Starting phenix.real_space_refine on Mon Jul 28 06:19:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k1l_36794/07_2025/8k1l_36794.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k1l_36794/07_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_36794/07_2025/8k1l_36794.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k1l_36794/07_2025/8k1l_36794.map" model { file = "/net/cci-nas-00/data/ceres_data/8k1l_36794/07_2025/8k1l_36794.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k1l_36794/07_2025/8k1l_36794.cif" } resolution = 3.44 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.51, per 1000 atoms: 0.75 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: 2.52 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.07 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: 3.45 Time building geometry restraints manager: 3.02 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: 8.480 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 27.210 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.280 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.034 0.002 TRP B 63 HIS 0.008 0.001 HIS B 187 PHE 0.011 0.001 PHE A 989 TYR 0.024 0.001 TYR B 281 ARG 0.004 0.001 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.22489 ( 447) hydrogen bonds : angle 8.15990 ( 1293) SS BOND : bond 0.00182 ( 3) SS BOND : angle 1.25131 ( 6) covalent geometry : bond 0.00443 (10257) covalent geometry : angle 1.16838 (13899) *********************** 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 : 1.042 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: 0.2359 time to fit residues: 40.6448 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 : 1.040 ------------------------------------------------------------------------------- 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 106 optimal weight: 2.9990 chunk 95 optimal weight: 0.5980 chunk 52 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 98 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 60 optimal weight: 10.0000 chunk 73 optimal weight: 0.5980 chunk 114 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 = 0.3846 r_free = 0.3846 target = 0.125280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.090869 restraints weight = 19994.637| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.99 r_work: 0.3184 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 10260 Z= 0.200 Angle : 0.667 11.838 13905 Z= 0.341 Chirality : 0.044 0.240 1540 Planarity : 0.005 0.043 1786 Dihedral : 4.617 28.030 1373 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.16 % Favored : 93.76 % Rotamer: Outliers : 3.57 % Allowed : 22.05 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.24), residues: 1267 helix: 0.61 (0.22), residues: 565 sheet: -1.18 (0.44), residues: 140 loop : -1.18 (0.27), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 63 HIS 0.004 0.001 HIS A 470 PHE 0.013 0.001 PHE A 989 TYR 0.019 0.001 TYR A 465 ARG 0.005 0.001 ARG A 992 Details of bonding type rmsd hydrogen bonds : bond 0.04815 ( 447) hydrogen bonds : angle 5.17742 ( 1293) SS BOND : bond 0.00186 ( 3) SS BOND : angle 1.28650 ( 6) covalent geometry : bond 0.00479 (10257) covalent geometry : angle 0.66684 (13899) *********************** 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 159 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 120 time to evaluate : 1.107 Fit side-chains revert: symmetry clash REVERT: A 465 TYR cc_start: 0.7405 (p90) cc_final: 0.7186 (p90) REVERT: B 56 MET cc_start: 0.7412 (tpt) cc_final: 0.7065 (tpt) outliers start: 39 outliers final: 30 residues processed: 151 average time/residue: 0.2159 time to fit residues: 47.5288 Evaluate side-chains 142 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 112 time to evaluate : 1.321 ------------------------------------------------------------------------------- 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 250 LEU 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 84 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 115 optimal weight: 0.4980 chunk 38 optimal weight: 8.9990 chunk 2 optimal weight: 9.9990 chunk 15 optimal weight: 4.9990 chunk 33 optimal weight: 0.0040 chunk 69 optimal weight: 0.3980 overall best weight: 0.5792 ------------------------------------------------------------------------------- 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 = 0.3879 r_free = 0.3879 