Starting phenix.real_space_refine on Sat Aug 23 05:51:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k1l_36794/08_2025/8k1l_36794.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k1l_36794/08_2025/8k1l_36794.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k1l_36794/08_2025/8k1l_36794.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k1l_36794/08_2025/8k1l_36794.map" model { file = "/net/cci-nas-00/data/ceres_data/8k1l_36794/08_2025/8k1l_36794.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k1l_36794/08_2025/8k1l_36794.cif" } resolution = 3.44 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= -0.002 sd= 0.037 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 Al 1 5.89 5 S 69 5.16 5 C 6420 2.51 5 N 1671 2.21 5 O 1861 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10026 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 979, 7657 Classifications: {'peptide': 979} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 44, 'TRANS': 934} Chain: "B" Number of atoms: 2364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2364 Classifications: {'peptide': 292} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 274} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'ALF': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.51, per 1000 atoms: 0.25 Number of scatterers: 10026 At special positions: 0 Unit cell: (88.736, 103.776, 166.192, 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) S 69 16.00 Al 1 13.00 F 4 9.00 O 1861 8.00 N 1671 7.00 C 6420 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 165 " - pdb=" SG CYS B 177 " distance=2.03 Simple disulfide: pdb=" SG CYS B 188 " - pdb=" SG CYS B 202 " distance=2.03 Simple disulfide: pdb=" SG CYS B 254 " - pdb=" SG CYS B 311 " distance=2.03 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: 0.96 Conformation dependent library (CDL) restraints added in 391.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2356 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 9 sheets defined 47.7% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 24 through 33 Processing helix chain 'A' and resid 41 through 52 Processing helix chain 'A' and resid 64 through 73 removed outlier: 3.528A pdb=" N LYS A 68 " --> pdb=" O PRO A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 99 Processing helix chain 'A' and resid 105 through 128 removed outlier: 4.114A pdb=" N TYR A 125 " --> pdb=" O GLY A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 138 Processing helix chain 'A' and resid 150 through 153 Processing helix chain 'A' and resid 212 through 216 removed outlier: 3.895A pdb=" N THR A 216 " --> pdb=" O PRO A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 253 Processing helix chain 'A' and resid 259 through 284 Processing helix chain 'A' and resid 284 through 289 removed outlier: 3.958A pdb=" N PHE A 288 " --> pdb=" O ALA A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 305 removed outlier: 3.923A pdb=" N GLY A 303 " --> pdb=" O ILE A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 330 removed outlier: 3.589A pdb=" N LYS A 330 " --> pdb=" O LYS A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 345 removed outlier: 3.756A pdb=" N GLU A 342 " --> pdb=" O GLU A 339 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N THR A 343 " --> pdb=" O ALA A 340 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU A 344 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 405 Processing helix chain 'A' and resid 427 through 442 Processing helix chain 'A' and resid 444 through 451 Processing helix chain 'A' and resid 485 through 491 removed outlier: 4.084A pdb=" N GLU A 491 " --> pdb=" O GLU A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 523 removed outlier: 3.674A pdb=" N MET A 523 " --> pdb=" O GLU A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 584 Processing helix chain 'A' and resid 595 through 607 Processing helix chain 'A' and resid 615 through 624 Processing helix chain 'A' and resid 641 through 647 removed outlier: 3.594A pdb=" N ASP A 647 " --> pdb=" O ASN A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 660 removed outlier: 3.528A pdb=" N TYR A 660 " --> pdb=" O ILE A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 682 removed outlier: 3.849A pdb=" N LEU A 674 " --> pdb=" O PRO A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 703 Processing helix chain 'A' and resid 714 through 720 Processing helix chain 'A' and resid 731 through 755 removed outlier: 3.521A pdb=" N THR A 735 " --> pdb=" O ALA A 731 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR A 753 " --> pdb=" O LYS A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 770 Proline residue: A 764 - end of helix Processing helix chain 'A' and resid 778 through 787 removed outlier: 3.507A pdb=" N CYS A 784 " --> pdb=" O VAL A 780 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE A 785 " --> pdb=" O THR A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 790 No H-bonds generated for 'chain 'A' and resid 788 through 790' Processing helix chain 'A' and resid 791 through 797 Processing helix chain 'A' and resid 798 through 800 No H-bonds generated for 'chain 'A' and resid 798 