Starting phenix.real_space_refine on Wed Jun 3 20:27:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9i3p_52603/06_2026/9i3p_52603.cif Found real_map, /net/cci-nas-00/data/ceres_data/9i3p_52603/06_2026/9i3p_52603.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9i3p_52603/06_2026/9i3p_52603.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9i3p_52603/06_2026/9i3p_52603.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9i3p_52603/06_2026/9i3p_52603.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9i3p_52603/06_2026/9i3p_52603.map" } resolution = 3.3 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= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 31 5.16 5 C 5319 2.51 5 N 1370 2.21 5 O 1565 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8285 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 490 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 4, 'TRANS': 55} Chain: "B" Number of atoms: 4268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4268 Classifications: {'peptide': 528} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 4, 'PTRANS': 32, 'TRANS': 491} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 3504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3504 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 25, 'TRANS': 426} Chain breaks: 1 Chain: "E" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'GLC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.31, per 1000 atoms: 0.28 Number of scatterers: 8285 At special positions: 0 Unit cell: (71.725, 110.985, 151.755, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 31 16.00 O 1565 8.00 N 1370 7.00 C 5319 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.04 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 Links applied ALPHA1-4 " GLC E 1 " - " GLC E 2 " Time building additional restraints: 0.76 Conformation dependent library (CDL) restraints added in 325.1 milliseconds 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1952 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 16 sheets defined 21.2% alpha, 34.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'B' and resid 4 through 11 Processing helix chain 'B' and resid 13 through 17 removed outlier: 3.508A pdb=" N LEU B 17 " --> pdb=" O LEU B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 276 Processing helix chain 'B' and resid 351 through 359 Processing helix chain 'B' and resid 445 through 452 Processing helix chain 'B' and resid 472 through 476 removed outlier: 3.701A pdb=" N ALA B 475 " --> pdb=" O VAL B 472 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N THR B 476 " --> pdb=" O LEU B 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 472 through 476' Processing helix chain 'C' and resid 130 through 144 Processing helix chain 'C' and resid 154 through 163 removed outlier: 3.646A pdb=" N PHE C 159 " --> pdb=" O LEU C 155 " (cutoff:3.500A) Proline residue: C 160 - end of helix Processing helix chain 'C' and resid 164 through 166 No H-bonds generated for 'chain 'C' and resid 164 through 166' Processing helix chain 'C' and resid 178 through 185 removed outlier: 4.168A pdb=" N SER C 185 " --> pdb=" O GLY C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 199 Processing helix chain 'C' and resid 204 through 210 Processing helix chain 'C' and resid 242 through 254 removed outlier: 4.774A pdb=" N ALA C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU C 250 " --> pdb=" O ALA C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 268 Processing helix chain 'C' and resid 269 through 274 Processing helix chain 'C' and resid 275 through 277 No H-bonds generated for 'chain 'C' and resid 275 through 277' Processing helix chain 'C' and resid 298 through 313 Processing helix chain 'C' and resid 321 through 330 Processing helix chain 'C' and resid 340 through 342 No H-bonds generated for 'chain 'C' and resid 340 through 342' Processing helix chain 'C' and resid 343 through 351 removed outlier: 3.552A pdb=" N SER C 350 " --> pdb=" O ASN C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 395 Processing helix chain 'C' and resid 398 through 409 removed outlier: 3.842A pdb=" N ASP C 408 " --> pdb=" O ALA C 404 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS C 409 " --> pdb=" O VAL C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 424 Processing helix chain 'C' and resid 426 through 439 Processing helix chain 'C' and resid 447 through 465 removed outlier: 3.610A pdb=" N ILE C 460 " --> pdb=" O ARG C 456 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 201 through 206 removed outlier: 6.608A pdb=" N LYS A 195 " --> pdb=" O MET A 186 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 84 through 89 removed outlier: 6.828A pdb=" N LEU B 85 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N THR B 199 " --> pdb=" O VAL B 89 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 84 through 89 removed outlier: 6.828A pdb=" N LEU B 85 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N THR B 199 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N THR B 222 " --> pdb=" O GLU B 62 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N GLU B 62 " --> pdb=" O THR B 222 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE B 224 " --> pdb=" O ILE B 60 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ILE B 60 " --> pdb=" O ILE B 224 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N LYS B 226 " --> pdb=" O LYS B 58 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N LYS B 58 " --> pdb=" O LYS B 226 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N VAL B 228 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N VAL B 56 " --> pdb=" O VAL B 228 