Starting phenix.real_space_refine on Fri Feb 14 10:30:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k1l_36794/02_2025/8k1l_36794.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k1l_36794/02_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_36794/02_2025/8k1l_36794.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k1l_36794/02_2025/8k1l_36794.map" model { file = "/net/cci-nas-00/data/ceres_data/8k1l_36794/02_2025/8k1l_36794.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k1l_36794/02_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-5592/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: 7.12, per 1000 atoms: 0.71 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: 2.50 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: 1.18 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: 3.62 Time building geometry restraints manager: 2.91 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: 5.620 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: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 26.370 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.660 ------------------------------------------------------------------------------- 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 10257 Z= 0.288 Angle : 1.168 71.224 13899 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 *********************** 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 : 1.193 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: 0.2293 time to fit residues: 39.2074 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 : 1.183 ------------------------------------------------------------------------------- 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 = 0.125281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.090899 restraints weight = 19994.600| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.98 r_work: 0.3180 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 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 10257 Z= 0.311 Angle : 0.667 11.838 13899 Z= 0.340 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 *********************** 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 : 1.113 Fit side-chains revert: symmetry clash REVERT: A 465 TYR cc_start: 0.7514 (p90) cc_final: 0.7290 (p90) REVERT: A 483 LYS cc_start: 0.6551 (pttm) cc_final: 0.6349 (pttm) REVERT: B 56 MET cc_start: 0.7383 (tpt) cc_final: 0.7032 (tpt) outliers start: 39 outliers final: 30 residues processed: 151 average time/residue: 0.2121 time to fit residues: 46.5521 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 : 1.093 ------------------------------------------------------------------------------- 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: 7.9990 chunk 115 optimal weight: 4.9990 chunk 38 optimal weight: 8.9990 chunk 2 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 33 optimal weight: 0.0040 chunk 69 optimal weight: 0.3980 overall best weight: 1.0794 ------------------------------------------------------------------------------- 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 = 0.3860 r_free = 0.3860 target = 0.126269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.092066 restraints weight = 20158.921| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 3.01 r_work: 0.3196 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10257 Z= 0.249 Angle : 0.610 8.255 13899 Z= 0.310 Chirality : 0.042 0.242 1540 Planarity : 0.004 0.045 1786 Dihedral : 4.578 37.376 1371 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.92 % Favored : 94.00 % Rotamer: Outliers : 3.84 % Allowed : 22.14 % 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: -0.36 (0.24), residues: 1267 helix: 0.89 (0.23), residues: 555 sheet: -1.20 (0.43), residues: 140 loop : -1.08 (0.27), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 63 HIS 0.003 0.001 HIS A 470 PHE 0.021 0.001 PHE A 145 TYR 0.015 0.001 TYR A 465 ARG 0.004 0.001 ARG A 741 *********************** 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 164 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 122 time to evaluate : 1.140 Fit side-chains REVERT: A 142 MET cc_start: 0.7816 (ppp) cc_final: 0.7574 (ppp) REVERT: B 56 MET cc_start: 0.7369 (tpt) cc_final: 0.6945 (tpt) outliers start: 42 outliers final: 26 residues processed: 156 average time/residue: 0.2103 time to fit residues: 48.8126 Evaluate side-chains 138 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 112 time to evaluate : 1.193 ------------------------------------------------------------------------------- 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 90 ILE 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 480 LEU Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 489 ILE 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 37 optimal weight: 9.9990 chunk 60 optimal weight: 0.0770 chunk 94 optimal weight: 0.9990 chunk 44 optimal weight: 0.3980 chunk 109 optimal weight: 7.9990 chunk 116 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 38 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 overall best weight: 0.6742 ------------------------------------------------------------------------------- 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 = 0.3879 r_free = 0.3879 target = 0.127672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.093025 restraints weight = 19839.114| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.77 r_work: 0.3244 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10257 Z= 0.193 Angle : 0.575 8.345 13899 Z= 0.291 Chirality : 0.041 0.251 1540 Planarity : 0.004 0.049 1786 Dihedral : 4.430 