Starting phenix.real_space_refine on Thu Aug 6 18:11:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9shn_54905/08_2026/9shn_54905_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9shn_54905/08_2026/9shn_54905.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9shn_54905/08_2026/9shn_54905.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9shn_54905/08_2026/9shn_54905.map" model { file = "/net/cci-nas-00/data/ceres_data/9shn_54905/08_2026/9shn_54905_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9shn_54905/08_2026/9shn_54905_trim.cif" } resolution = 2.18 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= 0.001 sd= 0.032 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: 7 Type Number sf(0) Gaussians Fe 2 7.16 5 P 2 5.49 5 S 44 5.16 5 C 5060 2.51 5 N 1386 2.21 5 O 1496 1.98 5 H 7970 0.53 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-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15960 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 7915 Classifications: {'peptide': 507} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 481} Chain: "A" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 65 Unusual residues: {'HEM': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 176 SG CYS A 52 67.445 78.610 69.540 1.00 21.59 S Restraints were copied for chains: B Time building chain proxies: 7.23, per 1000 atoms: 0.45 Number of scatterers: 15960 At special positions: 0 Unit cell: (96.728, 99.44, 91.304, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 2 26.01 S 44 16.00 P 2 15.00 O 1496 8.00 N 1386 7.00 C 5060 6.00 H 7970 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.20 Conformation dependent library (CDL) restraints added in 367.2 milliseconds 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1868 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 8 sheets defined 45.3% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 59 through 63 removed outlier: 3.729A pdb=" N GLU A 62 " --> pdb=" O PRO A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 94 through 99 Processing helix chain 'A' and resid 111 through 113 No H-bonds generated for 'chain 'A' and resid 111 through 113' Processing helix chain 'A' and resid 118 through 133 removed outlier: 4.172A pdb=" N ILE A 122 " --> pdb=" O VAL A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 162 Processing helix chain 'A' and resid 174 through 185 removed outlier: 3.667A pdb=" N VAL A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 213 Processing helix chain 'A' and resid 226 through 235 removed outlier: 3.857A pdb=" N HIS A 232 " --> pdb=" O ASN A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 244 Processing helix chain 'A' and resid 258 through 272 Processing helix chain 'A' and resid 290 through 295 removed outlier: 3.716A pdb=" N GLN A 295 " --> pdb=" O GLU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 320 removed outlier: 3.727A pdb=" N VAL A 319 " --> pdb=" O ASP A 316 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL A 320 " --> pdb=" O ARG A 317 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 316 through 320' Processing helix chain 'A' and resid 327 through 343 removed outlier: 3.517A pdb=" N GLY A 343 " --> pdb=" O ILE A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 361 removed outlier: 3.516A pdb=" N GLY A 351 " --> pdb=" O GLY A 347 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS A 359 " --> pdb=" O ALA A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 364 No H-bonds generated for 'chain 'A' and resid 362 through 364' Processing helix chain 'A' and resid 377 through 382 removed outlier: 3.885A pdb=" N ASN A 380 " --> pdb=" O SER A 377 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N MET A 382 " --> pdb=" O ARG A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 395 removed outlier: 3.612A pdb=" N MET A 391 " --> pdb=" O SER A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 405 removed outlier: 4.435A pdb=" N LYS A 405 " --> pdb=" O ASP A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 417 Processing helix chain 'A' and resid 430 through 442 Processing helix chain 'A' and resid 461 through 470 Processing helix chain 'A' and resid 495 through 504 Processing helix chain 'A' and resid 535 through 547 Processing helix chain 'B' and resid 59 through 63 removed outlier: 3.729A pdb=" N GLU B 62 " --> pdb=" O PRO B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 83 Processing helix chain 'B' and resid 94 through 99 Processing helix chain 'B' and resid 111 through 113 No H-bonds generated for 'chain 'B' and resid 111 through 113' Processing helix chain 'B' and resid 118 through 134 