target = 0.127675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.093793 restraints weight = 20081.460| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 3.04 r_work: 0.3220 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10260 Z= 0.127 Angle : 0.593 7.919 13905 Z= 0.302 Chirality : 0.041 0.236 1540 Planarity : 0.004 0.046 1786 Dihedral : 4.500 37.536 1371 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.29 % Favored : 94.63 % Rotamer: Outliers : 3.29 % Allowed : 22.69 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.24), residues: 1267 helix: 0.97 (0.23), residues: 555 sheet: -1.19 (0.43), residues: 140 loop : -1.04 (0.27), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 63 HIS 0.004 0.001 HIS A 470 PHE 0.023 0.001 PHE A 145 TYR 0.015 0.001 TYR A 465 ARG 0.004 0.000 ARG A 741 Details of bonding type rmsd hydrogen bonds : bond 0.03951 ( 447) hydrogen bonds : angle 4.65911 ( 1293) SS BOND : bond 0.00127 ( 3) SS BOND : angle 1.08312 ( 6) covalent geometry : bond 0.00299 (10257) covalent geometry : angle 0.59226 (13899) *********************** 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 156 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 120 time to evaluate : 1.056 Fit side-chains revert: symmetry clash REVERT: A 142 MET cc_start: 0.7750 (ppp) cc_final: 0.7519 (ppp) REVERT: B 56 MET cc_start: 0.7253 (tpt) cc_final: 0.6797 (tpt) outliers start: 36 outliers final: 20 residues processed: 149 average time/residue: 0.2062 time to fit residues: 44.5301 Evaluate side-chains 131 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 162 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 480 LEU Chi-restraints excluded: chain A residue 482 MET 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 813 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 301 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 37 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 chunk 94 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 109 optimal weight: 9.9990 chunk 116 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 chunk 38 optimal weight: 7.9990 chunk 14 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 360 GLN A 372 GLN ** B 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.125961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.091848 restraints weight = 19982.148| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 3.14 r_work: 0.3185 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1530 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= 0.175 Angle : 0.605 8.869 13905 Z= 0.306 Chirality : 0.043 0.255 1540 Planarity : 0.004 0.048 1786 Dihedral : 4.379 25.799 1370 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.16 % Favored : 93.76 % Rotamer: Outliers : 3.75 % Allowed : 22.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.24), residues: 1267 helix: 1.00 (0.23), residues: 556 sheet: -0.92 (0.45), residues: 128 loop : -1.09 (0.27), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 63 HIS 0.003 0.001 HIS A 414 PHE 0.010 0.001 PHE A 839 TYR 0.013 0.001 TYR B 281 ARG 0.004 0.000 ARG A 741 Details of bonding type rmsd hydrogen bonds : bond 0.03767 ( 447) hydrogen bonds : angle 4.56129 ( 1293) SS BOND : bond 0.00154 ( 3) SS BOND : angle 1.17069 ( 6) covalent geometry : bond 0.00425 (10257) covalent geometry : angle 0.60449 (13899) *********************** 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 164 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 123 time to evaluate : 1.041 Fit side-chains revert: symmetry clash REVERT: A 517 TYR cc_start: 0.8074 (t80) cc_final: 0.7826 (t80) REVERT: A 531 CYS cc_start: 0.6178 (OUTLIER) cc_final: 0.5564 (m) REVERT: B 55 PHE cc_start: 0.7452 (t80) cc_final: 0.7000 (t80) REVERT: B 56 MET cc_start: 0.7318 (tpt) cc_final: 0.6873 (tpt) outliers start: 41 outliers final: 25 residues processed: 156 average time/residue: 0.2221 time to fit residues: 50.4989 Evaluate side-chains 139 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 162 VAL Chi-restraints excluded: chain A residue 164 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 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 20 optimal weight: 0.4980 chunk 32 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 117 optimal weight: 0.5980 chunk 11 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 chunk 76 