Starting phenix.real_space_refine on Wed Aug 5 01:12:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uin_64198/08_2026/9uin_64198.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uin_64198/08_2026/9uin_64198.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9uin_64198/08_2026/9uin_64198.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uin_64198/08_2026/9uin_64198.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9uin_64198/08_2026/9uin_64198.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uin_64198/08_2026/9uin_64198.map" } resolution = 3.03 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= 0.039 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: 6 Type Number sf(0) Gaussians Cu 6 5.60 5 P 10 5.49 5 S 38 5.16 5 C 4854 2.51 5 N 1308 2.21 5 O 1474 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 67 residue(s): 0.00s 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: 7690 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 3741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3741 Classifications: {'peptide': 484} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 464} Chain: "A" Number of atoms: 3741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3741 Classifications: {'peptide': 484} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 464} Chain: "B" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 104 Unusual residues: {' CU': 3, 'FAD': 1, 'TXP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "A" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 104 Unusual residues: {' CU': 3, 'FAD': 1, 'TXP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 359 SG CYS B 59 34.739 33.083 38.357 1.00 55.17 S ATOM 391 SG CYS B 64 34.309 36.550 37.870 1.00 52.37 S ATOM 4100 SG CYS A 59 67.263 58.717 38.361 1.00 55.17 S ATOM 4132 SG CYS A 64 67.693 55.250 37.874 1.00 52.37 S Time building chain proxies: 1.51, per 1000 atoms: 0.20 Number of scatterers: 7690 At special positions: 0 Unit cell: (102.85, 92.65, 74.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cu 6 28.99 S 38 16.00 P 10 15.00 O 1474 8.00 N 1308 7.00 C 4854 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.52 Conformation dependent library (CDL) restraints added in 442.2 milliseconds 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1740 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 12 sheets defined 35.8% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'B' and resid 21 through 33 removed outlier: 3.578A pdb=" N LEU B 25 " --> pdb=" O GLY B 21 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN B 33 " --> pdb=" O LYS B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 62 removed outlier: 3.819A pdb=" N ASN B 61 " --> pdb=" O GLY B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 83 removed outlier: 3.857A pdb=" N GLN B 81 " --> pdb=" O GLY B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 87 removed outlier: 3.552A pdb=" N GLY B 87 " --> pdb=" O ARG B 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 84 through 87' Processing helix chain 'B' and resid 97 through 123 removed outlier: 3.678A pdb=" N MET B 101 " --> pdb=" O ASP B 97 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG B 121 " --> pdb=" O ARG B 117 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS B 123 " --> pdb=" O ALA B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 184 removed outlier: 3.628A pdb=" N LEU B 183 " --> pdb=" O SER B 179 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N PHE B 184 " --> pdb=" O SER B 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 179 through 184' Processing helix chain 'B' and resid 199 through 211 Processing helix chain 'B' and resid 229 through 244 Processing helix chain 'B' and resid 301 through 306 removed outlier: 4.367A pdb=" N VAL B 305 " --> pdb=" O GLY B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 359 removed outlier: 3.614A pdb=" N ALA B 346 " --> pdb=" O LEU B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 395 Processing helix chain 'B' and resid 409 through 413 removed outlier: 3.687A pdb=" N ILE B 413 " --> pdb=" O GLU B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 456 removed outlier: 3.567A pdb=" N VAL B 448 " --> pdb=" O ASN B 444 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY B 451 " --> pdb=" O GLU B 447 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE B 452 " --> pdb=" O VAL B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 468 Processing helix chain 'B' and resid 475 through 482 removed outlier: 3.516A pdb=" N VAL B 478 " --> pdb=" O CYS B 475 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU B 482 " --> pdb=" O PHE B 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 