removed outlier: 4.172A pdb=" N ILE B 122 " --> pdb=" O VAL B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 162 Processing helix chain 'B' and resid 174 through 185 removed outlier: 3.668A pdb=" N VAL B 178 " --> pdb=" O SER B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 213 Processing helix chain 'B' and resid 226 through 235 removed outlier: 3.857A pdb=" N HIS B 232 " --> pdb=" O ASN B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 244 Processing helix chain 'B' and resid 258 through 272 Processing helix chain 'B' and resid 290 through 295 removed outlier: 3.717A pdb=" N GLN B 295 " --> pdb=" O GLU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 320 removed outlier: 3.727A pdb=" N VAL B 319 " --> pdb=" O ASP B 316 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL B 320 " --> pdb=" O ARG B 317 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 316 through 320' Processing helix chain 'B' and resid 327 through 343 removed outlier: 3.518A pdb=" N GLY B 343 " --> pdb=" O ILE B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 361 removed outlier: 3.516A pdb=" N GLY B 351 " --> pdb=" O GLY B 347 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS B 359 " --> pdb=" O ALA B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 364 No H-bonds generated for 'chain 'B' and resid 362 through 364' Processing helix chain 'B' and resid 377 through 382 removed outlier: 3.885A pdb=" N ASN B 380 " --> pdb=" O SER B 377 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N MET B 382 " --> pdb=" O ARG B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 395 removed outlier: 3.612A pdb=" N MET B 391 " --> pdb=" O SER B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 405 removed outlier: 4.435A pdb=" N LYS B 405 " --> pdb=" O ASP B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 417 Processing helix chain 'B' and resid 430 through 442 Processing helix chain 'B' and resid 461 through 470 Processing helix chain 'B' and resid 495 through 504 Processing helix chain 'B' and resid 535 through 547 Processing sheet with id=AA1, first strand: chain 'A' and resid 89 through 92 removed outlier: 4.734A pdb=" N LEU A 105 " --> pdb=" O ILE A 92 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N MET A 250 " --> pdb=" O VAL A 371 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N ILE A 373 " --> pdb=" O MET A 250 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N VAL A 252 " --> pdb=" O ILE A 373 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N LEU A 251 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N VAL A 280 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ALA A 253 " --> pdb=" O VAL A 280 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 187 through 191 removed outlier: 6.097A pdb=" N ILE A 142 " --> pdb=" O ILE A 166 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N VAL A 168 " --> pdb=" O ILE A 142 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N GLU A 144 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N THR A 141 " --> pdb=" O HIS A 218 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 445 through 449 removed outlier: 3.982A pdb=" N GLY A 457 " --> pdb=" O VAL A 448 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 488 through 490 removed outlier: 6.763A pdb=" N HIS A 513 " --> pdb=" O VAL A 530 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N VAL A 530 " --> pdb=" O HIS A 513 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N GLN A 515 " --> pdb=" O GLN A 528 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLN A 528 " --> pdb=" O GLN A 515 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 89 through 92 removed outlier: 4.734A pdb=" N LEU B 105 " --> pdb=" O ILE B 92 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N MET B 250 " --> pdb=" O VAL B 371 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N ILE B 373 " --> pdb=" O MET B 250 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N VAL B 252 " --> pdb=" O ILE B 373 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N LEU B 251 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N VAL B 280 " --> pdb=" O LEU B 251 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ALA B 253 " --> pdb=" O VAL B 280 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 191 removed outlier: 6.097A pdb=" N ILE B 142 " --> pdb=" O ILE B 166 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N VAL B 168 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N GLU B 144 " --> pdb=" O VAL B 168 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N THR B 141 " --> pdb=" O HIS B 218 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 445 through 449 removed outlier: 3.983A pdb=" N GLY B 457 " --> pdb=" O VAL B 448 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 488 through 490 removed outlier: 6.764A pdb=" N HIS B 513 " --> pdb=" O VAL B 530 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N VAL B 530 " --> pdb=" O HIS B 513 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N GLN B 515 " --> pdb=" O GLN B 528 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N GLN B 528 " --> pdb=" O GLN B 515 " (cutoff:3.500A) 311 hydrogen bonds defined for protein. 