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N GLU B 230 " --> pdb=" O LEU B 54 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LEU B 54 " --> pdb=" O GLU B 230 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLN B 232 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL B 234 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS B 50 " --> pdb=" O VAL B 234 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU B 22 " --> pdb=" O LYS B 253 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLU B 251 " --> pdb=" O GLN B 24 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 159 through 164 removed outlier: 6.115A pdb=" N ALA B 153 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N LEU B 138 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 8.568A pdb=" N ALA B 155 " --> pdb=" O ILE B 136 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N ILE B 136 " --> pdb=" O ALA B 155 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 123 through 124 Processing sheet with id=AA6, first strand: chain 'B' and resid 268 through 269 removed outlier: 6.771A pdb=" N THR B 512 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N VAL B 284 " --> pdb=" O VAL B 516 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N ILE B 309 " --> pdb=" O SER B 493 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N SER B 493 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS B 311 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU B 483 " --> pdb=" O LEU B 319 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N SER B 321 " --> pdb=" O LEU B 481 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N LEU B 481 " --> pdb=" O SER B 321 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ASP B 494 " --> pdb=" O GLU B 500 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLU B 500 " --> pdb=" O ASP B 494 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 457 through 459 removed outlier: 5.424A pdb=" N LEU B 481 " --> pdb=" O SER B 321 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N SER B 321 " --> pdb=" O LEU B 481 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU B 483 " --> pdb=" O LEU B 319 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS B 311 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N SER B 493 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N ILE B 309 " --> pdb=" O SER B 493 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N HIS B 331 " --> pdb=" O ILE B 535 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 348 through 349 Processing sheet with id=AA9, first strand: chain 'B' and resid 389 through 391 removed outlier: 3.612A pdb=" N THR B 397 " --> pdb=" O VAL B 408 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL B 410 " --> pdb=" O GLU B 395 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLU B 395 " --> pdb=" O VAL B 410 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 389 through 391 Processing sheet with id=AB2, first strand: chain 'C' and resid 6 through 7 removed outlier: 3.663A pdb=" N THR C 78 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 10 through 11 removed outlier: 7.001A pdb=" N GLY C 10 " --> pdb=" O THR C 115 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL C 93 " --> pdb=" O GLN C 39 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA C 33 " --> pdb=" O ASP C 99 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N MET C 34 " --> pdb=" O ALA C 50 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ALA C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 10 through 11 removed outlier: 7.001A pdb=" N GLY C 10 " --> pdb=" O THR C 115 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR C 107 " --> pdb=" O ALA C 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 147 through 150 removed outlier: 6.467A pdb=" N LEU C 119 " --> pdb=" O THR C 148 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N GLU C 150 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE C 121 " --> pdb=" O GLU C 150 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE C 171 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ALA C 376 " --> pdb=" O PRO C 219 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 147 through 150 removed outlier: 6.467A pdb=" N LEU C 119 " --> pdb=" O THR C 148 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N GLU C 150 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE C 121 " --> pdb=" O GLU C 150 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE C 171 " --> pdb=" O VAL C 120 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 257 through 259 removed outlier: 6.525A pdb=" N ALA C 258 " --> pdb=" O MET C 336 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N ILE C 338 " --> pdb=" O ALA C 258 " (cutoff:3.500A) 290 hydrogen bonds defined for protein. 795 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.45 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2659 1.34 - 1.46: 1756 1.46 - 1.58: 4021 1.58 - 1.69: 0 1.69 - 1.81: 52 Bond restraints: 8488 Sorted by residual: bond pdb=" N VAL B 463 " pdb=" CA VAL B 463 " ideal model delta sigma weight residual 1.458 1.501 -0.043 1.17e-02 7.31e+03 1.34e+01 bond pdb=" CA SER B 462 " pdb=" CB SER B 462 " ideal model delta sigma weight residual 1.535 1.480 0.055 1.58e-02 4.01e+03 1.21e+01 bond pdb=" N TYR B 118 " pdb=" CA TYR B 118 " ideal model delta sigma weight residual 1.454 1.492 -0.039 1.23e-02 6.61e+03 9.92e+00 bond pdb=" CA SER B 467 " pdb=" CB SER B 467 " ideal model delta sigma weight residual 1.529 1.484 0.045 1.46e-02 4.69e+03 9.39e+00 bond pdb=" N VAL B 513 " pdb=" CA VAL B 513 " ideal model delta sigma weight residual 1.457 1.492 -0.034 1.14e-02 7.69e+03 9.09e+00 ... (remaining 8483 