33 removed outlier: 3.578A pdb=" N LEU A 25 " --> pdb=" O GLY A 21 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 62 removed outlier: 3.819A pdb=" N ASN A 61 " --> pdb=" O GLY A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 83 removed outlier: 3.858A pdb=" N GLN A 81 " --> pdb=" O GLY A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 87 removed outlier: 3.552A pdb=" N GLY A 87 " --> pdb=" O ARG A 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 84 through 87' Processing helix chain 'A' and resid 97 through 123 removed outlier: 3.678A pdb=" N MET A 101 " --> pdb=" O ASP A 97 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG A 121 " --> pdb=" O ARG A 117 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 184 removed outlier: 3.628A pdb=" N LEU A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N PHE A 184 " --> pdb=" O SER A 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 179 through 184' Processing helix chain 'A' and resid 199 through 211 Processing helix chain 'A' and resid 229 through 244 Processing helix chain 'A' and resid 301 through 306 removed outlier: 4.366A pdb=" N VAL A 305 " --> pdb=" O GLY A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 359 removed outlier: 3.614A pdb=" N ALA A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 395 Processing helix chain 'A' and resid 408 through 413 removed outlier: 3.575A pdb=" N THR A 412 " --> pdb=" O PRO A 408 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ILE A 413 " --> pdb=" O LEU A 409 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 408 through 413' Processing helix chain 'A' and resid 444 through 456 removed outlier: 3.567A pdb=" N VAL A 448 " --> pdb=" O ASN A 444 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY A 451 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE A 452 " --> pdb=" O VAL A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 468 Processing helix chain 'A' and resid 475 through 482 removed outlier: 3.516A pdb=" N VAL A 478 " --> pdb=" O CYS A 475 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU A 482 " --> pdb=" O PHE A 479 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 126 through 128 removed outlier: 6.123A pdb=" N VAL B 40 " --> pdb=" O GLU B 128 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE B 16 " --> pdb=" O LEU B 158 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 134 through 136 removed outlier: 4.254A pdb=" N GLY B 136 " --> pdb=" O ARG B 139 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 163 through 165 Processing sheet with id=AA4, first strand: chain 'B' and resid 246 through 249 removed outlier: 3.673A pdb=" N LYS B 246 " --> pdb=" O VAL B 216 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU B 194 " --> pdb=" O MET B 288 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 251 through 260 removed outlier: 6.524A pdb=" N VAL B 270 " --> pdb=" O ILE B 254 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL B 256 " --> pdb=" O ARG B 268 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ARG B 268 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N GLN B 258 " --> pdb=" O ARG B 266 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ARG B 266 " --> pdb=" O GLN B 258 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 372 through 374 removed outlier: 6.583A pdb=" N ILE B 426 " --> pdb=" O VAL B 436 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N PHE B 438 " --> pdb=" O LYS B 424 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N LYS B 424 " --> pdb=" O PHE B 438 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N VAL B 440 " --> pdb=" O TYR B 422 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N TYR B 422 " --> pdb=" O VAL B 440 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N CYS B 421 " --> pdb=" O PHE B 406 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 126 through 128 removed outlier: 6.123A pdb=" N VAL A 40 " --> pdb=" O GLU A 128 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE A 16 " --> pdb=" O LEU A 158 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 134 through 136 removed outlier: 4.254A pdb=" N GLY A 136 " --> pdb=" O ARG A 139 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 163 through 165 Processing sheet with id=AB1, first strand: chain 'A' and resid 246 through 249 removed outlier: 3.674A pdb=" N LYS A 246 " --> pdb=" O VAL A 216 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N LEU A 194 " --> pdb=" O MET A 288 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 251 through 260 removed outlier: 6.523A pdb=" N VAL A 270 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL A 256 " --> pdb=" O