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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** ** 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 = 0.126173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.092319 restraints weight = 19874.002| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 3.01 r_work: 0.3207 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10260 Z= 0.159 Angle : 0.602 9.270 13905 Z= 0.302 Chirality : 0.042 0.260 1540 Planarity : 0.004 0.047 1786 Dihedral : 4.349 24.621 1370 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.08 % Favored : 93.76 % Rotamer: Outliers : 3.66 % Allowed : 22.87 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.24), residues: 1267 helix: 1.05 (0.23), residues: 556 sheet: -0.80 (0.45), residues: 128 loop : -1.09 (0.27), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 63 HIS 0.003 0.001 HIS A 641 PHE 0.025 0.001 PHE A 145 TYR 0.018 0.001 TYR A 842 ARG 0.004 0.000 ARG A 741 Details of bonding type rmsd hydrogen bonds : bond 0.03619 ( 447) hydrogen bonds : angle 4.44705 ( 1293) SS BOND : bond 0.00117 ( 3) SS BOND : angle 1.20753 ( 6) covalent geometry : bond 0.00387 (10257) covalent geometry : angle 0.60198 (13899) *********************** 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 159 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 119 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 509 MET cc_start: 0.7422 (mmp) cc_final: 0.7189 (mmp) REVERT: A 517 TYR cc_start: 0.8074 (t80) cc_final: 0.7827 (t80) REVERT: A 531 CYS cc_start: 0.6194 (OUTLIER) cc_final: 0.5628 (m) REVERT: A 564 MET cc_start: 0.8102 (mmp) cc_final: 0.7889 (mmt) REVERT: B 56 MET cc_start: 0.7286 (tpt) cc_final: 0.6805 (tpt) outliers start: 40 outliers final: 31 residues processed: 146 average time/residue: 0.2162 time to fit residues: 46.2740 Evaluate side-chains 148 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 116 time to evaluate : 1.191 ------------------------------------------------------------------------------- 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 168 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 480 LEU 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 759 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 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 110 optimal weight: 0.5980 chunk 11 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 120 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- 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 ** 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 = 0.3862 r_free = 0.3862 target = 0.126331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.092670 restraints weight = 19946.329| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 3.11 r_work: 0.3205 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10260 Z= 0.150 Angle : 0.583 10.022 13905 Z= 0.293 Chirality : 0.042 0.260 1540 Planarity : 0.004 0.049 1786 Dihedral : 4.293 23.195 1370 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.08 % Favored : 93.76 % Rotamer: Outliers : 3.84 % Allowed : 22.60 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.24), residues: 1267 helix: 1.06 (0.23), residues: 564 sheet: -0.75 (0.45), residues: 127 loop : -1.03 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 63 HIS 0.003 0.001 HIS A 641 PHE 0.010 0.001 PHE A 665 TYR 0.016 0.001 TYR A 842 ARG 0.009 0.000 ARG A 633 Details of bonding type rmsd hydrogen bonds : bond 0.03479 ( 447) hydrogen bonds : angle 4.35209 ( 1293) SS BOND : bond 0.00126 ( 3) SS BOND : angle 1.20835 ( 6) covalent geometry : bond 0.00364 (10257) covalent geometry : angle 0.58210 (13899) *********************** 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 162 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 120 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 TYR cc_start: 0.6247 (OUTLIER) cc_final: 0.5539 (p90) REVERT: A 142 MET cc_start: 0.8023 (OUTLIER) cc_final: 0.6835 (ppp) REVERT: A 509 MET cc_start: 0.7435 (mmp) cc_final: 0.7214 (mmp) REVERT: A 517 TYR cc_start: 0.8041 (t80) cc_final: 0.7833 (t80) REVERT: A 564 MET cc_start: 0.8135 (mmp) cc_final: 0.7929 (mmt) REVERT: A 709 MET cc_start: 0.8795 (OUTLIER) cc_final: 0.8429 (mmm) REVERT: B 55 PHE cc_start: 0.7493 (t80) cc_final: 0.7026 (t80) REVERT: B 56 MET cc_start: 0.7191 (tpt) cc_final: 0.6699 (tpt) outliers start: 42 outliers final: 31 residues processed: 150 average