867 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: 3.80 Time building geometry restraints manager: 1.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.08: 7952 1.08 - 1.32: 1418 1.32 - 1.57: 6674 1.57 - 1.81: 64 1.81 - 2.05: 16 Bond restraints: 16124 Sorted by residual: bond pdb=" C3 KOU B 602 " pdb=" O3 KOU B 602 " ideal model delta sigma weight residual 1.328 1.425 -0.097 2.00e-02 2.50e+03 2.34e+01 bond pdb=" C3 KOU A 602 " pdb=" O3 KOU A 602 " ideal model delta sigma weight residual 1.328 1.424 -0.096 2.00e-02 2.50e+03 2.33e+01 bond pdb=" C4 KOU A 602 " pdb=" C4A KOU A 602 " ideal model delta sigma weight residual 1.464 1.558 -0.094 2.00e-02 2.50e+03 2.20e+01 bond pdb=" C4 KOU B 602 " pdb=" C4A KOU B 602 " ideal model delta sigma weight residual 1.464 1.558 -0.094 2.00e-02 2.50e+03 2.20e+01 bond pdb=" C5 KOU A 602 " pdb=" C5A KOU A 602 " ideal model delta sigma weight residual 1.505 1.569 -0.064 2.00e-02 2.50e+03 1.02e+01 ... (remaining 16119 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 28614 1.55 - 3.10: 566 3.10 - 4.64: 60 4.64 - 6.19: 12 6.19 - 7.74: 8 Bond angle restraints: 29260 Sorted by residual: angle pdb=" CA ARG B 498 " pdb=" CB ARG B 498 " pdb=" CG ARG B 498 " ideal model delta sigma weight residual 114.10 119.43 -5.33 2.00e+00 2.50e-01 7.10e+00 angle pdb=" CA ARG A 498 " pdb=" CB ARG A 498 " pdb=" CG ARG A 498 " ideal model delta sigma weight residual 114.10 119.37 -5.27 2.00e+00 2.50e-01 6.94e+00 angle pdb=" O3P KOU A 602 " pdb=" P KOU A 602 " pdb=" O4P KOU A 602 " ideal model delta sigma weight residual 100.35 108.09 -7.74 3.00e+00 1.11e-01 6.65e+00 angle pdb=" O KOU B 602 " pdb=" C KOU B 602 " pdb=" OXT KOU B 602 " ideal model delta sigma weight residual 127.50 119.79 7.71 3.00e+00 1.11e-01 6.61e+00 angle pdb=" O KOU A 602 " pdb=" C KOU A 602 " pdb=" OXT KOU A 602 " ideal model delta sigma weight residual 127.50 119.81 7.69 3.00e+00 1.11e-01 6.57e+00 ... (remaining 29255 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.10: 6735 16.10 - 32.20: 527 32.20 - 48.29: 145 48.29 - 64.39: 69 64.39 - 80.49: 16 Dihedral angle restraints: 7492 sinusoidal: 4214 harmonic: 3278 Sorted by residual: dihedral pdb=" CA GLU B 440 " pdb=" C GLU B 440 " pdb=" N LYS B 441 " pdb=" CA LYS B 441 " ideal model delta harmonic sigma weight residual 180.00 163.49 16.51 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA GLU A 440 " pdb=" C GLU A 440 " pdb=" N LYS A 441 " pdb=" CA LYS A 441 " ideal model delta harmonic sigma weight residual 180.00 163.52 16.48 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" C2D HEM B 601 " pdb=" C3D HEM B 601 " pdb=" CAD HEM B 601 " pdb=" CBD HEM B 601 " ideal model delta sinusoidal sigma weight residual 180.00 -110.88 -69.12 2 2.00e+01 2.50e-03 1.05e+01 ... (remaining 7489 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 734 0.028 - 0.055: 328 0.055 - 0.083: 83 0.083 - 0.111: 52 0.111 - 0.139: 45 Chirality restraints: 1242 Sorted by residual: chirality pdb=" CA ILE A 311 " pdb=" N ILE A 311 " pdb=" C ILE A 311 " pdb=" CB ILE A 311 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.80e-01 chirality pdb=" CA ILE B 311 " pdb=" N ILE B 311 " pdb=" C ILE B 311 " pdb=" CB ILE B 311 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.70e-01 chirality pdb=" CA ILE A 166 " pdb=" N ILE A 166 " pdb=" C ILE A 166 " pdb=" CB ILE A 166 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.70e-01 ... (remaining 1239 not shown) Planarity restraints: 2378 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 123 " 0.007 2.00e-02 2.50e+03 1.47e-02 2.16e+00 pdb=" C SER A 123 " -0.025 2.00e-02 2.50e+03 pdb=" O SER A 123 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU A 124 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 124 " -0.007 2.00e-02 2.50e+03 1.46e-02 2.14e+00 pdb=" C LEU B 124 " 0.025 2.00e-02 2.50e+03 pdb=" O LEU B 124 " -0.010 2.00e-02 2.50e+03 pdb=" N ARG B 125 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 123 " -0.007 2.00e-02 2.50e+03 1.46e-02 2.13e+00 pdb=" C SER B 123 " 0.025 2.00e-02 2.50e+03 pdb=" O SER B 123 " -0.010 2.00e-02 