ARG A 268 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ARG A 268 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N GLN A 258 " --> pdb=" O ARG A 266 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ARG A 266 " --> pdb=" O GLN A 258 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 372 through 374 removed outlier: 6.583A pdb=" N ILE A 426 " --> pdb=" O VAL A 436 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N PHE A 438 " --> pdb=" O LYS A 424 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N LYS A 424 " --> pdb=" O PHE A 438 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N VAL A 440 " --> pdb=" O TYR A 422 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N TYR A 422 " --> pdb=" O VAL A 440 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N CYS A 421 " --> pdb=" O PHE A 406 " (cutoff:3.500A) 273 hydrogen bonds defined for protein. 768 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: 1.07 Time building geometry restraints manager: 0.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1288 1.31 - 1.43: 2021 1.43 - 1.56: 4467 1.56 - 1.68: 22 1.68 - 1.81: 52 Bond restraints: 7850 Sorted by residual: bond pdb=" C3' TXP B 501 " pdb=" C4' TXP B 501 " ideal model delta sigma weight residual 1.544 1.294 0.250 2.00e-02 2.50e+03 1.56e+02 bond pdb=" C3' TXP A 501 " pdb=" C4' TXP A 501 " ideal model delta sigma weight residual 1.544 1.295 0.249 2.00e-02 2.50e+03 1.55e+02 bond pdb="C1'A TXP A 501 " pdb="C2'A TXP A 501 " ideal model delta sigma weight residual 1.526 1.300 0.226 2.00e-02 2.50e+03 1.28e+02 bond pdb="C1'A TXP B 501 " pdb="C2'A TXP B 501 " ideal model delta sigma weight residual 1.526 1.300 0.226 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C1' TXP B 501 " pdb=" C2' TXP B 501 " ideal model delta sigma weight residual 1.530 1.328 0.202 2.00e-02 2.50e+03 1.02e+02 ... (remaining 7845 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.87: 10436 2.87 - 5.73: 183 5.73 - 8.60: 31 8.60 - 11.47: 14 11.47 - 14.34: 6 Bond angle restraints: 10670 Sorted by residual: angle pdb=" N THR A 412 " pdb=" CA THR A 412 " pdb=" C THR A 412 " ideal model delta sigma weight residual 111.28 116.95 -5.67 1.09e+00 8.42e-01 2.71e+01 angle pdb=" N VAL B 220 " pdb=" CA VAL B 220 " pdb=" C VAL B 220 " ideal model delta sigma weight residual 107.80 114.94 -7.14 1.45e+00 4.76e-01 2.42e+01 angle pdb=" O1P FAD A 502 " pdb=" P FAD A 502 " pdb=" O2P FAD A 502 " ideal model delta sigma weight residual 122.50 108.16 14.34 3.00e+00 1.11e-01 2.28e+01 angle pdb=" O1P FAD B 502 " pdb=" P FAD B 502 " pdb=" O2P FAD B 502 " ideal model delta sigma weight residual 122.50 108.16 14.34 3.00e+00 1.11e-01 2.28e+01 angle pdb=" N GLY B 56 " pdb=" CA GLY B 56 " pdb=" C GLY B 56 " ideal model delta sigma weight residual 111.09 105.20 5.89 1.33e+00 5.65e-01 1.96e+01 ... (remaining 10665 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.79: 4518 34.79 - 69.58: 234 69.58 - 104.37: 42 104.37 - 139.17: 4 139.17 - 173.96: 2 Dihedral angle restraints: 4800 sinusoidal: 2052 harmonic: 2748 Sorted by residual: dihedral pdb=" O3 TXP B 501 " pdb=" PN TXP B 501 " pdb="O5'A TXP B 501 " pdb="C5'A TXP B 501 " ideal model delta sinusoidal sigma weight residual -146.00 27.96 -173.96 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O3 TXP A 501 " pdb=" PN TXP A 501 " pdb="O5'A TXP A 501 " pdb="C5'A TXP A 501 " ideal model delta sinusoidal sigma weight residual -146.00 20.76 -166.76 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" C3N TXP A 501 " pdb=" C2N TXP A 501 " pdb=" N1N TXP A 501 " pdb=" C6N TXP A 501 " ideal model delta sinusoidal sigma weight residual -67.86 59.04 -126.90 1 3.00e+01 1.11e-03 1.71e+01 ... (remaining 4797 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.064: 1188 1.064 - 2.128: 0 2.128 - 3.192: 0 3.192 - 4.256: 0 4.256 - 5.320: 2 Chirality restraints: 1190 Sorted by residual: chirality pdb=" C3N TXP B 501 " pdb=" C2N TXP B 501 " pdb=" C4N TXP B 501 " pdb=" C7N TXP B 501 " both_signs ideal model delta sigma weight residual False -2.65 2.67 -5.32 2.00e-01 2.50e+01 7.08e+02 chirality pdb=" C3N TXP A 501 " pdb=" C2N TXP A 501 " pdb=" C4N TXP A 501 " pdb=" C7N TXP A 501 " both_signs ideal model delta sigma weight residual False -2.65 2.67 -5.32 2.00e-01 2.50e+01 7.06e+02 chirality pdb=" CA THR A 412 " pdb=" N THR A 412 " pdb=" C THR A 412 " pdb=" CB THR A 412 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 1187 not shown) Planarity restraints: 1338 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 220 " 0.011 2.00e-02 2.50e+03 2.23e-02 4.99e+00 pdb=" C VAL A 220 " -0.039 2.00e-02 2.50e+03 pdb=" O VAL A 220 " 0.014 2.00e-02 2.50e+03 pdb=" N ARG A 