6878 (OUTLIER) cc_final: 0.5850 (tmtt) REVERT: D 295 GLU cc_start: 0.7533 (tt0) cc_final: 0.7172 (tt0) REVERT: D 415 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8439 (mttp) outliers start: 22 outliers final: 10 residues processed: 224 average time/residue: 3.4785 time to fit residues: 836.0101 Evaluate side-chains 216 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 198 time to evaluate : 1.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE 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 94 LYS 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 94 LYS 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 94 LYS Chi-restraints excluded: chain D residue 172 GLU 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 97 optimal weight: 7.9990 chunk 94 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 137 optimal weight: 8.9990 chunk 40 optimal weight: 8.9990 chunk 156 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 = 0.3474 r_free = 0.3474 target = 0.135348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.101808 restraints weight = 36187.132| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 1.37 r_work: 0.2866 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 13688 Z= 0.251 Angle : 0.579 5.376 18572 Z= 0.311 Chirality : 0.040 0.122 2140 Planarity : 0.006 0.096 2276 Dihedral : 4.224 18.332 1824 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.97 % Allowed : 13.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.20), residues: 1620 helix: 2.27 (0.14), residues: 1188 sheet: None (None), residues: 0 loop : -0.50 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 355 HIS 0.004 0.001 HIS C 197 PHE 0.019 0.002 PHE D 419 TYR 0.017 0.002 TYR D 353 ARG 0.011 0.001 ARG D 346 Details of bonding type rmsd hydrogen bonds : bond 0.05453 ( 984) hydrogen bonds : angle 4.12964 ( 2916) covalent geometry : bond 0.00565 (13688) covalent geometry : angle 0.57876 (18572) *********************** 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 229 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 200 time to evaluate : 1.953 Fit side-chains REVERT: A 94 LYS cc_start: 0.6920 (OUTLIER) cc_final: 0.5863 (tmtt) REVERT: A 295 GLU cc_start: 0.7563 (tt0) cc_final: 0.7182 (tt0) REVERT: A 415 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8552 (mttp) REVERT: B 94 LYS cc_start: 0.6926 (OUTLIER) cc_final: 0.5869 (tmtt) REVERT: B 295 GLU cc_start: 0.7561 (tt0) cc_final: 0.7176 (tt0) REVERT: B 415 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8551 (mttp) REVERT: C 94 LYS cc_start: 0.6922 (OUTLIER) cc_final: 0.5857 (tmtt) REVERT: C 196 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7475 (tm-30) REVERT: C 295 GLU cc_start: 0.7569 (tt0) cc_final: 0.7181 (tt0) REVERT: C 415 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8557 (mttp) REVERT: D 94 LYS cc_start: 0.6926 (OUTLIER) cc_final: 0.5865 (tmtt) REVERT: D 295 GLU cc_start: 0.7564 (tt0) cc_final: 0.7175 (tt0) REVERT: D 415 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8553 (mttp) outliers start: 29 outliers final: 16 residues processed: 221 average time/residue: 3.5779 time to fit residues: 848.5957 Evaluate side-chains 220 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 195 time to evaluate : 1.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 196 GLU 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 94 LYS Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 196 GLU 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 94 LYS Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 196 GLU 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 94 LYS Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 415 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 58 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 137 optimal weight: 0.8980 chunk 140 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.136803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.103355 restraints weight = 36127.292| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 1.38 r_work: 0.2888 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 13688 Z= 0.165 Angle : 0.526 5.352 18572 Z= 0.279 Chirality : 0.037 0.124 2140 Planarity : 0.006 0.101 2276 Dihedral : 4.087 17.086 1824 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.29 % Allowed : 13.79 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.20), residues: 1620 helix: 2.43 (0.14), residues: 1192 sheet: None (None), residues: 0 loop : -0.46 (0.27), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 