2.50e+03 pdb=" N LEU B 124 " -0.008 2.00e-02 2.50e+03 ... (remaining 2375 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.47: 10911 2.47 - 3.01: 37492 3.01 - 3.54: 43779 3.54 - 4.07: 59009 4.07 - 4.60: 85138 Nonbonded interactions: 236329 Sorted by model distance: nonbonded pdb="HD21 ASN A 228 " pdb=" HG1 THR A 257 " model vdw 1.943 2.100 nonbonded pdb="HD21 ASN B 228 " pdb=" HG1 THR B 257 " model vdw 1.943 2.100 nonbonded pdb=" HD3 ARG B 336 " pdb="HH11 ARG B 336 " model vdw 1.957 2.270 nonbonded pdb=" HD3 ARG A 336 " pdb="HH11 ARG A 336 " model vdw 1.957 2.270 nonbonded pdb=" HD2 ARG A 91 " pdb="HH11 ARG A 91 " model vdw 1.957 2.270 ... (remaining 236324 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 19.220 Find NCS groups from input model: 0.110 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:6.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 29.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 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 0.097 8156 Z= 0.209 Angle : 0.616 7.738 11072 Z= 0.304 Chirality : 0.042 0.139 1242 Planarity : 0.004 0.025 1416 Dihedral : 13.120 80.491 3056 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.26), residues: 1010 helix: -0.28 (0.27), residues: 400 sheet: -0.84 (0.39), residues: 158 loop : 0.01 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 276 TYR 0.009 0.001 TYR A 233 PHE 0.009 0.001 PHE A 111 TRP 0.009 0.001 TRP A 408 HIS 0.003 0.001 HIS A 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.21 ( 8154) covalent geometry : angle 0.61598 / 0.30 (11072) hydrogen bonds : bond 0.13158 / 8.44 ( 311) hydrogen bonds : angle 6.35862 / 4.53 ( 867) Misc. bond : bond 0.07483 / 3.75 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.428 Fit side-chains REVERT: A 247 LYS cc_start: 0.7702 (ptpp) cc_final: 0.7112 (tppp) REVERT: A 250 MET cc_start: 0.8537 (ttm) cc_final: 0.8300 (ttm) REVERT: A 416 GLU cc_start: 0.6794 (tt0) cc_final: 0.6378 (mm-30) REVERT: A 501 HIS cc_start: 0.7680 (m-70) cc_final: 0.7188 (t70) REVERT: B 86 ASP cc_start: 0.7042 (m-30) cc_final: 0.6818 (m-30) REVERT: B 247 LYS cc_start: 0.7801 (ptpp) cc_final: 0.7206 (tppp) REVERT: B 250 MET cc_start: 0.8541 (ttm) cc_final: 0.8306 (ttm) REVERT: B 416 GLU cc_start: 0.6711 (tt0) cc_final: 0.6315 (mm-30) REVERT: B 501 HIS cc_start: 0.7697 (m-70) cc_final: 0.7237 (t70) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 1.0413 time to fit residues: 128.8511 Evaluate side-chains 101 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 415 GLN A 507 HIS ** B 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 GLN B 507 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.165805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.134609 restraints weight = 21192.962| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.41 r_work: 0.3456 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 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 : 0.006 0.217 8156 Z= 0.199 Angle : 0.666 15.720 11072 Z= 0.319 Chirality : 0.045 0.155 1242 Planarity : 0.005 0.048 1416 Dihedral : 8.674 78.206 1130 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.78 % Favored : 98.02 % Rotamer: Outliers : 1.05 % Allowed : 7.69 % Favored : 91.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.27), residues: 1010 helix: 0.04 (0.26), residues: 400 sheet: -0.38 (0.40), residues: 160 loop : 0.78 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 317 TYR 0.013 0.003 TYR A 223 PHE 0.010 0.002 PHE A 111 TRP 0.008 0.001 TRP B 54 HIS 0.005 0.001 HIS A 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.20 ( 8154) covalent geometry : angle 0.66594 / 0.32 (11072) hydrogen bonds : bond 0.05110 / 3.37 ( 311) hydrogen bonds : angle 4.99341 / 3.63 ( 867) Misc. bond : bond 0.21516 / 10.79 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 109 time to evaluate : 0.441 Fit side-chains REVERT: A 247 LYS cc_start: 0.7896 (ptpp) cc_final: 0.7227 (tptt) REVERT: A 501 HIS cc_start: 0.7619 (m-70) cc_final: 0.6938 (t70) REVERT: B 247 LYS cc_start: 0.7907 (ptpp) cc_final: 0.7205 (tptt) REVERT: B 501 HIS cc_start: 0.7590 (m-70) cc_final: 0.6925 (t70) outliers start: 9 outliers final: 4 residues processed: 110 average time/residue: 1.1410 time to fit residues: 134.4824 Evaluate side-chains 108 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 104 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain B residue 540 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 89 optimal weight: 0.0170 chunk 41 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 overall best weight: 1.1222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.165284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.134239 restraints weight = 21409.067| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.42 r_work: 0.3453 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.132 8156 Z= 0.151 Angle : 0.577 11.079 11072 Z= 0.283 Chirality : 0.043 0.139 1242 Planarity : 0.004 0.043 1416 Dihedral : 8.767 83.268 1130 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.98 % Favored : 97.82 % Rotamer: Outliers : 1.28 % Allowed : 7.58 % Favored : 91.