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 11067 2.00 - 4.00: 388 4.00 - 6.01: 45 6.01 - 8.01: 14 8.01 - 10.01: 2 Bond angle restraints: 11516 Sorted by residual: angle pdb=" N MET B 543 " pdb=" CA MET B 543 " pdb=" C MET B 543 " ideal model delta sigma weight residual 113.97 106.04 7.93 1.28e+00 6.10e-01 3.84e+01 angle pdb=" C LYS B 236 " pdb=" CA LYS B 236 " pdb=" CB LYS B 236 " ideal model delta sigma weight residual 116.54 109.88 6.66 1.15e+00 7.56e-01 3.35e+01 angle pdb=" CA THR B 512 " pdb=" CB THR B 512 " pdb=" OG1 THR B 512 " ideal model delta sigma weight residual 109.60 102.64 6.96 1.50e+00 4.44e-01 2.15e+01 angle pdb=" CA ASP B 465 " pdb=" CB ASP B 465 " pdb=" CG ASP B 465 " ideal model delta sigma weight residual 112.60 117.03 -4.43 1.00e+00 1.00e+00 1.96e+01 angle pdb=" N ARG B 544 " pdb=" CA ARG B 544 " pdb=" C ARG B 544 " ideal model delta sigma weight residual 113.12 107.71 5.41 1.25e+00 6.40e-01 1.87e+01 ... (remaining 11511 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.62: 4399 16.62 - 33.25: 561 33.25 - 49.87: 121 49.87 - 66.50: 47 66.50 - 83.12: 9 Dihedral angle restraints: 5137 sinusoidal: 2111 harmonic: 3026 Sorted by residual: dihedral pdb=" C ASP B 465 " pdb=" N ASP B 465 " pdb=" CA ASP B 465 " pdb=" CB ASP B 465 " ideal model delta harmonic sigma weight residual -122.60 -113.11 -9.49 0 2.50e+00 1.60e-01 1.44e+01 dihedral pdb=" C ARG C 38 " pdb=" N ARG C 38 " pdb=" CA ARG C 38 " pdb=" CB ARG C 38 " ideal model delta harmonic sigma weight residual -122.60 -113.76 -8.84 0 2.50e+00 1.60e-01 1.25e+01 dihedral pdb=" CA TYR B 444 " pdb=" C TYR B 444 " pdb=" N PRO B 445 " pdb=" CA PRO B 445 " ideal model delta harmonic sigma weight residual 180.00 163.14 16.86 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 5134 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1015 0.060 - 0.119: 203 0.119 - 0.179: 36 0.179 - 0.238: 12 0.238 - 0.297: 2 Chirality restraints: 1268 Sorted by residual: chirality pdb=" C1 GLC E 2 " pdb=" O4 GLC E 1 " pdb=" C2 GLC E 2 " pdb=" O5 GLC E 2 " both_signs ideal model delta sigma weight residual False 2.40 2.27 0.13 2.00e-02 2.50e+03 4.04e+01 chirality pdb=" CA ASP B 465 " pdb=" N ASP B 465 " pdb=" C ASP B 465 " pdb=" CB ASP B 465 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CA ILE B 468 " pdb=" N ILE B 468 " pdb=" C ILE B 468 " pdb=" CB ILE B 468 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 1265 not shown) Planarity restraints: 1484 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 556 " 0.317 9.50e-02 1.11e+02 1.42e-01 1.24e+01 pdb=" NE ARG B 556 " -0.019 2.00e-02 2.50e+03 pdb=" CZ ARG B 556 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG B 556 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 556 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 464 " 0.315 9.50e-02 1.11e+02 1.41e-01 1.23e+01 pdb=" NE ARG B 464 " -0.020 2.00e-02 2.50e+03 pdb=" CZ ARG B 464 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG B 464 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 464 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 461 " 0.016 2.00e-02 2.50e+03 3.07e-02 9.43e+00 pdb=" C VAL B 461 " -0.053 2.00e-02 2.50e+03 pdb=" O VAL B 461 " 0.020 2.00e-02 2.50e+03 pdb=" N SER B 462 " 0.018 2.00e-02 2.50e+03 ... (remaining 1481 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1086 2.76 - 3.29: 7352 3.29 - 3.83: 12346 3.83 - 4.36: 14703 4.36 - 4.90: 25848 Nonbonded interactions: 61335 Sorted by model distance: nonbonded pdb=" OD1 ASP C 170 " pdb=" OG SER C 382 " model vdw 2.219 3.040 nonbonded pdb=" OG1 THR C 240 " pdb=" OE2 GLU C 243 " model vdw 2.224 3.040 nonbonded pdb=" OD2 ASP B 440 " pdb=" OH TYR B 444 " model vdw 2.230 3.040 nonbonded pdb=" O ASN C 74 " pdb=" OD1 ASN C 74 " model vdw 2.244 3.040 nonbonded pdb=" OH TYR B 338 " pdb=" OD2 ASP B 471 " model vdw 2.260 3.040 ... (remaining 61330 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.980 Find NCS groups from input model: 0.040 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 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 : 0.005 0.055 8490 Z= 0.342 Angle : 0.804 10.010 11521 Z= 0.512 Chirality : 0.054 0.297 1268 Planarity : 0.008 0.142 1484 Dihedral : 16.122 83.122 3182 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.89 % Allowed : 21.63 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.26), residues: 1024 helix: -0.25 (0.37), residues: 202 sheet: -0.24 (0.34), residues: 252 loop : -1.09 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 545 TYR 0.015 0.001 TYR C 419 PHE 0.019 0.001 PHE C 451 TRP 0.007 0.001 TRP A 193 HIS 0.004 0.001 HIS B 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.34 ( 8488) covalent geometry : angle 0.79858 / 0.51 (11516) SS BOND : bond 0.00452 / 0.30 ( 1) SS BOND : angle 0.34549 / 0.24 ( 2) hydrogen bonds : bond 0.18751 / 12.98 ( 262) hydrogen bonds : angle 7.64269 / 5.53 ( 795) link_ALPHA1-4 : bond 0.04643 / 3.10 ( 1) link_ALPHA1-4 : angle 5.64991 / 4.00 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: A 204 MET cc_start: 0.8064 (OUTLIER) cc_final: 0.7844 (mmm) REVERT: B 55 LYS cc_start: 0.7356 (ttpt) cc_final: 0.6711 (mmtt) REVERT: B 97 THR cc_start: 0.8416 (p) cc_final: 0.7987 (t) REVERT: B 116 CYS cc_start: 0.7902 (p) cc_final: 0.7530 (p) REVERT: B 139 ASN cc_start: 0.7910 (m-40) cc_final: 0.7423 (t0) REVERT: B 276 MET cc_start: 0.8490 (mtp) cc_final: 0.8231 (mtt) REVERT: B 371 LYS cc_start: 0.7929 (tttm) cc_final: 0.7527 (mtmm) REVERT: B 489 TYR cc_start: 0.8695 (m-80) cc_final: 0.8331 (m-80) REVERT: B 500 GLU cc_start: 0.6875 (pm20) cc_final: 0.6613 (pm20) REVERT: C 12 VAL cc_start: 0.8556 (p) cc_final: 0.8267 (m) REVERT: C 129 TYR cc_start: 0.7858 (p90) cc_final: 