through 800' Processing helix chain 'A' and resid 819 through 827 Processing helix chain 'A' and resid 828 through 850 removed outlier: 3.520A pdb=" N MET A 833 " --> pdb=" O GLN A 829 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR A 841 " --> pdb=" O GLY A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 857 removed outlier: 3.654A pdb=" N PHE A 857 " --> pdb=" O PRO A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 865 removed outlier: 3.568A pdb=" N GLU A 864 " --> pdb=" O ARG A 860 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER A 865 " --> pdb=" O LYS A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 912 removed outlier: 4.186A pdb=" N THR A 905 " --> pdb=" O ILE A 901 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP A 906 " --> pdb=" O VAL A 902 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR A 912 " --> pdb=" O ILE A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 921 Processing helix chain 'A' and resid 924 through 942 Processing helix chain 'A' and resid 964 through 984 Processing helix chain 'A' and resid 988 through 993 Processing helix chain 'B' and resid 59 through 90 Processing helix chain 'B' and resid 138 through 149 Processing helix chain 'B' and resid 153 through 159 removed outlier: 3.854A pdb=" N SER B 158 " --> pdb=" O THR B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 185 Processing helix chain 'B' and resid 189 through 196 removed outlier: 5.673A pdb=" N PHE B 194 " --> pdb=" O GLU B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 242 Processing helix chain 'B' and resid 243 through 248 Processing helix chain 'B' and resid 258 through 265 removed outlier: 4.223A pdb=" N GLU B 263 " --> pdb=" O ALA B 259 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 147 through 148 removed outlier: 3.963A pdb=" N PHE A 147 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLY A 233 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ARG A 232 " --> pdb=" O THR A 183 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE A 234 " --> pdb=" O ARG A 181 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ASP A 179 " --> pdb=" O ILE A 236 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 189 through 190 Processing sheet with id=AA3, first strand: chain 'A' and resid 333 through 335 removed outlier: 6.889A pdb=" N VAL A 687 " --> pdb=" O ILE A 705 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N VAL A 707 " --> pdb=" O VAL A 687 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N VAL A 689 " --> pdb=" O VAL A 707 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N MET A 709 " --> pdb=" O VAL A 689 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N VAL A 588 " --> pdb=" O ILE A 663 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N PHE A 665 " --> pdb=" O VAL A 588 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N MET A 590 " --> pdb=" O PHE A 665 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ALA A 638 " --> pdb=" O VAL A 664 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 373 through 376 removed outlier: 3.609A pdb=" N VAL A 375 " --> pdb=" O MET A 368 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N HIS A 367 " --> pdb=" O SER A 565 " (cutoff:3.500A) removed outlier: 9.921A pdb=" N LEU A 558 " --> pdb=" O GLU A 534 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N GLU A 534 " --> pdb=" O LEU A 558 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N PHE A 560 " --> pdb=" O ASP A 532 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N ASP A 532 " --> pdb=" O PHE A 560 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N TYR A 478 " --> pdb=" O LEU A 535 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS A 483 " --> pdb=" O GLN A 466 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN A 466 " --> pdb=" O LYS A 483 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL A 467 " --> pdb=" O GLU A 456 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLU A 456 " --> pdb=" O VAL A 467 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL A 469 " --> pdb=" O VAL A 454 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 373 through 376 removed outlier: 3.609A pdb=" N VAL A 375 " --> pdb=" O MET A 368 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N HIS A 367 " --> pdb=" O SER A 565 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N CYS A 493 " --> pdb=" O LEU A 558 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N PHE A 560 " --> pdb=" O CYS A 493 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N THR A 495 " --> pdb=" O PHE A 560 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N GLY A 562 " --> pdb=" O THR A 495 " (cutoff:3.500A) removed outlier: 9.240A pdb=" N LEU A 497 " --> pdb=" O GLY A 562 " (cutoff:3.500A) removed outlier: 12.386A pdb=" N MET A 564 " --> pdb=" O LEU A 497 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 409 through 410 removed outlier: 4.166A pdb=" N GLU A 409 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 871 through 872 Processing sheet with id=AA8, first strand: chain 'B' and resid 112 through 114 Processing sheet with id=AA9, first strand: chain 'B' and resid 127 through 130 removed outlier: 5.975A pdb=" N ILE B 128 " --> pdb=" O ARG B 334 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N MET B 335 " --> pdb=" O GLN B 305 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLN B 305 " --> pdb=" O MET B 335 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TRP B 251 " --> pdb=" O TRP B 314 " (cutoff:3.500A) 453 hydrogen bonds defined for protein. 