time/residue: 0.2092 time to fit residues: 45.8209 Evaluate side-chains 149 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 115 time to evaluate : 1.133 ------------------------------------------------------------------------------- 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 224 THR 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 38 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 59 optimal weight: 0.1980 chunk 13 optimal weight: 20.0000 chunk 26 optimal weight: 0.9990 chunk 95 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 82 optimal weight: 0.4980 chunk 18 optimal weight: 3.9990 chunk 54 optimal weight: 8.9990 chunk 15 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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** ** 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 = 0.3830 r_free = 0.3830 target = 0.127314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.092693 restraints weight = 19386.867| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.59 r_work: 0.3189 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10260 Z= 0.151 Angle : 0.585 10.523 13905 Z= 0.293 Chirality : 0.042 0.261 1540 Planarity : 0.004 0.049 1786 Dihedral : 4.264 22.473 1370 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.31 % Favored : 93.53 % Rotamer: Outliers : 4.48 % Allowed : 22.42 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.24), residues: 1267 helix: 1.05 (0.22), residues: 571 sheet: -0.63 (0.47), residues: 117 loop : -1.07 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 63 HIS 0.003 0.001 HIS A 267 PHE 0.010 0.001 PHE A 665 TYR 0.022 0.001 TYR A 842 ARG 0.004 0.000 ARG A 741 Details of bonding type rmsd hydrogen bonds : bond 0.03437 ( 447) hydrogen bonds : angle 4.31802 ( 1293) SS BOND : bond 0.00158 ( 3) SS BOND : angle 1.18590 ( 6) covalent geometry : bond 0.00367 (10257) covalent geometry : angle 0.58501 (13899) *********************** 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 167 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 118 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 TYR cc_start: 0.6242 (OUTLIER) cc_final: 0.5569 (p90) REVERT: A 142 MET cc_start: 0.7991 (OUTLIER) cc_final: 0.6884 (ppp) REVERT: A 509 MET cc_start: 0.7518 (mmp) cc_final: 0.7304 (mmp) REVERT: A 531 CYS cc_start: 0.6196 (OUTLIER) cc_final: 0.5676 (m) REVERT: A 709 MET cc_start: 0.8862 (OUTLIER) cc_final: 0.8451 (mmm) REVERT: B 55 PHE cc_start: 0.7385 (t80) cc_final: 0.7019 (t80) REVERT: B 56 MET cc_start: 0.6998 (tpt) cc_final: 0.6486 (tpt) outliers start: 49 outliers final: 35 residues processed: 156 average time/residue: 0.2191 time to fit residues: 49.9933 Evaluate side-chains 155 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 116 time to evaluate : 1.065 ------------------------------------------------------------------------------- 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 224 THR 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 489 ILE 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 555 ILE 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 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 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 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 42 optimal weight: 0.4980 chunk 111 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 119 optimal weight: 0.6980 chunk 57 optimal weight: 0.0170 chunk 72 optimal weight: 0.8980 chunk 122 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 74 optimal weight: 0.5980 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN ** 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 = 0.3856 r_free = 0.3856 target = 0.129324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.095124 restraints weight = 19198.211| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.58 r_work: 0.3228 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10260 Z= 0.110 Angle : 0.575 11.620 13905 Z= 0.285 Chirality : 0.041 0.257 1540 Planarity : 0.004 0.050 1786 Dihedral : 4.145 20.235 1370 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.68 % Favored : 94.24 % Rotamer: Outliers : 3.48 % Allowed : 23.79 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.24), residues: 1267 helix: 1.13 (0.22), residues: 578 sheet: -0.47 (0.48), residues: 116 loop : -1.09 (0.26), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 63 HIS 0.002 0.000 HIS