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.27), residues: 1010 helix: 0.27 (0.26), residues: 400 sheet: -0.30 (0.40), residues: 158 loop : 1.02 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 498 TYR 0.010 0.002 TYR A 223 PHE 0.009 0.002 PHE B 111 TRP 0.006 0.001 TRP A 390 HIS 0.004 0.001 HIS B 507 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 8154) covalent geometry : angle 0.57684 / 0.28 (11072) hydrogen bonds : bond 0.04525 / 2.96 ( 311) hydrogen bonds : angle 4.77118 / 3.47 ( 867) Misc. bond : bond 0.13221 / 6.63 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 0.351 Fit side-chains REVERT: A 97 LYS cc_start: 0.7448 (mttp) cc_final: 0.7180 (mppt) REVERT: A 137 LYS cc_start: 0.7790 (mppt) cc_final: 0.7485 (mptp) REVERT: A 501 HIS cc_start: 0.7536 (m-70) cc_final: 0.6908 (t70) REVERT: B 97 LYS cc_start: 0.7460 (mttp) cc_final: 0.7187 (mppt) REVERT: B 501 HIS cc_start: 0.7608 (m-70) cc_final: 0.6953 (t70) outliers start: 11 outliers final: 4 residues processed: 109 average time/residue: 1.0125 time to fit residues: 117.9303 Evaluate side-chains 107 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 103 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain B residue 540 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 78 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 18 optimal weight: 0.2980 chunk 50 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.163490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.131253 restraints weight = 20935.643| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.47 r_work: 0.3416 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.117 8156 Z= 0.123 Angle : 0.542 10.240 11072 Z= 0.266 Chirality : 0.043 0.139 1242 Planarity : 0.004 0.042 1416 Dihedral : 8.442 84.267 1130 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.98 % Favored : 97.82 % Rotamer: Outliers : 1.17 % Allowed : 8.16 % Favored : 90.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.27), residues: 1010 helix: 0.47 (0.27), residues: 400 sheet: -0.19 (0.40), residues: 158 loop : 1.12 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 121 TYR 0.009 0.002 TYR B 381 PHE 0.009 0.002 PHE A 111 TRP 0.005 0.001 TRP A 390 HIS 0.003 0.001 HIS A 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 ( 8154) covalent geometry : angle 0.54162 / 0.27 (11072) hydrogen bonds : bond 0.04052 / 2.67 ( 311) hydrogen bonds : angle 4.63900 / 3.38 ( 867) Misc. bond : bond 0.11636 / 5.84 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 0.451 Fit side-chains REVERT: A 97 LYS cc_start: 0.7488 (mttp) cc_final: 0.7229 (mppt) REVERT: A 460 THR cc_start: 0.8249 (m) cc_final: 0.7787 (p) REVERT: A 501 HIS cc_start: 0.7585 (m-70) cc_final: 0.6948 (t70) REVERT: B 97 LYS cc_start: 0.7481 (mttp) cc_final: 0.7226 (mppt) REVERT: B 137 LYS cc_start: 0.7766 (mppt) cc_final: 0.7439 (mptp) REVERT: B 460 THR cc_start: 0.8265 (m) cc_final: 0.7784 (p) REVERT: B 501 HIS cc_start: 0.7595 (m-70) cc_final: 0.6937 (t70) outliers start: 10 outliers final: 4 residues processed: 108 average time/residue: 0.9788 time to fit residues: 113.3226 Evaluate side-chains 107 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 103 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain B residue 540 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 42 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 1 optimal weight: 0.3980 chunk 56 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 chunk 76 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.164078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.133080 restraints weight = 21357.621| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 1.43 r_work: 0.3441 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 8156 Z= 0.142 Angle : 0.561 10.731 11072 Z= 0.275 Chirality : 0.043 0.139 1242 Planarity : 0.004 0.043 1416 Dihedral : 8.954 89.299 1130 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.78 % Favored : 98.02 % Rotamer: Outliers : 1.05 % Allowed : 8.97 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.27), residues: 1010 helix: 0.51 (0.27), residues: 400 sheet: -0.09 (0.40), residues: 158 loop : 1.29 