39.448 1371 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.92 % Favored : 93.92 % Rotamer: Outliers : 3.39 % Allowed : 22.42 % Favored : 74.20 % 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: -0.20 (0.24), residues: 1267 helix: 1.03 (0.23), residues: 562 sheet: -0.83 (0.45), residues: 128 loop : -1.12 (0.27), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 63 HIS 0.004 0.001 HIS A 414 PHE 0.010 0.001 PHE A 744 TYR 0.012 0.001 TYR A 768 ARG 0.003 0.000 ARG A 204 *********************** 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 160 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 123 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 509 MET cc_start: 0.7414 (mmp) cc_final: 0.7163 (mmp) REVERT: A 517 TYR cc_start: 0.8065 (t80) cc_final: 0.7811 (t80) REVERT: A 531 CYS cc_start: 0.6230 (OUTLIER) cc_final: 0.5704 (m) REVERT: B 55 PHE cc_start: 0.7292 (t80) cc_final: 0.6791 (t80) REVERT: B 56 MET cc_start: 0.7171 (tpt) cc_final: 0.6658 (tpt) outliers start: 37 outliers final: 22 residues processed: 151 average time/residue: 0.2194 time to fit residues: 47.9211 Evaluate side-chains 137 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 705 ILE 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 301 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 20 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 124 optimal weight: 0.0370 chunk 117 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 123 optimal weight: 0.0020 chunk 21 optimal weight: 5.9990 chunk 76 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 overall best weight: 1.1470 ------------------------------------------------------------------------------- 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 = 0.3862 r_free = 0.3862 target = 0.126529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.092442 restraints weight = 19918.475| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 3.08 r_work: 0.3200 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10257 Z= 0.255 Angle : 0.596 9.168 13899 Z= 0.298 Chirality : 0.042 0.258 1540 Planarity : 0.004 0.050 1786 Dihedral : 4.318 24.729 1370 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.08 % Favored : 93.76 % Rotamer: Outliers : 3.57 % Allowed : 22.78 % Favored : 73.65 % 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: -0.19 (0.24), residues: 1267 helix: 1.05 (0.23), residues: 563 sheet: -0.79 (0.45), residues: 128 loop : -1.13 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 63 HIS 0.002 0.001 HIS A 641 PHE 0.023 0.001 PHE A 145 TYR 0.015 0.001 TYR A 465 ARG 0.004 0.000 ARG A 978 *********************** 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 160 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 121 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 509 MET cc_start: 0.7362 (mmp) cc_final: 0.7140 (mmp) REVERT: A 517 TYR cc_start: 0.8053 (t80) cc_final: 0.7810 (t80) REVERT: A 531 CYS cc_start: 0.6100 (OUTLIER) cc_final: 0.5516 (m) REVERT: A 591 VAL cc_start: 0.9244 (t) cc_final: 0.9019 (m) REVERT: B 55 PHE cc_start: 0.7451 (t80) cc_final: 0.6978 (t80) REVERT: B 56 MET cc_start: 0.7278 (tpt) cc_final: 0.6768 (tpt) outliers start: 39 outliers final: 30 residues processed: 149 average time/residue: 0.2083 time to fit residues: 45.1106 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 : 1.174 ------------------------------------------------------------------------------- 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 156 GLN 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 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 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: 0.2980 chunk 11 optimal weight: 6.9990 chunk 34 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 120 optimal weight: 0.3980 chunk 33 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 12 optimal weight: 0.1980 chunk 55 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 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 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 = 0.3843 r_free = 0.3843 target = 0.128314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.093925 restraints weight = 19027.493| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.55 r_work: 0.3212 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10257 Z= 0.198 Angle : 0.568 10.056 13899 Z= 0.284 Chirality : 0.041 0.258 1540 Planarity : 0.004 0.050 1786 Dihedral : 4.251 23.816 1370 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.68 % Favored : 94.16 % Rotamer: Outliers : 3.02 % Allowed : 22.78 % Favored : 74.20 % 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: -0.07 (0.24), residues: 1267 helix: 1.15 (0.23), residues: 564 sheet: -0.73 (0.45), residues: 128 loop : -1.08 (0.27), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 63 HIS 0.003 0.001 HIS A 267 PHE 0.009 0.001 PHE A 665 TYR 0.013 0.001 TYR A 768 ARG 0.006 0.000 ARG A 633 *********************** 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 156 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 123 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 TYR cc_start: 0.6236 (OUTLIER) cc_final: 0.5352 (p90) REVERT: A 142 MET cc_start: 0.7916 (OUTLIER) cc_final: 0.6787 (ppp) REVERT: A 509 MET cc_start: 0.7461 (mmp) cc_final: 0.7229 (mmp) REVERT: A 517 TYR cc_start: 0.8095 (t80) cc_final: 0.7879 (t80) REVERT: A 531 CYS cc_start: 0.6163 (OUTLIER) cc_final: 0.5621 (m) REVERT: B 55 PHE cc_start: 0.7311 (t80) cc_final: 0.6943 (t80) REVERT: B 56 MET cc_start: 0.6940 (tpt) cc_final: 0.6384 (tpt) outliers start: 33 outliers final: 27 residues processed: 145 average