221 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 200 " 0.026 2.00e-02 2.50e+03 1.52e-02 4.59e+00 pdb=" CG TYR A 200 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR A 200 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR A 200 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 200 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 200 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 200 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 200 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 200 " -0.025 2.00e-02 2.50e+03 1.49e-02 4.47e+00 pdb=" CG TYR B 200 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR B 200 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR B 200 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 200 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR B 200 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR B 200 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 200 " -0.007 2.00e-02 2.50e+03 ... (remaining 1335 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 763 2.73 - 3.27: 6771 3.27 - 3.81: 11417 3.81 - 4.36: 14516 4.36 - 4.90: 26021 Nonbonded interactions: 59488 Sorted by model distance: nonbonded pdb=" O SER A 185 " pdb=" OG SER A 185 " model vdw 2.184 3.040 nonbonded pdb=" O SER B 185 " pdb=" OG SER B 185 " model vdw 2.185 3.040 nonbonded pdb=" SG CYS B 59 " pdb="CU CU B 503 " model vdw 2.206 2.600 nonbonded pdb=" SG CYS A 59 " pdb="CU CU A 503 " model vdw 2.206 2.600 nonbonded pdb=" OG SER B 276 " pdb=" N GLU B 277 " model vdw 2.210 3.120 ... (remaining 59483 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 'B' selection = chain 'A' } 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: 2.910 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.980 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 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 : 0.015 0.250 7850 Z= 0.666 Angle : 1.102 14.337 10670 Z= 0.574 Chirality : 0.225 5.320 1190 Planarity : 0.005 0.044 1338 Dihedral : 20.788 173.958 3060 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.57 % Favored : 92.22 % Rotamer: Outliers : 6.16 % Allowed : 12.81 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -2.83 (0.23), residues: 964 helix: -0.84 (0.26), residues: 276 sheet: -1.83 (0.32), residues: 238 loop : -2.55 (0.24), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 52 TYR 0.033 0.003 TYR A 200 PHE 0.034 0.004 PHE A 208 TRP 0.012 0.002 TRP A 407 HIS 0.005 0.002 HIS B 96 Details of bonding type rmsd/Z covalent geometry : bond 0.01466 / 0.67 ( 7850) covalent geometry : angle 1.10237 / 0.57 (10670) hydrogen bonds : bond 0.17320 / 11.36 ( 273) hydrogen bonds : angle 6.33693 / 4.29 ( 768) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 78 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 128 GLU cc_start: 0.6984 (OUTLIER) cc_final: 0.6613 (tm-30) REVERT: B 334 ASP cc_start: 0.8527 (m-30) cc_final: 0.8250 (m-30) REVERT: A 128 GLU cc_start: 0.6985 (OUTLIER) cc_final: 0.6618 (tm-30) REVERT: A 334 ASP cc_start: 0.8524 (m-30) cc_final: 0.8259 (m-30) outliers start: 49 outliers final: 40 residues processed: 122 average time/residue: 0.1003 time to fit residues: 16.0441 Evaluate side-chains 108 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 66 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 208 PHE Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 320 ASP Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 64 CYS Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 250 GLN Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 493 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 234 ASN B 369 ASN B 419 ASN B 428 ASN A 234 ASN A 369 ASN A 419 ASN A 428 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.145207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.117237 restraints weight = 8929.460| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.16 r_work: 0.3238 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7850 Z= 0.118 Angle : 0.543 9.858 10670 Z= 0.277 Chirality : 0.045 0.144 1190 Planarity : 0.004 0.035 1338 Dihedral : 16.472 172.627 1366 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 4.77 % Allowed : 16.21 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -1.44 (0.25), residues: 964 helix: 1.08 (0.29), residues: 268 sheet: -1.07 (0.34), residues: 228 loop : -2.17 (0.25), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 139 TYR 0.023 0.001 TYR A 200 PHE 0.019 0.001 PHE A 208 TRP 0.009 0.001 TRP A 407 HIS 0.002 0.001 HIS A 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 ( 7850) covalent geometry : angle 0.54264 / 0.28 (10670) hydrogen bonds : bond 0.04398 / 