0.7383 (p90) REVERT: C 336 MET cc_start: 0.6332 (mmp) cc_final: 0.5164 (mmm) outliers start: 8 outliers final: 3 residues processed: 89 average time/residue: 0.0967 time to fit residues: 11.9353 Evaluate side-chains 83 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 79 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 445 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.4980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.0670 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.0070 chunk 100 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN C 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.213168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.141135 restraints weight = 9614.726| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 4.25 r_work: 0.3378 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.0845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8490 Z= 0.114 Angle : 0.535 8.194 11521 Z= 0.276 Chirality : 0.042 0.145 1268 Planarity : 0.004 0.041 1484 Dihedral : 4.823 56.156 1163 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.12 % Allowed : 21.07 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.26), residues: 1024 helix: 0.11 (0.36), residues: 213 sheet: -0.15 (0.34), residues: 262 loop : -0.97 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 104 TYR 0.019 0.001 TYR B 546 PHE 0.019 0.001 PHE C 306 TRP 0.004 0.001 TRP C 270 HIS 0.003 0.001 HIS C 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 8488) covalent geometry : angle 0.53440 / 0.28 (11516) SS BOND : bond 0.00349 / 0.23 ( 1) SS BOND : angle 0.36272 / 0.25 ( 2) hydrogen bonds : bond 0.04805 / 3.29 ( 262) hydrogen bonds : angle 5.54785 / 4.02 ( 795) link_ALPHA1-4 : bond 0.00025 / 0.02 ( 1) link_ALPHA1-4 : angle 1.16645 / 0.85 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: A 188 ASN cc_start: 0.7724 (p0) cc_final: 0.7491 (p0) REVERT: B 55 LYS cc_start: 0.7310 (ttpt) cc_final: 0.6631 (mmtt) REVERT: B 97 THR cc_start: 0.8374 (p) cc_final: 0.7979 (t) REVERT: B 139 ASN cc_start: 0.7839 (m-40) cc_final: 0.7330 (t0) REVERT: B 371 LYS cc_start: 0.7856 (tttm) cc_final: 0.7392 (mtmm) REVERT: B 500 GLU cc_start: 0.6939 (pm20) cc_final: 0.6690 (pm20) REVERT: C 129 TYR cc_start: 0.7876 (p90) cc_final: 0.7350 (p90) REVERT: C 223 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7905 (mt-10) REVERT: C 249 LYS cc_start: 0.7625 (OUTLIER) cc_final: 0.7385 (tppt) REVERT: C 336 MET cc_start: 0.6559 (mmp) cc_final: 0.5416 (mmm) outliers start: 19 outliers final: 9 residues processed: 95 average time/residue: 0.0891 time to fit residues: 11.8943 Evaluate side-chains 81 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 409 ASN Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 249 LYS Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 445 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 88 optimal weight: 10.0000 chunk 100 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 21 optimal weight: 0.0770 chunk 77 optimal weight: 0.0050 chunk 56 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 68 optimal weight: 0.5980 chunk 94 optimal weight: 0.4980 overall best weight: 0.4152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 74 ASN C 437 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.212891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.137569 restraints weight = 9586.608| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 4.04 r_work: 0.3316 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 8490 Z= 0.104 Angle : 0.505 8.549 11521 Z= 0.258 Chirality : 0.042 0.143 1268 Planarity : 0.004 0.044 1484 Dihedral : 4.100 36.501 1156 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.01 % Allowed : 20.74 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.26), residues: 1024 helix: 0.24 (0.36), residues: 213 sheet: -0.16 (0.33), residues: 279 loop : -0.90 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 243 TYR 0.013 0.001 TYR B 546 PHE 0.015 0.001 PHE C 451 TRP 0.006 0.001 TRP C 270 HIS 0.002 0.001 HIS B 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.10 ( 8488) covalent geometry : angle 0.50503 / 0.26 (11516) SS BOND : bond 0.00335 / 0.22 ( 1) SS BOND : angle 0.28680 / 0.20 ( 2) hydrogen bonds : bond 0.03883 / 2.61 ( 262) hydrogen bonds : angle 5.12066 / 3.69 ( 795) link_ALPHA1-4 : bond 0.00086 / 0.06 ( 1) link_ALPHA1-4 : angle 0.93507 / 0.68 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 77 time to evaluate : 0.404 Fit side-chains revert: symmetry clash REVERT: A 188 ASN cc_start: 0.7891 (p0) cc_final: 0.7531 (p0) REVERT: B 7 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7324 (mt-10) REVERT: B 55 LYS cc_start: 0.7406 (ttpt) cc_final: 0.6739 (mmtt) REVERT: B 97 THR cc_start: 0.8468 (p) cc_final: 0.8098 (t) REVERT: B 139 ASN cc_start: 0.7942 (m-40) cc_final: 0.7440 (t0) REVERT: B 371 LYS cc_start: 0.7873 (tttm) cc_final: 0.7386 (mtmm) REVERT: B 500 GLU cc_start: 0.7010 (pm20) cc_final: 0.6805 (pm20) REVERT: C 129 TYR cc_start: 0.7886 (p90) cc_final: 0.7377 (p90) REVERT: C 223 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7996 (mt-10) REVERT: C 260 MET cc_start: 0.4899 (mmt) cc_final: 0.4309 (ptt) REVERT: C 336 MET cc_start: 0.6552 (mmp) cc_final: 0.5149 (mmm) outliers start: 27 outliers final: 13 residues processed: 98 average time/residue: 0.0910 time to fit residues: 12.7005 Evaluate side-chains 85 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 409 ASN Chi-restraints excluded: chain B residue 430 MET Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 552 HIS Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 445 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 91 optimal weight: 4.9990 