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 121 TYR 0.009 0.002 TYR B 381 PHE 0.009 0.002 PHE B 111 TRP 0.007 0.001 TRP A 390 HIS 0.004 0.001 HIS A 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 ( 8154) covalent geometry : angle 0.56084 / 0.27 (11072) hydrogen bonds : bond 0.04293 / 2.84 ( 311) hydrogen bonds : angle 4.62787 / 3.38 ( 867) Misc. bond : bond 0.11177 / 5.61 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 109 time to evaluate : 0.494 Fit side-chains REVERT: A 97 LYS cc_start: 0.7492 (mttp) cc_final: 0.7203 (mppt) REVERT: A 137 LYS cc_start: 0.7753 (mppt) cc_final: 0.7488 (mptp) REVERT: A 247 LYS cc_start: 0.8227 (ptpp) cc_final: 0.7235 (tppp) REVERT: A 460 THR cc_start: 0.8179 (m) cc_final: 0.7888 (p) REVERT: A 501 HIS cc_start: 0.7624 (m-70) cc_final: 0.6984 (t70) REVERT: B 97 LYS cc_start: 0.7499 (mttp) cc_final: 0.7207 (mppt) REVERT: B 137 LYS cc_start: 0.7740 (mppt) cc_final: 0.7444 (mptp) REVERT: B 247 LYS cc_start: 0.8235 (ptpp) cc_final: 0.7239 (tppp) REVERT: B 460 THR cc_start: 0.8188 (m) cc_final: 0.7852 (p) REVERT: B 501 HIS cc_start: 0.7626 (m-70) cc_final: 0.6966 (t70) outliers start: 9 outliers final: 4 residues processed: 111 average time/residue: 1.1900 time to fit residues: 141.3034 Evaluate side-chains 109 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 105 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain B residue 540 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 57 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.159993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.127965 restraints weight = 20828.707| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.42 r_work: 0.3374 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.126 8156 Z= 0.208 Angle : 0.648 12.146 11072 Z= 0.321 Chirality : 0.045 0.152 1242 Planarity : 0.005 0.061 1416 Dihedral : 8.942 75.670 1130 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.88 % Favored : 97.92 % Rotamer: Outliers : 1.40 % Allowed : 8.28 % Favored : 90.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.27), residues: 1010 helix: 0.31 (0.26), residues: 390 sheet: -0.22 (0.39), residues: 158 loop : 1.30 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 91 TYR 0.012 0.003 TYR A 381 PHE 0.009 0.002 PHE A 531 TRP 0.010 0.002 TRP A 390 HIS 0.003 0.001 HIS B 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.21 ( 8154) covalent geometry : angle 0.64808 / 0.32 (11072) hydrogen bonds : bond 0.05017 / 3.33 ( 311) hydrogen bonds : angle 4.86209 / 3.56 ( 867) Misc. bond : bond 0.12596 / 6.32 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.434 Fit side-chains REVERT: A 97 LYS cc_start: 0.7508 (mttp) cc_final: 0.7204 (mppt) REVERT: A 137 LYS cc_start: 0.7766 (mppt) cc_final: 0.7482 (mptp) REVERT: A 440 GLU cc_start: 0.5540 (OUTLIER) cc_final: 0.5282 (tt0) REVERT: A 460 THR cc_start: 0.8234 (m) cc_final: 0.7870 (p) REVERT: A 501 HIS cc_start: 0.7572 (m-70) cc_final: 0.6862 (t70) REVERT: A 540 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7634 (mp) REVERT: B 97 LYS cc_start: 0.7500 (mttp) cc_final: 0.7201 (mppt) REVERT: B 137 LYS cc_start: 0.7815 (mppt) cc_final: 0.7501 (mptp) REVERT: B 440 GLU cc_start: 0.5460 (OUTLIER) cc_final: 0.5219 (tt0) REVERT: B 460 THR cc_start: 0.8243 (m) cc_final: 0.7873 (p) REVERT: B 501 HIS cc_start: 0.7592 (m-70) cc_final: 0.6898 (t70) outliers start: 12 outliers final: 5 residues processed: 115 average time/residue: 1.0334 time to fit residues: 126.8343 Evaluate side-chains 117 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 440 GLU Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain B residue 540 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 85 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 ASN A 218 HIS B 216 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.160922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.129816 restraints weight = 20996.348| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.42 r_work: 0.3399 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.123 8156 Z= 0.209 Angle : 0.644 12.255 11072 Z= 0.317 Chirality : 0.045 0.149 1242 Planarity : 0.005 0.057 1416 Dihedral : 8.797 75.359 1130 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.88 % Favored : 97.92 % Rotamer: Outliers : 1.86 % Allowed : 9.21 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.27), residues: 1010 helix: 0.22 (0.26), residues: 390 sheet: -0.07 (0.39), residues: 156 loop : 1.23 (0.31), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 91 TYR 0.011 0.003 TYR A 223 PHE 0.011 0.002 PHE A 531 TRP 0.010 0.002 TRP A 390 HIS 0.004 0.001 HIS A 