A 267 PHE 0.010 0.001 PHE A 410 TYR 0.022 0.001 TYR A 842 ARG 0.008 0.000 ARG A 633 Details of bonding type rmsd hydrogen bonds : bond 0.03242 ( 447) hydrogen bonds : angle 4.21752 ( 1293) SS BOND : bond 0.00135 ( 3) SS BOND : angle 1.13543 ( 6) covalent geometry : bond 0.00259 (10257) covalent geometry : angle 0.57468 (13899) *********************** 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 162 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 124 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 TYR cc_start: 0.6218 (OUTLIER) cc_final: 0.5570 (p90) REVERT: A 142 MET cc_start: 0.7915 (OUTLIER) cc_final: 0.6846 (ppp) REVERT: A 517 TYR cc_start: 0.7911 (t80) cc_final: 0.7485 (t80) REVERT: A 531 CYS cc_start: 0.6056 (OUTLIER) cc_final: 0.5593 (m) REVERT: A 709 MET cc_start: 0.8801 (OUTLIER) cc_final: 0.8397 (mmm) REVERT: B 48 TRP cc_start: 0.4869 (t-100) cc_final: 0.4491 (t-100) REVERT: B 55 PHE cc_start: 0.7310 (t80) cc_final: 0.7021 (t80) REVERT: B 56 MET cc_start: 0.6894 (tpt) cc_final: 0.6384 (tpt) outliers start: 38 outliers final: 31 residues processed: 150 average time/residue: 0.2136 time to fit residues: 46.5303 Evaluate side-chains 151 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 116 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 TYR 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 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 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 555 ILE 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 63 TRP 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 198 LEU Chi-restraints excluded: chain B residue 202 CYS 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 122 optimal weight: 2.9990 chunk 59 optimal weight: 0.0370 chunk 71 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 47 optimal weight: 9.9990 chunk 90 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 16 optimal weight: 0.3980 chunk 28 optimal weight: 0.5980 overall best weight: 0.6062 ------------------------------------------------------------------------------- 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 = 0.129365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.096775 restraints weight = 19072.070| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.76 r_work: 0.3229 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2060 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= 0.116 Angle : 0.587 12.672 13905 Z= 0.289 Chirality : 0.041 0.257 1540 Planarity : 0.004 0.049 1786 Dihedral : 4.068 18.103 1370 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.92 % Favored : 94.00 % Rotamer: Outliers : 3.75 % Allowed : 23.88 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.24), residues: 1267 helix: 1.26 (0.22), residues: 572 sheet: -0.38 (0.48), residues: 116 loop : -1.08 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 63 HIS 0.003 0.000 HIS A 267 PHE 0.009 0.001 PHE A 410 TYR 0.024 0.001 TYR A 842 ARG 0.010 0.000 ARG A 633 Details of bonding type rmsd hydrogen bonds : bond 0.03188 ( 447) hydrogen bonds : angle 4.16166 ( 1293) SS BOND : bond 0.00131 ( 3) SS BOND : angle 1.14987 ( 6) covalent geometry : bond 0.00279 (10257) covalent geometry : angle 0.58629 (13899) *********************** 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 156 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 115 time to evaluate : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 TYR cc_start: 0.6298 (OUTLIER) cc_final: 0.5689 (p90) REVERT: A 517 TYR cc_start: 0.7796 (t80) cc_final: 0.7457 (t80) REVERT: A 531 CYS cc_start: 0.5996 (OUTLIER) cc_final: 0.5533 (m) REVERT: A 709 MET cc_start: 0.8804 (OUTLIER) cc_final: 0.8387 (mmm) REVERT: B 48 TRP cc_start: 0.5007 (t-100) cc_final: 0.4599 (t-100) REVERT: B 55 PHE cc_start: 0.7362 (t80) cc_final: 0.7037 (t80) REVERT: B 56 MET cc_start: 0.6995 (tpt) cc_final: 0.6492 (tpt) outliers start: 41 outliers final: 32 residues processed: 143 average time/residue: 0.2213 time to fit residues: 46.7213 Evaluate side-chains 149 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 114 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 97 TYR Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 164 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 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 531 CYS Chi-restraints excluded: chain A residue 555 ILE 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 