chunk 56 optimal weight: 0.0870 chunk 19 optimal weight: 20.0000 chunk 70 optimal weight: 0.0370 chunk 17 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 overall best weight: 0.9440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 326 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.210915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.148511 restraints weight = 9675.155| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 2.78 r_work: 0.3387 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8490 Z= 0.151 Angle : 0.549 9.262 11521 Z= 0.279 Chirality : 0.043 0.142 1268 Planarity : 0.004 0.047 1484 Dihedral : 4.234 39.399 1156 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.23 % Allowed : 20.29 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.26), residues: 1024 helix: 0.35 (0.36), residues: 214 sheet: -0.19 (0.33), residues: 279 loop : -0.93 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 544 TYR 0.019 0.001 TYR B 546 PHE 0.013 0.001 PHE B 332 TRP 0.008 0.001 TRP C 270 HIS 0.003 0.001 HIS B 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.15 ( 8488) covalent geometry : angle 0.54887 / 0.28 (11516) SS BOND : bond 0.00306 / 0.20 ( 1) SS BOND : angle 0.49142 / 0.31 ( 2) hydrogen bonds : bond 0.04004 / 2.65 ( 262) hydrogen bonds : angle 5.07105 / 3.65 ( 795) link_ALPHA1-4 : bond 0.00131 / 0.09 ( 1) link_ALPHA1-4 : angle 0.87563 / 0.63 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 70 time to evaluate : 0.320 Fit side-chains REVERT: A 188 ASN cc_start: 0.7898 (p0) cc_final: 0.7511 (p0) REVERT: B 7 GLU cc_start: 0.7559 (mt-10) cc_final: 0.7278 (mt-10) REVERT: B 55 LYS cc_start: 0.7323 (ttpt) cc_final: 0.6629 (mmtt) REVERT: B 97 THR cc_start: 0.8552 (p) cc_final: 0.8074 (t) REVERT: B 139 ASN cc_start: 0.7905 (m-40) cc_final: 0.7370 (t0) REVERT: B 371 LYS cc_start: 0.7905 (tttm) cc_final: 0.7399 (mtmm) REVERT: B 500 GLU cc_start: 0.7044 (pm20) cc_final: 0.6842 (pm20) REVERT: C 129 TYR cc_start: 0.7820 (p90) cc_final: 0.7291 (p90) REVERT: C 249 LYS cc_start: 0.7606 (OUTLIER) cc_final: 0.7231 (tppt) REVERT: C 260 MET cc_start: 0.4660 (mmt) cc_final: 0.4255 (ptt) REVERT: C 336 MET cc_start: 0.6287 (mmp) cc_final: 0.4992 (mmm) outliers start: 29 outliers final: 19 residues processed: 95 average time/residue: 0.0867 time to fit residues: 11.7695 Evaluate side-chains 86 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 66 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 409 ASN Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 430 MET Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 551 SER Chi-restraints excluded: chain B residue 552 HIS Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 249 LYS Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 445 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 63 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 29 optimal weight: 9.9990 chunk 3 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 85 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 15 optimal weight: 0.4980 chunk 12 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 326 ASN C 437 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.214679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 113)---------------| | r_work = 0.3656 r_free = 0.3656 target = 0.139171 restraints weight = 9744.149| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 4.11 r_work: 0.3334 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8490 Z= 0.129 Angle : 0.519 9.302 11521 Z= 0.266 Chirality : 0.042 0.139 1268 Planarity : 0.004 0.048 1484 Dihedral : 4.136 36.485 1156 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.68 % Allowed : 20.85 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.26), residues: 1024 helix: 0.48 (0.36), residues: 214 sheet: -0.12 (0.34), residues: 276 loop : -0.93 (0.26), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 243 TYR 0.018 0.001 TYR B 546 PHE 0.016 0.001 PHE C 306 TRP 0.007 0.001 TRP B 190 HIS 0.003 0.001 HIS C 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 ( 8488) covalent geometry : angle 0.51907 / 0.27 (11516) SS BOND : bond 0.00312 / 0.21 ( 1) SS BOND : angle 0.37779 / 0.24 ( 2) hydrogen bonds : bond 0.03661 / 2.41 ( 262) hydrogen bonds : angle 4.89859 / 3.52 ( 795) link_ALPHA1-4 : bond 0.00038 / 0.03 ( 1) link_ALPHA1-4 : angle 0.86840 / 0.64 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 72 time to evaluate : 0.350 Fit side-chains REVERT: A 188 ASN cc_start: 0.8004 (p0) cc_final: 0.7622 (p0) REVERT: B 7 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7294 (mt-10) REVERT: B 55 LYS cc_start: 0.7364 (ttpt) cc_final: 0.6675 (mmtt) REVERT: B 97 THR cc_start: 0.8602 (p) cc_final: 0.8129 (t) REVERT: B 139 ASN cc_start: 0.7887 (m-40) cc_final: 0.7371 (t0) REVERT: B 237 PHE cc_start: 0.5496 (OUTLIER) cc_final: 0.4782 (m-80) REVERT: B 371 LYS cc_start: 0.7965 (tttm) cc_final: 0.7460 (mtmm) REVERT: B 500 GLU cc_start: 0.7098 (pm20) cc_final: 0.6896 (pm20) REVERT: C 129 TYR cc_start: 0.7866 (p90) cc_final: 0.7355 (p90) REVERT: C 223 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7951 (mt-10) REVERT: C 249 LYS cc_start: 0.7664 (OUTLIER) cc_final: 0.7272 (tppt) REVERT: C 260 MET cc_start: 0.4776 (mmt) cc_final: 0.4349 (ptt) outliers start: 33 outliers final: 21 residues processed: 100 average time/residue: 0.0891 time to fit residues: 12.6263 Evaluate side-chains 90 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 66 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 237 PHE Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 409 ASN Chi-restraints excluded: chain B residue 430 MET Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 542 MET Chi-restraints