355 HIS 0.002 0.001 HIS A 197 PHE 0.013 0.002 PHE B 66 TYR 0.015 0.002 TYR C 353 ARG 0.012 0.001 ARG B 346 Details of bonding type rmsd hydrogen bonds : bond 0.04924 ( 984) hydrogen bonds : angle 4.03382 ( 2916) covalent geometry : bond 0.00355 (13688) covalent geometry : angle 0.52555 (18572) *********************** 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 230 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 211 time to evaluate : 1.906 Fit side-chains revert: symmetry clash REVERT: A 94 LYS cc_start: 0.6903 (OUTLIER) cc_final: 0.5843 (tmtt) REVERT: A 258 PHE cc_start: 0.8481 (t80) cc_final: 0.8153 (t80) REVERT: A 295 GLU cc_start: 0.7505 (tt0) cc_final: 0.7149 (tt0) REVERT: A 415 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8522 (mttp) REVERT: B 94 LYS cc_start: 0.6901 (OUTLIER) cc_final: 0.5846 (tmtt) REVERT: B 258 PHE cc_start: 0.8495 (t80) cc_final: 0.8164 (t80) REVERT: B 295 GLU cc_start: 0.7512 (tt0) cc_final: 0.7134 (tt0) REVERT: B 344 LYS cc_start: 0.7408 (tppt) cc_final: 0.6337 (tmtt) REVERT: B 415 LYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8524 (mttp) REVERT: C 94 LYS cc_start: 0.6906 (OUTLIER) cc_final: 0.5849 (tmtt) REVERT: C 258 PHE cc_start: 0.8491 (t80) cc_final: 0.8162 (t80) REVERT: C 295 GLU cc_start: 0.7511 (tt0) cc_final: 0.7130 (tt0) REVERT: C 415 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8526 (mttp) REVERT: D 94 LYS cc_start: 0.6907 (OUTLIER) cc_final: 0.5847 (tmtt) REVERT: D 258 PHE cc_start: 0.8488 (t80) cc_final: 0.8120 (t80) REVERT: D 295 GLU cc_start: 0.7518 (tt0) cc_final: 0.7153 (tt0) REVERT: D 415 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8525 (mttp) outliers start: 19 outliers final: 10 residues processed: 221 average time/residue: 3.5040 time to fit residues: 831.9623 Evaluate side-chains 221 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 203 time to evaluate : 2.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 94 LYS 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 94 LYS 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 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 75 ILE Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain D residue 172 GLU 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 10 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 17 optimal weight: 9.9990 chunk 130 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 128 optimal weight: 0.8980 chunk 52 optimal weight: 0.5980 chunk 149 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 150 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3519 r_free = 0.3519 target = 0.138867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.105722 restraints weight = 36209.099| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.36 r_work: 0.2923 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 13688 Z= 0.129 Angle : 0.496 5.440 18572 Z= 0.262 Chirality : 0.036 0.130 2140 Planarity : 0.006 0.105 2276 Dihedral : 3.947 15.867 1824 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.29 % Allowed : 14.13 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.81 (0.20), residues: 1620 helix: 2.62 (0.14), residues: 1192 sheet: None (None), residues: 0 loop : -0.39 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 355 HIS 0.002 0.001 HIS B 118 PHE 0.011 0.001 PHE B 66 TYR 0.012 0.001 TYR A 353 ARG 0.014 0.001 ARG C 346 Details of bonding type rmsd hydrogen bonds : bond 0.04611 ( 984) hydrogen bonds : angle 3.92771 ( 2916) covalent geometry : bond 0.00265 (13688) covalent geometry : angle 0.49557 (18572) *********************** 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 230 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 211 time to evaluate : 1.931 Fit side-chains REVERT: A 94 LYS cc_start: 0.6867 (OUTLIER) cc_final: 0.5831 (tmtt) REVERT: A 258 PHE cc_start: 0.8465 (t80) cc_final: 0.8122 (t80) REVERT: A 295 GLU cc_start: 0.7537 (tt0) cc_final: 0.7175 (tt0) REVERT: B 94 LYS cc_start: 0.6874 (OUTLIER) cc_final: 0.5839 (tmtt) REVERT: B 258 PHE cc_start: 0.8464 (t80) cc_final: 0.8113 (t80) REVERT: C 94 LYS cc_start: 0.6884 (OUTLIER) cc_final: 0.5848 (tmtt) REVERT: C 258 PHE cc_start: 0.8484 (t80) cc_final: 0.8136 (t80) REVERT: D 94 LYS cc_start: 0.6910 (OUTLIER) cc_final: 0.5859 (tmtt) REVERT: D 258 PHE cc_start: 0.8468 (t80) cc_final: 0.8131 (t80) REVERT: D 295 GLU cc_start: 0.7528 (tt0) cc_final: 0.7165 (tt0) outliers start: 19 outliers final: 11 residues processed: 221 average time/residue: 3.5373 time to fit residues: 838.7143 Evaluate side-chains 216 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 201 time to evaluate : 1.