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 58 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 11 optimal weight: 0.0970 chunk 37 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 113 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 108 optimal weight: 8.9990 chunk 107 optimal weight: 0.6980 chunk 117 optimal weight: 0.5980 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 ** 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 = 0.3866 r_free = 0.3866 target = 0.129934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.097268 restraints weight = 19203.667| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.75 r_work: 0.3245 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10260 Z= 0.114 Angle : 0.587 13.067 13905 Z= 0.289 Chirality : 0.041 0.255 1540 Planarity : 0.004 0.051 1786 Dihedral : 4.024 16.306 1370 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.45 % Favored : 94.48 % Rotamer: Outliers : 3.29 % Allowed : 24.25 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.24), residues: 1267 helix: 1.31 (0.22), residues: 572 sheet: -0.24 (0.48), residues: 116 loop : -1.07 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 63 HIS 0.003 0.000 HIS A 267 PHE 0.029 0.001 PHE A 145 TYR 0.025 0.001 TYR A 842 ARG 0.011 0.000 ARG A 633 Details of bonding type rmsd hydrogen bonds : bond 0.03154 ( 447) hydrogen bonds : angle 4.10632 ( 1293) SS BOND : bond 0.00130 ( 3) SS BOND : angle 1.12213 ( 6) covalent geometry : bond 0.00271 (10257) covalent geometry : angle 0.58692 (13899) ********************** 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: 36 poor density : 118 time to evaluate : 1.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 TYR cc_start: 0.6326 (OUTLIER) cc_final: 0.5712 (p90) REVERT: A 142 MET cc_start: 0.7736 (OUTLIER) cc_final: 0.6691 (ppp) REVERT: A 517 TYR cc_start: 0.7751 (t80) cc_final: 0.7451 (t80) REVERT: A 531 CYS cc_start: 0.5951 (OUTLIER) cc_final: 0.5446 (m) REVERT: A 709 MET cc_start: 0.8784 (OUTLIER) cc_final: 0.8366 (mmm) REVERT: B 55 PHE cc_start: 0.7377 (t80) cc_final: 0.6994 (t80) REVERT: B 56 MET cc_start: 0.6965 (tpt) cc_final: 0.6442 (tpt) outliers start: 36 outliers final: 29 residues processed: 142 average time/residue: 0.2532 time to fit residues: 53.9817 Evaluate side-chains 148 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 115 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 TYR 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 157 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 164 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 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 555 ILE 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 61 VAL 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 118 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 chunk 3 optimal weight: 0.2980 chunk 94 optimal weight: 0.0270 chunk 73 optimal weight: 2.9990 chunk 59 optimal weight: 0.0000 overall best weight: 0.4644 ------------------------------------------------------------------------------- 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 = 0.3876 r_free = 0.3876 target = 0.130698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.096620 restraints weight = 19129.119| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.60 r_work: 0.3251 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2295 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= 0.108 Angle : 0.580 13.115 13905 Z= 0.285 Chirality : 0.041 0.252 1540 Planarity : 0.004 0.054 1786 Dihedral : 3.921 15.935 1369 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.45 % Favored : 94.48 % Rotamer: Outliers : 3.11 % Allowed : 24.43 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.24), residues: 1267 helix: 1.30 (0.23), residues: 580 sheet: -0.15 (0.48), residues: 116 loop : -0.97 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 63 HIS 0.002 0.000 HIS A 267 PHE 0.010 0.001 PHE A 410 TYR 0.024 0.001 TYR A 842 ARG 0.011 0.000 ARG A 633 Details of bonding type rmsd hydrogen bonds : bond 0.03053 ( 447) hydrogen bonds : angle 4.03839 ( 1293) SS BOND : bond 0.00122 ( 3) SS BOND : angle 1.12000 ( 6) covalent geometry : bond 0.00255 (10257) covalent geometry : angle 0.57967 (13899) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5490.75 seconds wall clock time: 97 minutes 55.93 seconds (5875.93 seconds total)