1293 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: 1.78 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2575 1.33 - 1.45: 2001 1.45 - 1.58: 5566 1.58 - 1.70: 0 1.70 - 1.82: 115 Bond restraints: 10257 Sorted by residual: bond pdb=" F1 ALF A1001 " pdb="AL ALF A1001 " ideal model delta sigma weight residual 1.684 1.785 -0.101 2.00e-02 2.50e+03 2.53e+01 bond pdb=" F2 ALF A1001 " pdb="AL ALF A1001 " ideal model delta sigma weight residual 1.685 1.785 -0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" F3 ALF A1001 " pdb="AL ALF A1001 " ideal model delta sigma weight residual 1.685 1.783 -0.098 2.00e-02 2.50e+03 2.40e+01 bond pdb=" F4 ALF A1001 " pdb="AL ALF A1001 " ideal model delta sigma weight residual 1.686 1.783 -0.097 2.00e-02 2.50e+03 2.36e+01 bond pdb=" N ILE A 180 " pdb=" CA ILE A 180 " ideal model delta sigma weight residual 1.458 1.492 -0.035 1.14e-02 7.69e+03 9.39e+00 ... (remaining 10252 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.24: 13893 14.24 - 28.49: 4 28.49 - 42.73: 0 42.73 - 56.98: 0 56.98 - 71.22: 2 Bond angle restraints: 13899 Sorted by residual: angle pdb=" F1 ALF A1001 " pdb="AL ALF A1001 " pdb=" F2 ALF A1001 " ideal model delta sigma weight residual 108.68 179.90 -71.22 3.00e+00 1.11e-01 5.64e+02 angle pdb=" F3 ALF A1001 " pdb="AL ALF A1001 " pdb=" F4 ALF A1001 " ideal model delta sigma weight residual 109.63 179.36 -69.73 3.00e+00 1.11e-01 5.40e+02 angle pdb=" F2 ALF A1001 " pdb="AL ALF A1001 " pdb=" F4 ALF A1001 " ideal model delta sigma weight residual 110.21 90.25 19.96 3.00e+00 1.11e-01 4.43e+01 angle pdb=" F1 ALF A1001 " pdb="AL ALF A1001 " pdb=" F3 ALF A1001 " ideal model delta sigma weight residual 109.69 89.90 19.79 3.00e+00 1.11e-01 4.35e+01 angle pdb=" F2 ALF A1001 " pdb="AL ALF A1001 " pdb=" F3 ALF A1001 " ideal model delta sigma weight residual 109.59 90.02 19.57 3.00e+00 1.11e-01 4.26e+01 ... (remaining 13894 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 5208 17.13 - 34.27: 722 34.27 - 51.40: 163 51.40 - 68.54: 38 68.54 - 85.67: 8 Dihedral angle restraints: 6139 sinusoidal: 2472 harmonic: 3667 Sorted by residual: dihedral pdb=" CB CYS B 188 " pdb=" SG CYS B 188 " pdb=" SG CYS B 202 " pdb=" CB CYS B 202 " ideal model delta sinusoidal sigma weight residual 93.00 159.64 -66.64 1 1.00e+01 1.00e-02 5.79e+01 dihedral pdb=" CA TYR B 280 " pdb=" C TYR B 280 " pdb=" N TYR B 281 " pdb=" CA TYR B 281 " ideal model delta harmonic sigma weight residual -180.00 -150.38 -29.62 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" CA SER A 406 " pdb=" C SER A 406 " pdb=" N ARG A 407 " pdb=" CA ARG A 407 " ideal model delta harmonic sigma weight residual 180.00 158.95 21.05 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 6136 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1239 0.052 - 0.103: 238 0.103 - 0.155: 51 0.155 - 0.206: 9 0.206 - 0.258: 3 Chirality restraints: 1540 Sorted by residual: chirality pdb=" CB ILE A 759 " pdb=" CA ILE A 759 " pdb=" CG1 ILE A 759 " pdb=" CG2 ILE A 759 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CA ILE A 625 " pdb=" N ILE A 625 " pdb=" C ILE A 625 " pdb=" CB ILE A 625 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CG LEU B 76 " pdb=" CB LEU B 76 " pdb=" CD1 LEU B 76 " pdb=" CD2 LEU B 76 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 1537 not shown) Planarity restraints: 1786 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 622 " 0.616 9.50e-02 1.11e+02 2.76e-01 4.65e+01 pdb=" NE ARG A 622 " -0.038 2.00e-02 2.50e+03 pdb=" CZ ARG A 622 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 622 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 622 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 983 " -0.335 9.50e-02 1.11e+02 1.50e-01 1.38e+01 pdb=" NE ARG A 983 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG A 983 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 983 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 983 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 175 " -0.237 9.50e-02 1.11e+02 1.06e-01 6.95e+00 pdb=" NE ARG A 175 " 0.014 2.00e-02 2.50e+03 pdb=" CZ ARG A 175 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 175 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 175 " -0.008 2.00e-02 2.50e+03 ... (remaining 1783 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 195 2.63 - 3.20: 9671 3.20 - 3.77: 15847 3.77 - 4.33: 21704 4.33 - 4.90: 35452 Nonbonded interactions: 82869 Sorted by model distance: nonbonded pdb=" O ALA A 431 " pdb=" CE LYS A 435 " model vdw 2.067 3.440 nonbonded pdb=" OD2 ASP A 353 " pdb=" F2 ALF A1001 " model vdw 2.125 2.990 nonbonded pdb=" O ASP B 227 " pdb=" OD1 ASP B 227 " model vdw 2.146 3.040 nonbonded pdb=" O GLY A 312 " pdb=" OG1 THR A 316 " model vdw 2.179 3.040 nonbonded pdb=" OD1 ASP A 353 " pdb=" F3 ALF A1001 " model vdw 2.179 2.990 ... (remaining 82864 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.640 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: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.010 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 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 : 0.004 0.101 10260 Z= 0.251 Angle : 1.168 71.224 13905 Z= 0.518 Chirality : 0.046 0.258 1540 Planarity : 0.009 0.276 1786 Dihedral : 16.417 85.672 3774 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 19.