2.86 ( 273) hydrogen bonds : angle 4.54433 / 3.11 ( 768) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 76 time to evaluate : 0.292 Fit side-chains REVERT: B 116 TYR cc_start: 0.7748 (m-80) cc_final: 0.7523 (m-80) REVERT: B 128 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7228 (tm-30) REVERT: B 152 TYR cc_start: 0.7572 (OUTLIER) cc_final: 0.7205 (p90) REVERT: B 337 GLU cc_start: 0.8080 (tt0) cc_final: 0.7859 (tt0) REVERT: A 128 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7236 (tm-30) REVERT: A 152 TYR cc_start: 0.7549 (OUTLIER) cc_final: 0.7182 (p90) REVERT: A 337 GLU cc_start: 0.8076 (tt0) cc_final: 0.7856 (tt0) outliers start: 38 outliers final: 25 residues processed: 111 average time/residue: 0.0885 time to fit residues: 13.6395 Evaluate side-chains 90 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 61 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 152 TYR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 64 CYS Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 250 GLN Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 493 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 54 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 48 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 42 optimal weight: 8.9990 chunk 65 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.146261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.119779 restraints weight = 8791.561| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.05 r_work: 0.3261 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7850 Z= 0.106 Angle : 0.505 9.556 10670 Z= 0.254 Chirality : 0.044 0.135 1190 Planarity : 0.004 0.040 1338 Dihedral : 14.021 159.401 1329 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.64 % Allowed : 16.71 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -0.99 (0.26), residues: 964 helix: 1.41 (0.30), residues: 280 sheet: -0.70 (0.35), residues: 230 loop : -2.02 (0.25), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 139 TYR 0.024 0.001 TYR A 200 PHE 0.015 0.001 PHE A 208 TRP 0.007 0.001 TRP A 98 HIS 0.001 0.001 HIS B 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 ( 7850) covalent geometry : angle 0.50472 / 0.25 (10670) hydrogen bonds : bond 0.04032 / 2.62 ( 273) hydrogen bonds : angle 4.23168 / 2.90 ( 768) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 73 time to evaluate : 0.295 Fit side-chains REVERT: B 29 LYS cc_start: 0.8138 (OUTLIER) cc_final: 0.7812 (mttp) REVERT: B 116 TYR cc_start: 0.7545 (m-80) cc_final: 0.7000 (m-80) REVERT: B 152 TYR cc_start: 0.7505 (OUTLIER) cc_final: 0.7299 (p90) REVERT: A 29 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7819 (mttp) REVERT: A 116 TYR cc_start: 0.7680 (m-80) cc_final: 0.7207 (m-80) outliers start: 29 outliers final: 21 residues processed: 98 average time/residue: 0.0957 time to fit residues: 12.8604 Evaluate side-chains 84 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 60 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 LYS Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 152 TYR Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 208 PHE Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 493 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 62 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 70 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 1 optimal weight: 8.9990 chunk 14 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.143652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.116015 restraints weight = 8717.477| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.15 r_work: 0.3220 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7850 Z= 0.127 Angle : 0.518 9.774 10670 Z= 0.261 Chirality : 0.045 0.143 1190 Planarity : 0.004 0.038 1338 Dihedral : 12.402 116.504 1310 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.89 % Allowed : 17.09 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -0.74 (0.26), residues: 964 helix: 1.59 (0.30), residues: 280 sheet: -0.53 (0.35), residues: 230 loop : -1.86 (0.26), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 139 TYR 0.023 0.001 TYR B 200 PHE 0.017 0.002 PHE B 208 TRP 0.007 0.001 TRP A 88 HIS 0.001 0.001 HIS B 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 7850) covalent geometry : angle 0.51756 / 0.26 (10670) hydrogen bonds : bond 0.04366 / 2.83 ( 273) hydrogen bonds : angle 4.22483 / 2.91 ( 768) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 64 time to evaluate : 0.182 Fit side-chains REVERT: B 29 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7809 (mttp) REVERT: B 116 TYR cc_start: 0.7559 (m-80) cc_final: 0.7065 (m-80) REVERT: B 152 TYR cc_start: 0.7553 (OUTLIER) cc_final: 0.7350 (p90) REVERT: B 348 GLN cc_start: 0.7415 (tt0) cc_final: 0.7156 (mt0) REVERT: A 29 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7780 (mttp) REVERT: A 116 TYR cc_start: 0.7608 (m-80) cc_final: 0.7094 (m-80) REVERT: A 348 GLN cc_start: 0.7401 (tt0) cc_final: 0.7141 (mt0) outliers start: 31 outliers final: 23 residues processed: 89 average time/residue: 0.0878 time to fit residues: 10.9941 Evaluate side-chains 86 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 60 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 LYS Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 152 TYR Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 208 PHE Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 493 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 0.0060 chunk 62 optimal weight: 3.9990 chunk 44 optimal weight: 0.3980 chunk 30 optimal weight: 6.9990 chunk 79 optimal weight: 0.0980 chunk 0 optimal weight: 4.9990 chunk 20 optimal weight: 0.0770 chunk 53 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 76 optimal weight: 0.2980 chunk 80 optimal weight: 0.9980 overall best weight: 0.1754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.149673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.122905 restraints weight = 8591.196| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.11 r_work: 0.3316 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7850 Z= 0.075 Angle : 0.449 9.973 10670 Z= 0.223 Chirality : 0.042 0.145 1190 Planarity : 0.004 0.045 1338 Dihedral : 10.635 105.849 1310 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.51 % Allowed : 19.22 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -0.20 (0.27), residues: 964 helix: 1.85 (0.30), residues: 284 sheet: -0.04 (0.37), residues: 218 loop : -1.50 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 139 TYR 0.022 0.001 TYR A 200 PHE 0.008 0.001 PHE A 406 TRP 0.010 0.001 TRP B 98 HIS 0.001 0.000 HIS B 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00158 / 0.07 ( 7850) covalent geometry : angle 0.44852 / 0.22 (10670) hydrogen bonds : bond 0.02564 / 1.69 ( 273) hydrogen bonds : angle 3.92575 / 2.68 ( 768) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 83 time to evaluate : 0.245 Fit side-chains REVERT: B 116 TYR cc_start: 0.7434 (m-80) cc_final: 0.7110 (m-80) REVERT: B 348 GLN cc_start: 0.7413 (tt0) cc_final: 0.7168 (mt0) REVERT: A 116 TYR cc_start: 0.7474 (m-80) cc_final: 0.7170 (m-80) REVERT: A 348 GLN cc_start: 0.7417 (tt0) cc_final: 0.7172 (mt0) outliers start: 20 outliers final: 14 residues processed: 96 average time/residue: 0.0663 time to fit residues: 9.2099 Evaluate side-chains 87 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 208 PHE Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 250 GLN Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 493 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 45 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 82 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 75 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.143917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.116184 restraints weight = 8745.393| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.15 r_work: 0.3208 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 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 : 0.004 0.030 7850 Z= 0.144 Angle : 0.519 10.019 10670 Z= 0.259 Chirality : 0.045 0.147 1190 Planarity : 0.004 0.046 1338 Dihedral : 11.451 109.955 1310 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.27 % Allowed : 17.71 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -0.21 (0.27), residues: 964 helix: 1.83 (0.30), residues: 284 sheet: -0.15 (0.36), residues: 230 loop : -1.47 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 139 TYR 0.021 0.001 TYR B 200 PHE 0.018 0.002 PHE B 208 TRP 0.007 0.001 TRP A 88 HIS 0.002 0.001 HIS B 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.14 ( 7850) covalent geometry : angle 0.51880 / 0.26 (10670) hydrogen bonds : bond 0.04463 / 2.88 ( 273) hydrogen bonds : angle 4.12006 / 2.83 ( 768) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 61 time to evaluate : 0.297 Fit side-chains REVERT: B 116 TYR cc_start: 0.7537 (m-80) cc_final: 0.7102 (m-80) REVERT: B 348 GLN cc_start: 0.7446 (tt0) cc_final: 0.7165 (mt0) REVERT: B 394 PHE cc_start: 0.7929 (m-80) cc_final: 0.7726 (m-80) REVERT: A 116 TYR cc_start: 0.7590 (m-80) cc_final: 0.7119 (m-80) REVERT: A 348 GLN cc_start: 0.7435 (tt0) cc_final: 0.7153 (mt0) outliers start: 34 outliers final: 26 residues processed: 89 average time/residue: 0.0757 time to fit residues: 9.8186 Evaluate side-chains 86 