time/residue: 0.2151 time to fit residues: 45.4103 Evaluate side-chains 146 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 116 time to evaluate : 1.191 ------------------------------------------------------------------------------- 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 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 63 TRP 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: 0.8980 chunk 20 optimal weight: 0.7980 chunk 59 optimal weight: 0.0970 chunk 13 optimal weight: 0.0980 chunk 26 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 chunk 82 optimal weight: 0.4980 chunk 18 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- 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 = 0.3863 r_free = 0.3863 target = 0.129930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.095669 restraints weight = 19435.586| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.58 r_work: 0.3237 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10257 Z= 0.168 Angle : 0.558 11.286 13899 Z= 0.279 Chirality : 0.041 0.259 1540 Planarity : 0.004 0.051 1786 Dihedral : 4.134 21.935 1370 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.52 % Favored : 94.32 % Rotamer: Outliers : 3.66 % Allowed : 22.51 % 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 (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: 0.06 (0.24), residues: 1267 helix: 1.30 (0.23), residues: 565 sheet: -0.57 (0.45), residues: 127 loop : -1.08 (0.26), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 63 HIS 0.003 0.001 HIS A 267 PHE 0.030 0.001 PHE A 145 TYR 0.018 0.001 TYR A 842 ARG 0.003 0.000 ARG A 362 *********************** 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 168 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 128 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 TYR cc_start: 0.6195 (OUTLIER) cc_final: 0.5507 (p90) REVERT: A 483 LYS cc_start: 0.6351 (pttm) cc_final: 0.6124 (pttm) REVERT: A 509 MET cc_start: 0.7476 (mmp) cc_final: 0.7262 (mmp) REVERT: A 709 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.8318 (mmm) REVERT: B 55 PHE cc_start: 0.7272 (t80) cc_final: 0.6874 (t80) REVERT: B 56 MET cc_start: 0.6853 (tpt) cc_final: 0.6303 (tpt) outliers start: 40 outliers final: 30 residues processed: 156 average time/residue: 0.2213 time to fit residues: 49.4535 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 : 1.155 ------------------------------------------------------------------------------- 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 168 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 42 optimal weight: 0.9980 chunk 111 optimal weight: 0.3980 chunk 19 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 119 optimal weight: 0.8980 chunk 57 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 122 optimal weight: 0.4980 chunk 83 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3861 r_free = 0.3861 target = 0.129735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.095279 restraints weight = 19296.817| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.62 r_work: 0.3225 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10257 Z= 0.186 Angle : 0.573 11.864 13899 Z= 0.286 Chirality : 0.041 0.258 1540 Planarity : 0.004 0.051 1786 Dihedral : 4.071 20.294 1370 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.92 % Favored : 93.92 % Rotamer: Outliers : 3.48 % Allowed : 22.87 % Favored : 73.65 % 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: 0.07 (0.24), residues: 1267 helix: 1.27 (0.22), residues: 571 sheet: -0.42 (0.45), residues: 126 loop : -1.10 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 63 HIS 0.003 0.001 HIS B 187 PHE 0.010 0.001 PHE A 410 TYR 0.016 0.001 TYR A 842 ARG 0.009 0.000 ARG A 633 *********************** 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 156 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 118 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 TYR cc_start: 0.6179 (OUTLIER) cc_final: 0.5541 (p90) REVERT: A 142 MET cc_start: 0.7929 (OUTLIER) cc_final: 0.6836 (ppp) REVERT: A 517 TYR cc_start: 0.7884 (t80) cc_final: 0.7498 (t80) REVERT: A 531 CYS cc_start: 0.5983 (OUTLIER) cc_final: 0.5547 (m) REVERT: A 709 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.8350 (mmm) REVERT: B 55 PHE cc_start: 0.7276 (t80) cc_final: 0.6866 (t80) REVERT: B 56 MET cc_start: 0.6839 (tpt) cc_final: 0.6295 (tpt) outliers start: 38 outliers final: 29 residues processed: 144 average time/residue: 0.2297 time to fit residues: 47.5406 Evaluate side-chains 149 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 116 time to evaluate : 1.320 ------------------------------------------------------------------------------- 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 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 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 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: 0.8980 chunk 71 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 40 optimal weight: 0.4980 chunk 20 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 24 optimal weight: 0.1980 chunk 16 optimal weight: 2.9990 chunk 28 optimal weight: 0.0980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3849 r_free = 0.3849 target = 0.128777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.095398 restraints weight = 19107.151| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.73 r_work: 0.3214 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10257 Z= 0.221 Angle : 0.593 12.648 13899 Z= 0.294 Chirality : 0.042 0.257 1540 Planarity : 0.004 0.054 1786 Dihedral : 4.096 18.978 1370 