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 0.37 % Allowed : 24.06 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -1.16 (0.24), residues: 1267 helix: -0.05 (0.22), residues: 562 sheet: -1.08 (0.49), residues: 129 loop : -1.36 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 214 TYR 0.024 0.001 TYR B 281 PHE 0.011 0.001 PHE A 989 TRP 0.034 0.002 TRP B 63 HIS 0.008 0.001 HIS B 187 Details of bonding type rmsd covalent geometry : bond 0.00443 (10257) covalent geometry : angle 1.16838 (13899) SS BOND : bond 0.00182 ( 3) SS BOND : angle 1.25131 ( 6) hydrogen bonds : bond 0.22489 ( 447) hydrogen bonds : angle 8.15990 ( 1293) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 117 time to evaluate : 0.390 Fit side-chains REVERT: A 523 MET cc_start: 0.8016 (mpp) cc_final: 0.7549 (pmm) outliers start: 4 outliers final: 3 residues processed: 120 average time/residue: 0.1090 time to fit residues: 18.6449 Evaluate side-chains 115 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 112 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain A residue 627 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 7.9990 chunk 49 optimal weight: 9.9990 chunk 97 optimal weight: 0.0070 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 overall best weight: 1.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.124953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.090404 restraints weight = 20099.728| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 3.09 r_work: 0.3186 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.0970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 10260 Z= 0.215 Angle : 0.670 10.436 13905 Z= 0.344 Chirality : 0.044 0.246 1540 Planarity : 0.005 0.043 1786 Dihedral : 4.629 28.292 1373 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.47 % Favored : 93.45 % Rotamer: Outliers : 3.57 % Allowed : 22.51 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.62 (0.24), residues: 1267 helix: 0.59 (0.22), residues: 565 sheet: -1.19 (0.44), residues: 140 loop : -1.19 (0.27), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 622 TYR 0.018 0.001 TYR A 465 PHE 0.012 0.001 PHE A 410 TRP 0.018 0.001 TRP B 63 HIS 0.004 0.001 HIS A 470 Details of bonding type rmsd covalent geometry : bond 0.00516 (10257) covalent geometry : angle 0.66975 (13899) SS BOND : bond 0.00196 ( 3) SS BOND : angle 1.28213 ( 6) hydrogen bonds : bond 0.04981 ( 447) hydrogen bonds : angle 5.25186 ( 1293) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 119 time to evaluate : 0.408 Fit side-chains revert: symmetry clash REVERT: A 30 ARG cc_start: 0.7527 (mmp-170) cc_final: 0.7256 (mmp-170) REVERT: A 465 TYR cc_start: 0.7491 (p90) cc_final: 0.7269 (p90) REVERT: B 56 MET cc_start: 0.7424 (tpt) cc_final: 0.7078 (tpt) outliers start: 39 outliers final: 29 residues processed: 150 average time/residue: 0.1006 time to fit residues: 21.9270 Evaluate side-chains 140 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 111 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 70 CYS Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 156 GLN Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 991 GLU Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 202 CYS Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 309 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 52 optimal weight: 5.9990 chunk 95 optimal weight: 0.8980 chunk 48 optimal weight: 9.9990 chunk 42 optimal weight: 0.2980 chunk 101 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 985 ASN ** B 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.125804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.091592 restraints weight = 20033.172| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.99 r_work: 0.3193 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10260 Z= 0.172 Angle : 0.617 8.137 13905 Z= 0.315 Chirality : 0.043 0.243 1540 Planarity : 0.004 0.045 1786 Dihedral : 4.623 37.619 1371 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.00 % Favored : 93.92 % Rotamer: Outliers : 4.03 % Allowed : 22.05 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.42 (0.24), residues: 1267 helix: 0.83 (0.23), residues: 557 sheet: -1.20 (0.44), residues: 140 loop : -1.11 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 741 TYR 0.016 0.001 TYR B 281 PHE 0.022 0.001 PHE A 980 TRP 0.013 0.001 TRP B 63 HIS 0.004 0.001 HIS A 470 Details of bonding type rmsd covalent geometry : bond 0.00416 (10257) covalent geometry : angle 0.61697 (13899) SS BOND : bond 0.00144 ( 3) SS BOND : angle 1.16861 ( 6) hydrogen bonds : bond 0.04147 ( 447) hydrogen bonds : angle 4.77929 ( 1293) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 122 time to evaluate : 0.415 Fit side-chains REVERT: A 142 MET cc_start: 0.7822 (ppp) cc_final: 0.7589 (ppp) REVERT: A 368 MET cc_start: 0.6756 (mtm) cc_final: 0.6367 (mtm) REVERT: B 56 MET cc_start: 0.7351 (tpt) cc_final: 0.6969 (tpt) outliers start: 44 outliers final: 29 residues processed: 157 average time/residue: 0.0983 time to fit residues: 22.6171 Evaluate side-chains 140 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 111 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 70 CYS Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 202 CYS Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 309 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 93 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 63 optimal weight: 0.0270 chunk 73 optimal weight: 0.8980 chunk 39 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 123 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 118 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 overall best weight: 0.8840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 GLN A 372 GLN ** B 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.127007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.093062 restraints weight = 20176.985| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 3.14 r_work: 0.3208 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10260 Z= 0.140 Angle : 0.586 8.484 13905 Z= 0.297 Chirality : 0.042 0.259 1540 Planarity : 0.004 0.049 1786 Dihedral : 4.472 40.304 1371 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.16 % Favored : 93.69 % Rotamer: Outliers : 3.57 % Allowed : 22.32 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.23 (0.24), residues: 1267 helix: 0.98 (0.23), residues: 563 sheet: -0.82 (0.48), residues: 118 loop : -1.11 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 741 TYR 0.012 0.001 TYR A 768 PHE 0.009 0.001 PHE A 410 TRP 0.012 0.001 TRP B 63 HIS 0.003 0.001 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00336 (10257) covalent geometry : angle 0.58547 (13899) SS BOND : bond 0.00146 ( 3) SS BOND : angle 1.07717 ( 6) hydrogen bonds : bond 0.03612 ( 447) hydrogen bonds : angle 4.49894 ( 1293) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 124 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 509 MET cc_start: 0.7370 (mmp) cc_final: 0.7111 (mmp) REVERT: A 517 TYR cc_start: 0.8084 (t80) cc_final: 0.7832 (t80) REVERT: A 531 CYS cc_start: 0.6218 (OUTLIER) cc_final: 0.5649 (m) REVERT: B 55 PHE cc_start: 0.7389 (t80) cc_final: 0.6883 (t80) REVERT: B 56 MET cc_start: 0.7260 (tpt) cc_final: 0.6778 (tpt) outliers start: 39 outliers final: 27 residues processed: 154 average time/residue: 0.1016 time to fit residues: 22.5604 Evaluate side-chains 143 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 115 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 97 TYR Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 156 GLN Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 515 ASN Chi-restraints excluded: chain A residue 531 CYS Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 301 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 91 optimal weight: 0.9980 chunk 50 optimal weight: 7.9990 chunk 67 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 60 optimal weight: 8.9990 chunk 28 optimal weight: 0.7980 chunk 118 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.127483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.093759 restraints weight = 20082.119| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 3.16 r_work: 0.3214 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10260 Z= 0.126 Angle : 0.578 9.360 13905 Z= 0.289 Chirality : 0.042 0.258 1540 Planarity : 0.004 0.049 1786 Dihedral : 4.449 40.975 1371 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.52 % Favored : 94.32 % Rotamer: Outliers : 3.66 % Allowed : 22.60 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.15 (0.24), residues: 1267 helix: 1.09 (0.23), residues: 562 sheet: -0.77 (0.45), residues: 128 loop : -1.13 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 741 TYR 0.014 0.001 TYR A 465 PHE 0.025 0.001 PHE A 145 TRP 0.011 0.001 TRP B 63 HIS 0.002 0.001 HIS A 641 Details of bonding type rmsd covalent geometry : bond 0.00303 (10257) covalent geometry : angle 0.57790 (13899) SS BOND : bond 0.00632 ( 3) SS BOND : angle 1.18749 ( 6) hydrogen bonds : bond 0.03443 ( 447) hydrogen bonds : angle 4.37948 ( 1293) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 121 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.7999 (OUTLIER) cc_final: 0.6904 (ppp) REVERT: A 509 MET cc_start: 0.7356 (mmp) cc_final: 0.7138 (mmp) REVERT: A 517 TYR cc_start: 0.8018 (t80) cc_final: 0.7773 (t80) REVERT: A 531 CYS cc_start: 0.6186 (OUTLIER) cc_final: 0.5581 (m) REVERT: B 55 PHE cc_start: 0.7434 (t80) cc_final: 0.6946 (t80) REVERT: B 56 MET cc_start: 0.7260 (tpt) cc_final: 0.6755 (tpt) outliers start: 40 outliers final: 30 residues processed: 148 average time/residue: 0.0979 time to fit residues: 21.1406 Evaluate side-chains 147 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 115 