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain B residue 75 ILE 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 C residue 75 ILE 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 75 ILE 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 2 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 150 optimal weight: 3.9990 chunk 138 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.139030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.105946 restraints weight = 36178.603| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 1.37 r_work: 0.2910 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 13688 Z= 0.140 Angle : 0.508 5.366 18572 Z= 0.267 Chirality : 0.036 0.128 2140 Planarity : 0.006 0.102 2276 Dihedral : 3.945 16.023 1824 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.29 % Allowed : 14.13 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.86 (0.20), residues: 1620 helix: 2.66 (0.14), residues: 1192 sheet: None (None), residues: 0 loop : -0.37 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 355 HIS 0.002 0.001 HIS A 197 PHE 0.012 0.001 PHE C 66 TYR 0.014 0.002 TYR C 353 ARG 0.011 0.001 ARG D 346 Details of bonding type rmsd hydrogen bonds : bond 0.04687 ( 984) hydrogen bonds : angle 3.91207 ( 2916) covalent geometry : bond 0.00294 (13688) covalent geometry : angle 0.50752 (18572) ********************** 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 227 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 208 time to evaluate : 2.130 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 LYS cc_start: 0.6900 (OUTLIER) cc_final: 0.5853 (tmtt) REVERT: A 258 PHE cc_start: 0.8464 (t80) cc_final: 0.8132 (t80) REVERT: A 295 GLU cc_start: 0.7520 (tt0) cc_final: 0.7154 (tt0) REVERT: A 344 LYS cc_start: 0.7403 (tppt) cc_final: 0.6339 (tmtt) REVERT: B 94 LYS cc_start: 0.6905 (OUTLIER) cc_final: 0.5869 (tmtt) REVERT: B 258 PHE cc_start: 0.8463 (t80) cc_final: 0.8122 (t80) REVERT: B 295 GLU cc_start: 0.7525 (tt0) cc_final: 0.7158 (tt0) REVERT: B 344 LYS cc_start: 0.7413 (tppt) cc_final: 0.6345 (tmtt) REVERT: C 94 LYS cc_start: 0.6914 (OUTLIER) cc_final: 0.5866 (tmtt) REVERT: C 258 PHE cc_start: 0.8470 (t80) cc_final: 0.8125 (t80) REVERT: C 295 GLU cc_start: 0.7530 (tt0) cc_final: 0.7155 (tt0) REVERT: D 94 LYS cc_start: 0.6900 (OUTLIER) cc_final: 0.5852 (tmtt) REVERT: D 258 PHE cc_start: 0.8467 (t80) cc_final: 0.8138 (t80) REVERT: D 295 GLU cc_start: 0.7533 (tt0) cc_final: 0.7165 (tt0) REVERT: D 344 LYS cc_start: 0.7397 (tppt) cc_final: 0.6325 (tmtt) outliers start: 19 outliers final: 14 residues processed: 217 average time/residue: 3.3959 time to fit residues: 792.8614 Evaluate side-chains 222 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 204 time to evaluate : 3.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain B residue 75 ILE 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 179 SER Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 94 LYS Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 179 SER 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 84 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 138 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 133 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 85 optimal weight: 0.7980 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.3524 r_free = 0.3524 target = 0.139069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.106088 restraints weight = 35999.104| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.35 r_work: 0.2914 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 13688 Z= 0.141 Angle : 0.507 5.366 18572 Z= 0.266 Chirality : 0.036 0.128 2140 Planarity : 0.006 0.098 2276 Dihedral : 3.937 15.977 1824 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.56 % Allowed : 13.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.89 (0.20), residues: 1620 helix: 2.68 (0.14), residues: 1192 sheet: None (None), residues: 0 loop : -0.35 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 355 HIS 0.002 0.001 HIS C 197 PHE 0.012 0.001 PHE D 66 TYR 0.014 0.002 TYR D 353 ARG 0.013 0.001 ARG A 346 Details of bonding type rmsd hydrogen bonds : bond 0.04684 ( 984) hydrogen bonds : angle 3.90684 ( 2916) covalent geometry : bond 0.00297 (13688) covalent geometry : angle 0.50653 (18572) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20091.27 seconds wall clock time: 343 minutes 33.93 seconds (20613.93 seconds total)