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.08 % Favored : 93.76 % Rotamer: Outliers : 3.66 % Allowed : 22.96 % 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 (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: 0.06 (0.24), residues: 1267 helix: 1.25 (0.22), residues: 572 sheet: -0.32 (0.45), residues: 126 loop : -1.14 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 63 HIS 0.003 0.001 HIS A 267 PHE 0.030 0.001 PHE A 145 TYR 0.017 0.001 TYR A 842 ARG 0.010 0.001 ARG A 633 *********************** 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 157 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 117 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 TYR cc_start: 0.6222 (OUTLIER) cc_final: 0.5579 (p90) REVERT: A 142 MET cc_start: 0.7954 (OUTLIER) cc_final: 0.6781 (ppp) REVERT: A 517 TYR cc_start: 0.7867 (t80) cc_final: 0.7485 (t80) REVERT: A 531 CYS cc_start: 0.6048 (OUTLIER) cc_final: 0.5546 (m) REVERT: A 709 MET cc_start: 0.8804 (OUTLIER) cc_final: 0.8381 (mmm) REVERT: B 48 TRP cc_start: 0.5052 (t-100) cc_final: 0.4590 (t-100) REVERT: B 55 PHE cc_start: 0.7351 (t80) cc_final: 0.7045 (t80) REVERT: B 56 MET cc_start: 0.6927 (tpt) cc_final: 0.6407 (tpt) outliers start: 40 outliers final: 32 residues processed: 144 average time/residue: 0.2185 time to fit residues: 45.1296 Evaluate side-chains 152 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 116 time to evaluate : 1.052 ------------------------------------------------------------------------------- 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 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 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 301 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 58 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 11 optimal weight: 0.2980 chunk 37 optimal weight: 8.9990 chunk 12 optimal weight: 3.9990 chunk 119 optimal weight: 0.7980 chunk 113 optimal weight: 0.4980 chunk 38 optimal weight: 1.9990 chunk 108 optimal weight: 0.0670 chunk 107 optimal weight: 0.5980 chunk 117 optimal weight: 1.9990 overall best weight: 0.4518 ------------------------------------------------------------------------------- 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 = 0.3876 r_free = 0.3876 target = 0.130769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.096504 restraints weight = 19278.038| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.60 r_work: 0.3252 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10257 Z= 0.169 Angle : 0.582 13.185 13899 Z= 0.287 Chirality : 0.041 0.249 1540 Planarity : 0.004 0.054 1786 Dihedral : 4.007 16.683 1370 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.45 % Favored : 94.40 % Rotamer: Outliers : 3.02 % Allowed : 23.70 % Favored : 73.28 % 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: 0.17 (0.24), residues: 1267 helix: 1.36 (0.23), residues: 572 sheet: -0.25 (0.46), residues: 126 loop : -1.11 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 63 HIS 0.003 0.001 HIS A 267 PHE 0.009 0.001 PHE A 410 TYR 0.023 0.001 TYR A 842 ARG 0.011 0.000 ARG A 633 ********************** 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: 33 poor density : 121 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 TYR cc_start: 0.6303 (OUTLIER) cc_final: 0.5669 (p90) REVERT: A 142 MET cc_start: 0.7896 (OUTLIER) cc_final: 0.6814 (ppp) REVERT: A 517 TYR cc_start: 0.7769 (t80) cc_final: 0.7474 (t80) REVERT: A 531 CYS cc_start: 0.6000 (OUTLIER) cc_final: 0.5490 (m) REVERT: A 709 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.8314 (mmm) REVERT: B 55 PHE cc_start: 0.7247 (t80) cc_final: 0.6849 (t80) REVERT: B 56 MET cc_start: 0.6828 (tpt) cc_final: 0.6299 (tpt) outliers start: 33 outliers final: 26 residues processed: 143 average time/residue: 0.2360 time to fit residues: 48.9839 Evaluate side-chains 147 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 117 time to evaluate : 1.063 ------------------------------------------------------------------------------- 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 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 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 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: 5.9990 chunk 83 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 101 optimal weight: 0.4980 chunk 3 optimal weight: 0.7980 chunk 94 optimal weight: 0.0670 chunk 73 optimal weight: 0.4980 chunk 59 optimal weight: 0.6980 overall best weight: 0.5118 ------------------------------------------------------------------------------- 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 = 0.3875 r_free = 0.3875 target = 0.130610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.096273 restraints weight = 19151.842| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.59 r_work: 0.3250 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10257 Z= 0.174 Angle : 0.590 12.923 13899 Z= 0.289 Chirality : 0.041 0.264 1540 Planarity : 0.004 0.054 1786 Dihedral : 3.941 16.106 1369 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.68 % Favored : 94.16 % Rotamer: Outliers : 2.84 % Allowed : 23.88 % Favored : 73.28 % 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: 0.25 (0.24), residues: 1267 helix: 1.32 (0.22), residues: 579 sheet: 0.00 (0.48), residues: 116 loop : -1.01 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 63 HIS 0.002 0.001 HIS A 414 PHE 0.009 0.001 PHE A 410 TYR 0.024 0.001 TYR A 842 ARG 0.011 0.000 ARG A 633 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4878.32 seconds wall clock time: 87 minutes 54.91 seconds (5274.91 seconds total)