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 CYS Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 97 TYR Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 515 ASN Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 531 CYS Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain B residue 70 TYR Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 202 CYS Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 301 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 118 optimal weight: 6.9990 chunk 94 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 87 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 109 optimal weight: 9.9990 chunk 75 optimal weight: 0.4980 chunk 59 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN ** B 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.128736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.094170 restraints weight = 19189.262| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.57 r_work: 0.3218 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10260 Z= 0.124 Angle : 0.558 10.355 13905 Z= 0.281 Chirality : 0.041 0.256 1540 Planarity : 0.004 0.051 1786 Dihedral : 4.360 42.046 1371 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.68 % Favored : 94.16 % Rotamer: Outliers : 3.75 % Allowed : 22.42 % Favored : 73.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.06 (0.24), residues: 1267 helix: 1.17 (0.23), residues: 565 sheet: -0.70 (0.45), residues: 128 loop : -1.10 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 633 TYR 0.013 0.001 TYR A 768 PHE 0.008 0.001 PHE B 194 TRP 0.012 0.001 TRP B 63 HIS 0.002 0.000 HIS A 641 Details of bonding type rmsd covalent geometry : bond 0.00299 (10257) covalent geometry : angle 0.55782 (13899) SS BOND : bond 0.00175 ( 3) SS BOND : angle 1.14848 ( 6) hydrogen bonds : bond 0.03298 ( 447) hydrogen bonds : angle 4.28209 ( 1293) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 126 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 TYR cc_start: 0.6206 (OUTLIER) cc_final: 0.5486 (p90) REVERT: A 509 MET cc_start: 0.7470 (mmp) cc_final: 0.7247 (mmp) REVERT: A 531 CYS cc_start: 0.6146 (OUTLIER) cc_final: 0.5709 (m) REVERT: B 55 PHE cc_start: 0.7320 (t80) cc_final: 0.6854 (t80) REVERT: B 56 MET cc_start: 0.6927 (tpt) cc_final: 0.6383 (tpt) outliers start: 41 outliers final: 29 residues processed: 155 average time/residue: 0.1016 time to fit residues: 22.6472 Evaluate side-chains 148 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 117 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 70 CYS Chi-restraints excluded: chain A residue 97 TYR Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 156 GLN Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 515 ASN Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 531 CYS Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 70 TYR Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 202 CYS Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 301 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 118 optimal weight: 4.9990 chunk 97 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 chunk 100 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 192 ASN ** 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 = 0.3851 r_free = 0.3851 target = 0.128921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.095916 restraints weight = 19234.884| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.88 r_work: 0.3212 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10260 Z= 0.128 Angle : 0.566 10.459 13905 Z= 0.283 Chirality : 0.041 0.261 1540 Planarity : 0.004 0.050 1786 Dihedral : 4.326 43.195 1371 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.00 % Favored : 93.84 % Rotamer: Outliers : 3.84 % Allowed : 22.78 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.08 (0.24), residues: 1267 helix: 1.15 (0.22), residues: 571 sheet: -0.62 (0.45), residues: 127 loop : -1.17 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 978 TYR 0.018 0.001 TYR A 465 PHE 0.028 0.001 PHE A 145 TRP 0.012 0.001 TRP B 63 HIS 0.002 0.001 HIS A 641 Details of bonding type rmsd covalent geometry : bond 0.00311 (10257) covalent geometry : angle 0.56603 (13899) SS BOND : bond 0.00149 ( 3) SS BOND : angle 1.13919 ( 6) hydrogen bonds : bond 0.03280 ( 447) hydrogen bonds : angle 4.22664 ( 1293) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 122 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 TYR cc_start: 0.6233 (OUTLIER) cc_final: 0.5576 (p90) REVERT: A 142 MET cc_start: 0.7976 (OUTLIER) cc_final: 0.6885 (ppp) REVERT: A 517 TYR cc_start: 0.7918 (t80) cc_final: 0.7488 (t80) REVERT: A 531 CYS cc_start: 0.6049 (OUTLIER) cc_final: 0.5661 (m) REVERT: A 709 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.8379 (mmm) REVERT: B 55 PHE cc_start: 0.7413 (t80) cc_final: 0.6950 (t80) REVERT: B 56 MET cc_start: 0.7017 (tpt) cc_final: 0.6481 (tpt) outliers start: 42 outliers final: 31 residues processed: 154 average time/residue: 0.1026 time to fit residues: 22.8944 Evaluate side-chains 152 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 117 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 70 CYS Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 