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 60 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 208 PHE Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 410 GLU Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 250 GLN Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 493 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 3 optimal weight: 0.0670 chunk 19 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 49 optimal weight: 8.9990 chunk 60 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 40 optimal weight: 0.0470 chunk 58 optimal weight: 3.9990 overall best weight: 0.4416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.147611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.120225 restraints weight = 8606.988| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.13 r_work: 0.3274 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7850 Z= 0.081 Angle : 0.456 10.181 10670 Z= 0.227 Chirality : 0.043 0.146 1190 Planarity : 0.004 0.046 1338 Dihedral : 10.615 105.793 1310 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.89 % Allowed : 18.84 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.04 (0.27), residues: 964 helix: 1.98 (0.30), residues: 284 sheet: 0.19 (0.38), residues: 220 loop : -1.35 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 139 TYR 0.022 0.001 TYR A 200 PHE 0.008 0.001 PHE A 208 TRP 0.008 0.001 TRP A 98 HIS 0.001 0.000 HIS B 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00178 / 0.08 ( 7850) covalent geometry : angle 0.45582 / 0.23 (10670) hydrogen bonds : bond 0.03089 / 2.02 ( 273) hydrogen bonds : angle 3.92209 / 2.70 ( 768) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 65 time to evaluate : 0.266 Fit side-chains REVERT: B 116 TYR cc_start: 0.7516 (m-80) cc_final: 0.7115 (m-80) REVERT: A 116 TYR cc_start: 0.7594 (m-80) cc_final: 0.7256 (m-80) outliers start: 23 outliers final: 18 residues processed: 83 average time/residue: 0.0849 time to fit residues: 10.0142 Evaluate side-chains 78 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 60 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 208 PHE Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 250 GLN Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 493 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 46 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 76 optimal weight: 0.0020 chunk 39 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 12 optimal weight: 0.5980 chunk 1 optimal weight: 10.0000 chunk 72 optimal weight: 0.1980 chunk 45 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.147419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.119933 restraints weight = 8627.388| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.13 r_work: 0.3269 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7850 Z= 0.084 Angle : 0.451 9.906 10670 Z= 0.226 Chirality : 0.043 0.141 1190 Planarity : 0.004 0.049 1338 Dihedral : 10.307 105.677 1310 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.14 % Allowed : 18.72 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.14 (0.28), residues: 964 helix: 2.14 (0.31), residues: 280 sheet: 0.21 (0.38), residues: 222 loop : -1.31 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 139 TYR 0.020 0.001 TYR A 200 PHE 0.010 0.001 PHE B 208 TRP 0.007 0.001 TRP A 98 HIS 0.001 0.000 HIS B 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00186 / 0.08 ( 7850) covalent geometry : angle 0.45118 / 0.23 (10670) hydrogen bonds : bond 0.03260 / 2.12 ( 273) hydrogen bonds : angle 3.89976 / 2.68 ( 768) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 59 time to evaluate : 0.257 Fit side-chains REVERT: B 116 TYR cc_start: 0.7525 (m-80) cc_final: 0.7143 (m-80) REVERT: A 116 TYR cc_start: 0.7620 (m-80) cc_final: 0.7245 (m-80) outliers start: 25 outliers final: 24 residues processed: 79 average time/residue: 0.0686 time to fit residues: 7.8895 Evaluate side-chains 83 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 59 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 208 PHE Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 410 GLU Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 250 GLN Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 493 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 41 optimal weight: 2.9990 chunk 44 optimal weight: 0.0670 chunk 37 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.145954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.118488 restraints weight = 8661.461| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.13 r_work: 0.3256 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7850 Z= 0.097 Angle : 0.466 9.795 10670 Z= 0.233 Chirality : 0.043 0.139 1190 Planarity : 0.004 0.047 1338 Dihedral : 10.347 107.012 1310 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.39 % Allowed : 18.59 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.14 (0.28), residues: 964 helix: 2.13 (0.31), residues: 280 sheet: 0.24 (0.37), residues: 222 loop : -1.32 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 139 TYR 0.021 0.001 TYR A 200 PHE 0.011 0.001 PHE B 208 TRP 0.006 0.001 TRP B 98 HIS 0.001 0.000 HIS B 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 ( 7850) covalent geometry : angle 0.46571 / 0.23 (10670) hydrogen bonds : bond 0.03602 / 2.33 ( 273) hydrogen bonds : angle 3.95435 / 2.72 ( 768) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 60 time to evaluate : 0.235 Fit side-chains REVERT: B 116 TYR cc_start: 0.7539 (m-80) cc_final: 0.7140 (m-80) REVERT: A 116 TYR cc_start: 0.7636 (m-80) cc_final: 0.7244 (m-80) outliers start: 27 outliers final: 26 residues processed: 82 average time/residue: 0.0756 time to fit residues: 8.9401 Evaluate side-chains 84 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 58 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 208 PHE Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 410 GLU Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 250 GLN Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 493 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 91 optimal weight: 2.9990 chunk 12 optimal weight: 0.0970 chunk 70 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 21 optimal weight: 0.0470 chunk 85 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 81 GLN B 323 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.146675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.119227 restraints weight = 8626.913| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.13 r_work: 0.3265 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7850 Z= 0.089 Angle : 0.453 9.761 10670 Z= 0.227 Chirality : 0.043 0.138 1190 Planarity : 0.003 0.048 1338 Dihedral : 10.217 107.128 1310 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.39 % Allowed : 18.59 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.22 (0.28), residues: 964 helix: 2.15 (0.31), residues: 280 sheet: 0.35 (0.38), residues: 220 loop : -1.27 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 139 TYR 0.020 0.001 TYR A 200 PHE 0.010 0.001 PHE B 208 TRP 0.007 0.001 TRP B 98 HIS 0.001 0.000 HIS B 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.09 ( 7850) covalent geometry : angle 0.45336 / 0.23 (10670) hydrogen bonds : bond 0.03379 / 2.19 ( 273) hydrogen bonds : angle 3.92675 / 2.71 ( 768) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 58 time to evaluate : 0.212 Fit side-chains REVERT: B 116 TYR cc_start: 0.7540 (m-80) cc_final: 0.7143 (m-80) REVERT: A 116 TYR cc_start: 0.7620 (m-80) cc_final: 0.7239 (m-80) outliers start: 27 outliers final: 27 residues processed: 80 average time/residue: 0.0686 time to fit residues: 8.0900 Evaluate side-chains 85 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 58 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 208 PHE Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 410 GLU Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 250 GLN Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 493 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 90 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 64 optimal weight: 0.0370 chunk 10 optimal weight: 0.2980 chunk 80 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.8462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.145584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.117989 restraints weight = 8674.672| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.14 r_work: 0.3246 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7850 Z= 0.104 Angle : 0.471 9.735 10670 Z= 0.236 Chirality : 0.044 0.139 1190 Planarity : 0.004 0.048 1338 Dihedral : 10.405 109.013 1310 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.64 % Allowed : 18.34 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.16 (0.28), residues: 964 helix: 2.12 (0.31), residues: 280 sheet: 0.21 (0.37), residues: 230 loop : -1.28 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 139 TYR 0.021 0.001 TYR B 200 PHE 0.012 0.001 PHE A 208 TRP 0.006 0.001 TRP B 88 HIS 0.001 0.000 HIS B 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.10 ( 7850) covalent geometry : angle 0.47086 / 0.24 (10670) hydrogen bonds : bond 0.03807 / 2.46 ( 273) hydrogen bonds : angle 3.98995 / 2.75 ( 768) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1923.26 seconds wall clock time: 33 minutes 32.25 seconds (2012.25 seconds total)