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.21 ( 8154) covalent geometry : angle 0.64393 / 0.32 (11072) hydrogen bonds : bond 0.05012 / 3.32 ( 311) hydrogen bonds : angle 4.87497 / 3.57 ( 867) Misc. bond : bond 0.12236 / 6.14 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.443 Fit side-chains REVERT: A 97 LYS cc_start: 0.7561 (mttp) cc_final: 0.7216 (mppt) REVERT: A 292 GLU cc_start: 0.6980 (mp0) cc_final: 0.6740 (mp0) REVERT: A 440 GLU cc_start: 0.5611 (OUTLIER) cc_final: 0.5408 (tt0) REVERT: A 460 THR cc_start: 0.8208 (m) cc_final: 0.7838 (p) REVERT: A 501 HIS cc_start: 0.7601 (m-70) cc_final: 0.6889 (t70) REVERT: A 540 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7644 (mp) REVERT: B 97 LYS cc_start: 0.7559 (mttp) cc_final: 0.7219 (mppt) REVERT: B 137 LYS cc_start: 0.7797 (mppt) cc_final: 0.7481 (mptp) REVERT: B 460 THR cc_start: 0.8210 (m) cc_final: 0.7869 (p) REVERT: B 501 HIS cc_start: 0.7592 (m-70) cc_final: 0.6894 (t70) outliers start: 16 outliers final: 6 residues processed: 117 average time/residue: 1.1673 time to fit residues: 145.3734 Evaluate side-chains 116 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 108 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 440 GLU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 483 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 9 optimal weight: 0.3980 chunk 51 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 ASN ** B 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.161919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.130374 restraints weight = 20843.031| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.43 r_work: 0.3407 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.113 8156 Z= 0.163 Angle : 0.600 11.322 11072 Z= 0.294 Chirality : 0.044 0.142 1242 Planarity : 0.005 0.047 1416 Dihedral : 8.409 73.158 1130 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.98 % Favored : 97.82 % Rotamer: Outliers : 1.75 % Allowed : 9.79 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.27), residues: 1010 helix: 0.41 (0.27), residues: 390 sheet: -0.02 (0.39), residues: 156 loop : 1.27 (0.31), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 121 TYR 0.010 0.002 TYR B 381 PHE 0.011 0.002 PHE B 111 TRP 0.008 0.001 TRP A 390 HIS 0.004 0.001 HIS B 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 ( 8154) covalent geometry : angle 0.60005 / 0.29 (11072) hydrogen bonds : bond 0.04519 / 3.00 ( 311) hydrogen bonds : angle 4.75701 / 3.48 ( 867) Misc. bond : bond 0.11170 / 5.61 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 0.326 Fit side-chains REVERT: A 97 LYS cc_start: 0.7539 (mttp) cc_final: 0.7195 (mppt) REVERT: A 292 GLU cc_start: 0.7066 (mp0) cc_final: 0.6835 (mp0) REVERT: A 460 THR cc_start: 0.8213 (m) cc_final: 0.7886 (p) REVERT: A 501 HIS cc_start: 0.7551 (m-70) cc_final: 0.6844 (t70) REVERT: A 540 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7654 (mp) REVERT: B 97 LYS cc_start: 0.7539 (mttp) cc_final: 0.7198 (mppt) REVERT: B 137 LYS cc_start: 0.7793 (mppt) cc_final: 0.7481 (mptp) REVERT: B 460 THR cc_start: 0.8209 (m) cc_final: 0.7886 (p) REVERT: B 501 HIS cc_start: 0.7547 (m-70) cc_final: 0.6867 (t70) outliers start: 15 outliers final: 6 residues processed: 111 average time/residue: 1.0849 time to fit residues: 128.6759 Evaluate side-chains 110 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 103 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 483 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 33 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 ASN B 216 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.161119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.130071 restraints weight = 21101.268| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.42 r_work: 0.3402 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.117 8156 Z= 0.193 Angle : 0.630 12.021 11072 Z= 0.310 Chirality : 0.045 0.146 1242 Planarity : 0.005 0.056 1416 Dihedral : 8.682 74.785 1130 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.88 % Favored : 97.92 % Rotamer: Outliers : 1.52 % Allowed : 10.02 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.27), residues: 1010 helix: 0.27 (0.26), residues: 390 sheet: -0.06 (0.39), residues: 156 loop : 1.25 (0.31), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 91 TYR 0.011 0.003 TYR A 223 PHE 0.010 0.002 PHE B 111 TRP 0.009 0.001 TRP A 390 HIS 0.003 0.001 HIS A 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.19 ( 8154) covalent geometry : angle 0.63032 / 0.31 (11072) hydrogen bonds : bond 0.04878 / 3.23 ( 311) hydrogen bonds : angle 4.83722 / 3.54 ( 867) Misc. bond : bond 0.11555 / 5.81 