excluded: chain B residue 551 SER Chi-restraints excluded: chain B residue 552 HIS Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 249 LYS Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 445 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 20 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 43 optimal weight: 0.0470 chunk 94 optimal weight: 0.0570 chunk 6 optimal weight: 0.0670 chunk 44 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 overall best weight: 0.3934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 326 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.215966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.153587 restraints weight = 9633.974| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 2.46 r_work: 0.3452 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 8490 Z= 0.100 Angle : 0.506 9.364 11521 Z= 0.257 Chirality : 0.042 0.138 1268 Planarity : 0.004 0.049 1484 Dihedral : 4.037 36.619 1156 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.45 % Allowed : 22.19 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.26), residues: 1024 helix: 0.57 (0.36), residues: 214 sheet: -0.04 (0.34), residues: 276 loop : -0.89 (0.26), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 243 TYR 0.016 0.001 TYR B 546 PHE 0.024 0.001 PHE C 451 TRP 0.004 0.001 TRP C 241 HIS 0.002 0.001 HIS B 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 ( 8488) covalent geometry : angle 0.50570 / 0.26 (11516) SS BOND : bond 0.00313 / 0.21 ( 1) SS BOND : angle 0.33565 / 0.22 ( 2) hydrogen bonds : bond 0.03362 / 2.22 ( 262) hydrogen bonds : angle 4.79984 / 3.45 ( 795) link_ALPHA1-4 : bond 0.00130 / 0.09 ( 1) link_ALPHA1-4 : angle 0.84040 / 0.63 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 73 time to evaluate : 0.329 Fit side-chains REVERT: A 188 ASN cc_start: 0.7936 (p0) cc_final: 0.7544 (p0) REVERT: B 7 GLU cc_start: 0.7513 (mt-10) cc_final: 0.7289 (mp0) REVERT: B 55 LYS cc_start: 0.7179 (ttpt) cc_final: 0.6483 (mmtt) REVERT: B 97 THR cc_start: 0.8543 (p) cc_final: 0.8034 (t) REVERT: B 132 GLN cc_start: 0.6986 (tt0) cc_final: 0.6156 (tm-30) REVERT: B 139 ASN cc_start: 0.7800 (m-40) cc_final: 0.7295 (t0) REVERT: B 237 PHE cc_start: 0.5462 (OUTLIER) cc_final: 0.4752 (m-80) REVERT: B 371 LYS cc_start: 0.7857 (tttm) cc_final: 0.7384 (mtmm) REVERT: C 129 TYR cc_start: 0.7796 (p90) cc_final: 0.7286 (p90) REVERT: C 223 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7860 (mt-10) REVERT: C 249 LYS cc_start: 0.7633 (OUTLIER) cc_final: 0.7253 (tppt) REVERT: C 260 MET cc_start: 0.4618 (mmt) cc_final: 0.4291 (ptt) REVERT: C 336 MET cc_start: 0.6237 (mmp) cc_final: 0.5034 (mmm) outliers start: 22 outliers final: 15 residues processed: 90 average time/residue: 0.0993 time to fit residues: 12.4688 Evaluate side-chains 85 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 237 PHE Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 409 ASN Chi-restraints excluded: chain B residue 430 MET Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 542 MET Chi-restraints excluded: chain B residue 552 HIS Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 249 LYS Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 445 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 91 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 19 optimal weight: 8.9990 chunk 14 optimal weight: 0.0370 chunk 98 optimal weight: 0.9990 chunk 6 optimal weight: 0.4980 chunk 62 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 86 optimal weight: 7.9990 chunk 23 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 overall best weight: 0.8662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 326 ASN C 437 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.214521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.164178 restraints weight = 9805.455| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 2.52 r_work: 0.3340 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8490 Z= 0.143 Angle : 0.541 9.622 11521 Z= 0.273 Chirality : 0.042 0.139 1268 Planarity : 0.004 0.050 1484 Dihedral : 4.121 35.560 1156 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.57 % Allowed : 22.30 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.26), residues: 1024 helix: 0.65 (0.36), residues: 212 sheet: -0.12 (0.33), residues: 276 loop : -0.93 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 243 TYR 0.012 0.001 TYR B 546 PHE 0.021 0.002 PHE C 451 TRP 0.006 0.001 TRP B 190 HIS 0.003 0.001 HIS C 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.14 ( 8488) covalent geometry : angle 0.54136 / 0.27 (11516) SS BOND : bond 0.00311 / 0.21 ( 1) SS BOND : angle 0.45217 / 0.29 ( 2) hydrogen bonds : bond 0.03660 / 2.40 ( 262) hydrogen bonds : angle 4.85292 / 3.48 ( 795) link_ALPHA1-4 : bond 0.00020 / 0.01 ( 1) link_ALPHA1-4 : angle 0.86877 / 0.64 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 70 time to evaluate : 0.326 Fit side-chains REVERT: A 188 ASN cc_start: 0.8034 (p0) cc_final: 0.7651 (p0) REVERT: B 7 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7397 (mt-10) REVERT: B 55 LYS cc_start: 0.7610 (ttpt) cc_final: 0.6985 (mmtt) REVERT: B 97 THR cc_start: 0.8739 (p) cc_final: 0.8275 (t) REVERT: B 132 GLN cc_start: 0.6982 (tt0) cc_final: 0.6247 (tm-30) REVERT: B 139 ASN cc_start: 0.8095 (m-40) cc_final: 0.7638 (t0) REVERT: B 237 PHE cc_start: 0.5443 (OUTLIER) cc_final: 0.4723 (m-80) REVERT: B 371 LYS cc_start: 0.7970 (tttm) cc_final: 0.7569 (mtmm) REVERT: B 500 GLU cc_start: 0.7195 (pm20) cc_final: 0.6934 (pm20) REVERT: C 129 TYR cc_start: 0.7892 (p90) cc_final: 0.7390 (p90) REVERT: C 249 LYS cc_start: 0.7322 (OUTLIER) cc_final: 0.7057 (tppt) REVERT: C 260 MET cc_start: 