97 TYR Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 515 ASN Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 531 CYS Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 70 TYR Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 202 CYS Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 301 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 6.9990 chunk 29 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 111 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 93 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 192 ASN ** 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 = 0.3823 r_free = 0.3823 target = 0.126790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.094021 restraints weight = 19139.182| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.62 r_work: 0.3180 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 10260 Z= 0.185 Angle : 0.619 11.358 13905 Z= 0.308 Chirality : 0.043 0.265 1540 Planarity : 0.004 0.050 1786 Dihedral : 4.480 48.744 1371 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.47 % Favored : 93.37 % Rotamer: Outliers : 3.93 % Allowed : 22.87 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.16 (0.24), residues: 1267 helix: 1.03 (0.22), residues: 573 sheet: -0.68 (0.45), residues: 126 loop : -1.14 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 633 TYR 0.015 0.001 TYR A 768 PHE 0.010 0.001 PHE B 331 TRP 0.011 0.001 TRP B 63 HIS 0.003 0.001 HIS A 641 Details of bonding type rmsd covalent geometry : bond 0.00450 (10257) covalent geometry : angle 0.61873 (13899) SS BOND : bond 0.00165 ( 3) SS BOND : angle 1.21860 ( 6) hydrogen bonds : bond 0.03543 ( 447) hydrogen bonds : angle 4.33562 ( 1293) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 117 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8169 (tppt) cc_final: 0.7957 (tppt) REVERT: A 52 TYR cc_start: 0.6282 (OUTLIER) cc_final: 0.5610 (p90) REVERT: A 142 MET cc_start: 0.7943 (OUTLIER) cc_final: 0.6861 (ppp) REVERT: A 517 TYR cc_start: 0.7941 (t80) cc_final: 0.7558 (t80) REVERT: A 531 CYS cc_start: 0.6083 (OUTLIER) cc_final: 0.5740 (m) REVERT: A 709 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.8478 (mmm) REVERT: B 55 PHE cc_start: 0.7431 (t80) cc_final: 0.7054 (t80) REVERT: B 56 MET cc_start: 0.7072 (tpt) cc_final: 0.6577 (tpt) outliers start: 43 outliers final: 35 residues processed: 149 average time/residue: 0.1021 time to fit residues: 22.1513 Evaluate side-chains 154 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 115 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 70 CYS Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 97 TYR Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 515 ASN Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 531 CYS Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 70 TYR Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 202 CYS Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 301 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 41 optimal weight: 8.9990 chunk 85 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 3 optimal weight: 9.9990 chunk 29 optimal weight: 0.7980 chunk 113 optimal weight: 0.5980 chunk 39 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 chunk 46 optimal weight: 9.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 192 ASN ** 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 = 0.3823 r_free = 0.3823 target = 0.126726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.094044 restraints weight = 19136.537| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.62 r_work: 0.3179 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10260 Z= 0.182 Angle : 0.629 12.369 13905 Z= 0.311 Chirality : 0.043 0.260 1540 Planarity : 0.004 0.049 1786 Dihedral : 4.574 54.800 1371 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.08 % Favored : 93.76 % Rotamer: Outliers : 3.93 % Allowed : 23.42 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.18 (0.24), residues: 1267 helix: 1.01 (0.22), residues: 573 sheet: -0.65 (0.46), residues: 117 loop : -1.15 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 633 TYR 0.016 0.001 TYR A 465 PHE 0.029 0.001 PHE A 145 TRP 0.013 0.001 TRP B 63 HIS 0.003 0.001 HIS A 641 Details of bonding type rmsd covalent geometry : bond 0.00443 (10257) covalent geometry : angle 0.62814 (13899) SS BOND : bond 0.00175 ( 3) SS BOND : angle 1.21294 ( 6) hydrogen bonds : bond 0.03520 ( 447) hydrogen bonds : angle 4.34062 ( 1293) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 118 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8203 (tppt) cc_final: 0.7972 (tppt) REVERT: A 52 TYR cc_start: 0.6432 (OUTLIER) cc_final: 0.5695 (p90) REVERT: A 149 ILE cc_start: 0.8210 (mt) cc_final: 0.7832 (mt) REVERT: A 175 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.7345 (ttp-170) REVERT: A 517 TYR cc_start: 0.7954 (t80) cc_final: 0.7626 (t80) REVERT: A 531 CYS cc_start: 0.6030 (OUTLIER) cc_final: 0.5452 (m) REVERT: A 709 MET cc_start: 0.8928 (OUTLIER) cc_final: 0.8530 (mmm) REVERT: B 55 PHE cc_start: 0.7565 (t80) cc_final: 0.7179 (t80) REVERT: B 56 MET cc_start: 0.7130 (tpt) cc_final: 0.6631 (tpt) outliers start: 43 outliers final: 36 residues processed: 151 average time/residue: 0.1056 time to fit residues: 22.6816 Evaluate side-chains 155 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 115 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 70 CYS Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 97 TYR Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 175 ARG Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 515 ASN Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 531 CYS Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 70 TYR Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 202 CYS Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 301 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 97 optimal weight: 9.9990 chunk 33 optimal weight: 0.7980 chunk 70 optimal weight: 0.6980 chunk 11 optimal weight: 0.1980 chunk 86 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 26 optimal weight: 0.0970 chunk 71 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 192 ASN ** 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 = 0.3859 r_free = 0.3859 target = 0.129302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.095432 restraints weight = 18843.084| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.45 r_work: 0.3238 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 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 : 0.003 0.035 10260 Z= 0.114 Angle : 0.603 13.287 13905 Z= 0.296 Chirality : 0.041 0.257 1540 Planarity : 0.004 0.049 1786 Dihedral : 4.459 58.527 1371 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.68 % Favored : 94.16 % Rotamer: Outliers : 3.20 % Allowed : 24.25 % Favored : 72.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.01 (0.24), residues: 1267 helix: 1.22 (0.22), residues: 573 sheet: -0.40 (0.47), residues: 116 loop : -1.15 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 633 TYR 0.019 0.001 TYR A 465 PHE 0.011 0.001 PHE A 665 TRP 0.015 0.001 TRP B 63 HIS 0.003 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00270 (10257) covalent geometry : angle 0.60253 (13899) SS BOND : bond 0.00144 ( 3) SS BOND : angle 1.13591 ( 6) hydrogen bonds : bond 0.03230 ( 447) hydrogen bonds : angle 4.17668 ( 1293) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 119 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 TYR cc_start: 0.6432 (OUTLIER) cc_final: 0.5750 (p90) REVERT: A 142 MET cc_start: 0.7965 (OUTLIER) cc_final: 0.7097 (ppp) REVERT: A 175 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.7373 (ttp-170) REVERT: A 517 TYR cc_start: 0.7881 (t80) cc_final: 0.7559 (t80) REVERT: A 709 MET cc_start: 0.8820 (OUTLIER) cc_final: 0.8400 (mmm) REVERT: B 48 TRP cc_start: 0.4992 (t-100) cc_final: 0.4652 (t-100) REVERT: B 55 PHE cc_start: 0.7369 (t80) cc_final: 0.7110 (t80) REVERT: B 56 MET cc_start: 0.7021 (tpt) cc_final: 0.6489 (tpt) outliers start: 35 outliers final: 29 residues processed: 144 average time/residue: 0.1110 time to fit residues: 22.6266 Evaluate side-chains 151 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 118 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 70 CYS Chi-restraints excluded: chain A residue 97 TYR Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 175 ARG Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 515 ASN Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 70 TYR Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 202 CYS Chi-restraints excluded: chain B residue 301 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 79 optimal weight: 0.9980 chunk 119 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 87 optimal weight: 0.0870 chunk 20 optimal weight: 0.3980 chunk 63 optimal weight: 2.9990 chunk 110 optimal weight: 0.2980 chunk 50 optimal weight: 0.0010 chunk 76 optimal weight: 0.5980 chunk 109 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.2764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 451 GLN B 192 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.131085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.097268 restraints weight = 19069.688| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.59 r_work: 0.3260 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10260 Z= 0.104 Angle : 0.586 13.122 13905 Z= 0.287 Chirality : 0.041 0.247 1540 Planarity : 0.004 0.055 1786 Dihedral : 4.278 57.558 1370 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.37 % Favored : 94.48 % Rotamer: Outliers : 2.84 % Allowed : 24.61 % Favored : 72.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.20 (0.24), residues: 1267 helix: 1.29 (0.23), residues: 579 sheet: -0.12 (0.48), residues: 116 loop : -1.03 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 667 TYR 0.011 0.001 TYR A 768 PHE 0.009 0.001 PHE A 665 TRP 0.014 0.001 TRP B 63 HIS 0.002 0.000 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00239 (10257) covalent geometry : angle 0.58518 (13899) SS BOND : bond 0.00117 ( 3) SS BOND : angle 1.12009 ( 6) hydrogen bonds : bond 0.03051 ( 447) hydrogen bonds : angle 4.06964 ( 1293) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2574.73 seconds wall clock time: 45 minutes 8.33 seconds (2708.33 seconds total)