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.7586 (mttp) cc_final: 0.7217 (mppt) REVERT: A 137 LYS cc_start: 0.7790 (mppt) cc_final: 0.7512 (mptp) REVERT: A 292 GLU cc_start: 0.7069 (mp0) cc_final: 0.6786 (mp0) REVERT: A 460 THR cc_start: 0.8198 (m) cc_final: 0.7867 (p) REVERT: A 501 HIS cc_start: 0.7565 (m-70) cc_final: 0.6857 (t70) REVERT: A 540 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7638 (mp) REVERT: B 97 LYS cc_start: 0.7578 (mttp) cc_final: 0.7207 (mppt) REVERT: B 137 LYS cc_start: 0.7816 (mppt) cc_final: 0.7499 (mptp) REVERT: B 460 THR cc_start: 0.8199 (m) cc_final: 0.7902 (p) REVERT: B 501 HIS cc_start: 0.7575 (m-70) cc_final: 0.6882 (t70) outliers start: 13 outliers final: 9 residues processed: 111 average time/residue: 1.0045 time to fit residues: 118.9399 Evaluate side-chains 115 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 483 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 24 optimal weight: 0.1980 chunk 88 optimal weight: 1.9990 chunk 74 optimal weight: 0.1980 chunk 9 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 ASN B 216 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.163277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.132525 restraints weight = 21208.756| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 1.42 r_work: 0.3432 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 8156 Z= 0.130 Angle : 0.571 10.578 11072 Z= 0.279 Chirality : 0.043 0.137 1242 Planarity : 0.004 0.041 1416 Dihedral : 7.989 70.524 1130 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.18 % Favored : 97.62 % Rotamer: Outliers : 1.05 % Allowed : 10.96 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.27), residues: 1010 helix: 0.52 (0.27), residues: 400 sheet: 0.08 (0.40), residues: 152 loop : 1.33 (0.31), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 121 TYR 0.010 0.002 TYR B 381 PHE 0.011 0.001 PHE B 111 TRP 0.007 0.001 TRP A 390 HIS 0.004 0.001 HIS B 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 ( 8154) covalent geometry : angle 0.57127 / 0.28 (11072) hydrogen bonds : bond 0.04075 / 2.70 ( 311) hydrogen bonds : angle 4.62211 / 3.37 ( 867) Misc. bond : bond 0.10090 / 5.07 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 109 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.7558 (mttp) cc_final: 0.7206 (mppt) REVERT: A 247 LYS cc_start: 0.8163 (ptpp) cc_final: 0.7154 (tppp) REVERT: A 292 GLU cc_start: 0.7074 (mp0) cc_final: 0.6863 (mp0) REVERT: A 460 THR cc_start: 0.8164 (m) cc_final: 0.7876 (p) REVERT: A 501 HIS cc_start: 0.7554 (m-70) cc_final: 0.6867 (t70) REVERT: B 97 LYS cc_start: 0.7551 (mttp) cc_final: 0.7201 (mppt) REVERT: B 137 LYS cc_start: 0.7801 (mppt) cc_final: 0.7471 (mptp) REVERT: B 247 LYS cc_start: 0.8185 (ptpp) cc_final: 0.7174 (tppp) REVERT: B 460 THR cc_start: 0.8173 (m) cc_final: 0.7897 (p) REVERT: B 501 HIS cc_start: 0.7564 (m-70) cc_final: 0.6858 (t70) outliers start: 9 outliers final: 8 residues processed: 114 average time/residue: 1.1027 time to fit residues: 134.0451 Evaluate side-chains 116 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 108 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 393 GLN Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 483 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 40 optimal weight: 3.9990 chunk 53 optimal weight: 0.2980 chunk 37 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 chunk 59 optimal weight: 0.3980 chunk 22 optimal weight: 1.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.164157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.133489 restraints weight = 21002.690| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 1.42 r_work: 0.3443 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 8156 Z= 0.116 Angle : 0.536 10.417 11072 Z= 0.262 Chirality : 0.042 0.140 1242 Planarity : 0.004 0.040 1416 Dihedral : 7.782 67.279 1130 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.82 % Allowed : 11.54 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.27), residues: 1010 helix: 0.64 (0.27), residues: 400 sheet: 0.08 (0.40), residues: 152 loop : 1.36 (0.31), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 121 TYR 0.009 0.002 TYR B 381 PHE 0.011 0.001 PHE B 111 TRP 0.007 0.001 TRP A 390 HIS 0.005 0.001 HIS B 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 ( 8154) covalent geometry : angle 0.53626 / 0.26 (11072) hydrogen bonds : bond 0.03867 / 2.56 ( 311) hydrogen bonds : angle 4.52826 / 3.31 ( 867) Misc. bond : bond 0.09000 / 4.52 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5991.69 seconds wall clock time: 101 minutes 52.68 seconds (6112.68 seconds total)