0.4780 (mmt) cc_final: 0.4506 (ptt) REVERT: C 336 MET cc_start: 0.6168 (mmp) cc_final: 0.5004 (mmm) outliers start: 32 outliers final: 23 residues processed: 97 average time/residue: 0.0960 time to fit residues: 12.9342 Evaluate side-chains 94 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 69 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 237 PHE Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 409 ASN Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 430 MET Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 542 MET Chi-restraints excluded: chain B residue 551 SER Chi-restraints excluded: chain B residue 552 HIS Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 249 LYS Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 445 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 63 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 17 optimal weight: 0.0270 chunk 52 optimal weight: 3.9990 chunk 44 optimal weight: 0.1980 chunk 6 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 326 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.215638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.154278 restraints weight = 9709.249| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 2.45 r_work: 0.3444 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8490 Z= 0.110 Angle : 0.512 9.675 11521 Z= 0.261 Chirality : 0.042 0.137 1268 Planarity : 0.004 0.052 1484 Dihedral : 4.017 34.994 1156 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.34 % Allowed : 22.19 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.26), residues: 1024 helix: 0.64 (0.36), residues: 214 sheet: -0.09 (0.33), residues: 276 loop : -0.88 (0.26), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 243 TYR 0.012 0.001 TYR B 546 PHE 0.010 0.001 PHE B 163 TRP 0.005 0.001 TRP C 241 HIS 0.002 0.001 HIS C 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 ( 8488) covalent geometry : angle 0.51220 / 0.26 (11516) SS BOND : bond 0.00326 / 0.22 ( 1) SS BOND : angle 0.35052 / 0.22 ( 2) hydrogen bonds : bond 0.03322 / 2.18 ( 262) hydrogen bonds : angle 4.76330 / 3.42 ( 795) link_ALPHA1-4 : bond 0.00135 / 0.09 ( 1) link_ALPHA1-4 : angle 0.84348 / 0.64 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 72 time to evaluate : 0.411 Fit side-chains REVERT: A 188 ASN cc_start: 0.8066 (p0) cc_final: 0.7688 (p0) REVERT: B 1 MET cc_start: 0.4661 (mtt) cc_final: 0.3358 (tmm) REVERT: B 7 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7301 (mt-10) REVERT: B 55 LYS cc_start: 0.7371 (ttpt) cc_final: 0.6677 (mmtt) REVERT: B 97 THR cc_start: 0.8556 (p) cc_final: 0.8052 (t) REVERT: B 132 GLN cc_start: 0.6978 (tt0) cc_final: 0.6114 (tm-30) REVERT: B 139 ASN cc_start: 0.7924 (m-40) cc_final: 0.7395 (t0) REVERT: B 237 PHE cc_start: 0.5528 (OUTLIER) cc_final: 0.4575 (m-80) REVERT: B 371 LYS cc_start: 0.7976 (tttm) cc_final: 0.7427 (mtmm) REVERT: B 500 GLU cc_start: 0.6905 (pm20) cc_final: 0.6582 (pm20) REVERT: C 129 TYR cc_start: 0.7889 (p90) cc_final: 0.7309 (p90) REVERT: C 249 LYS cc_start: 0.7658 (OUTLIER) cc_final: 0.7255 (tppt) REVERT: C 260 MET cc_start: 0.4567 (mmt) cc_final: 0.4196 (ptt) REVERT: C 336 MET cc_start: 0.6230 (mmp) cc_final: 0.5043 (mmm) outliers start: 30 outliers final: 21 residues processed: 96 average time/residue: 0.0945 time to fit residues: 12.7172 Evaluate side-chains 90 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 67 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 237 PHE Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 409 ASN Chi-restraints excluded: chain B residue 430 MET Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 542 MET Chi-restraints excluded: chain B residue 551 SER Chi-restraints excluded: chain B residue 552 HIS Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 249 LYS Chi-restraints excluded: chain C residue 445 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 42 optimal weight: 1.9990 chunk 13 optimal weight: 0.0010 chunk 73 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 5 optimal weight: 0.0070 chunk 37 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 9 optimal weight: 0.1980 overall best weight: 0.8408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 326 ASN C 437 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.214567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.152990 restraints weight = 9678.674| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 2.44 r_work: 0.3424 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8490 Z= 0.139 Angle : 0.535 9.812 11521 Z= 0.272 Chirality : 0.042 0.138 1268 Planarity : 0.004 0.054 1484 Dihedral : 4.112 34.756 1156 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.01 % Allowed : 22.97 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.26), residues: 1024 helix: 0.71 (0.36), residues: 212 sheet: -0.14 (0.33), residues: 276 loop : -0.93 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 243 TYR 0.011 0.001 TYR C 95 PHE 0.014 0.002 PHE B 373 TRP 0.006 0.001 TRP B 190 HIS 0.003 0.001 HIS C 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.14 ( 8488) covalent geometry : angle 0.53539 / 0.27 (11516) SS BOND : bond 0.00285 / 0.19 ( 1) SS BOND : angle 0.48575 / 0.31 ( 2) hydrogen bonds : bond 0.03563 / 2.32 ( 262) hydrogen bonds : angle 4.82449 / 3.46 ( 795) link_ALPHA1-4 : bond 0.00057 / 0.04 ( 1) link_ALPHA1-4 : angle 0.82722 / 0.62 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 68 time to evaluate : 0.338 Fit side-chains REVERT: A 188 ASN cc_start: 0.7966 (p0) cc_final: 0.7583 (p0) REVERT: B 1 MET cc_start: 0.4479 (mtt) cc_final: 0.3271 (tmm) REVERT: B 7 GLU cc_start: 0.7544 (mt-10) cc_final: 0.7206 (mt-10) REVERT: B 55 LYS cc_start: 0.7239 (ttpt) cc_final: 0.6533 (mmtt) REVERT: B 97 THR cc_start: 0.8469 (p) cc_final: 0.7975 (t) REVERT: B 139 ASN cc_start: 0.7899 (m-40) cc_final: 0.7391 (t0) REVERT: B 237 PHE cc_start: 0.5416 (OUTLIER) cc_final: 0.4691 (m-80) REVERT: B 371 LYS cc_start: 0.7908 (tttm) cc_final: 0.7460 (mtmm) REVERT: B 500 GLU cc_start: 0.7071 (pm20) cc_final: 0.6742 (pm20) REVERT: C 129 TYR cc_start: 0.7840 (p90) cc_final: 0.7283 (p90) REVERT: C 249 LYS cc_start: 0.7553 (OUTLIER) cc_final: 0.7185 (tppt) REVERT: C 260 MET cc_start: 0.4524 (mmt) cc_final: 0.4164 (ptt) REVERT: C 336 MET cc_start: 0.6226 (mmp) cc_final: 0.5044 (mmm) outliers start: 27 outliers final: 23 residues processed: 89 average time/residue: 0.0954 time to fit residues: 11.9418 Evaluate side-chains 92 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 67 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 237 PHE Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 409 ASN Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 542 MET Chi-restraints excluded: chain B residue 551 SER Chi-restraints excluded: chain B residue 552 HIS Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 249 LYS Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 445 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 21 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 11 optimal weight: 0.2980 chunk 75 optimal weight: 0.4980 chunk 36 optimal weight: 0.1980 chunk 45 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 = 0.4397 r_free = 0.4397 target = 0.216049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.154447 restraints weight = 9715.113| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 2.48 r_work: 0.3449 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 8490 Z= 0.101 Angle : 0.507 9.643 11521 Z= 0.259 Chirality : 0.042 0.139 1268 Planarity : 0.004 0.056 1484 Dihedral : 3.979 34.468 1156 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.56 % Allowed : 23.19 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.26), residues: 1024 helix: 0.65 (0.36), residues: 215 sheet: -0.06 (0.34), residues: 276 loop : -0.86 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 243 TYR 0.011 0.001 TYR B 546 PHE 0.024 0.001 PHE C 306 TRP 0.005 0.001 TRP C 241 HIS 0.002 0.001 HIS C 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.10 ( 8488) covalent geometry : angle 0.50681 / 0.26 (11516) SS BOND : bond 0.00304 / 0.20 ( 1) SS BOND : angle 0.30648 / 0.19 ( 2) hydrogen bonds : bond 0.03184 / 2.08 ( 262) hydrogen bonds : angle 4.69825 / 3.36 ( 795) link_ALPHA1-4 : bond 0.00178 / 0.12 ( 1) link_ALPHA1-4 : angle 0.82535 / 0.64 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 70 time to evaluate : 0.321 Fit side-chains REVERT: A 188 ASN cc_start: 0.7980 (p0) cc_final: 0.7601 (p0) REVERT: B 1 MET cc_start: 0.4434 (mtt) cc_final: 0.3161 (tmm) REVERT: B 55 LYS cc_start: 0.7222 (ttpt) cc_final: 0.6541 (mmtt) REVERT: B 97 THR cc_start: 0.8446 (p) cc_final: 0.7940 (t) REVERT: B 132 GLN cc_start: 0.6912 (tt0) cc_final: 0.6040 (tm-30) REVERT: B 139 ASN cc_start: 0.7875 (m-40) cc_final: 0.7369 (t0) REVERT: B 237 PHE cc_start: 0.5462 (OUTLIER) cc_final: 0.4726 (m-80) REVERT: B 371 LYS cc_start: 0.7879 (tttm) cc_final: 0.7409 (mtmm) REVERT: B 500 GLU cc_start: 0.7072 (pm20) cc_final: 0.6759 (pm20) REVERT: C 129 TYR cc_start: 0.7831 (p90) cc_final: 0.7258 (p90) REVERT: C 249 LYS cc_start: 0.7572 (OUTLIER) cc_final: 0.7205 (tppt) REVERT: C 260 MET cc_start: 0.4448 (mmt) cc_final: 0.4061 (ptt) REVERT: C 336 MET cc_start: 0.6233 (mmp) cc_final: 0.5081 (mmm) outliers start: 23 outliers final: 21 residues processed: 87 average time/residue: 0.0951 time to fit residues: 11.7190 Evaluate side-chains 91 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 68 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 237 PHE Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 409 ASN Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 542 MET Chi-restraints excluded: chain B residue 551 SER Chi-restraints excluded: chain B residue 552 HIS Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 249 LYS Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 445 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 20.0000 chunk 78 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 chunk 98 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 92 optimal weight: 8.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4386 r_free = 0.4386 target = 0.214842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.152795 restraints weight = 9700.143| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 2.46 r_work: 0.3430 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8490 Z= 0.138 Angle : 0.539 9.802 11521 Z= 0.273 Chirality : 0.042 0.136 1268 Planarity : 0.004 0.055 1484 Dihedral : 4.063 34.320 1156 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.90 % Allowed : 22.85 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.26), residues: 1024 helix: 0.67 (0.36), residues: 213 sheet: -0.09 (0.34), residues: 275 loop : -0.89 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 243 TYR 0.010 0.001 TYR C 95 PHE 0.028 0.002 PHE C 306 TRP 0.005 0.001 TRP B 190 HIS 0.003 0.001 HIS C 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.14 ( 8488) covalent geometry : angle 0.53917 / 0.27 (11516) SS BOND : bond 0.00291 / 0.19 ( 1) SS BOND : angle 0.47364 / 0.30 ( 2) hydrogen bonds : bond 0.03460 / 2.26 ( 262) hydrogen bonds : angle 4.77176 / 3.42 ( 795) link_ALPHA1-4 : bond 0.00061 / 0.04 ( 1) link_ALPHA1-4 : angle 0.85182 / 0.64 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2552.03 seconds wall clock time: 44 minutes 23.39 seconds (2663.39 seconds total)