Starting phenix.real_space_refine on Wed Feb 4 02:42:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m5x_63652/02_2026/9m5x_63652.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m5x_63652/02_2026/9m5x_63652.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9m5x_63652/02_2026/9m5x_63652.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m5x_63652/02_2026/9m5x_63652.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9m5x_63652/02_2026/9m5x_63652.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m5x_63652/02_2026/9m5x_63652.map" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.030 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 43 5.16 5 C 5279 2.51 5 N 1417 2.21 5 O 1519 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8259 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1036, 8258 Classifications: {'peptide': 1036} Link IDs: {'PTRANS': 55, 'TRANS': 980} Chain breaks: 10 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2893 SG CYS A 800 52.434 39.905 28.905 1.00153.26 S ATOM 3544 SG CYS A 880 50.015 39.250 25.986 1.00170.97 S ATOM 3563 SG CYS A 883 53.037 41.583 25.524 1.00175.86 S Time building chain proxies: 1.92, per 1000 atoms: 0.23 Number of scatterers: 8259 At special positions: 0 Unit cell: (93.3222, 103.927, 130.439, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 43 16.00 O 1519 8.00 N 1417 7.00 C 5279 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.68 Conformation dependent library (CDL) restraints added in 324.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1601 " pdb="ZN ZN A1601 " - pdb=" NE2 HIS A 773 " pdb="ZN ZN A1601 " - pdb=" SG CYS A 800 " pdb="ZN ZN A1601 " - pdb=" SG CYS A 883 " pdb="ZN ZN A1601 " - pdb=" SG CYS A 880 " Number of angles added : 3 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1932 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 12 sheets defined 31.3% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 350 through 355 removed outlier: 3.769A pdb=" N ILE A 354 " --> pdb=" O ASN A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 411 Processing helix chain 'A' and resid 494 through 515 Proline residue: A 500 - end of helix Processing helix chain 'A' and resid 527 through 536 removed outlier: 3.655A pdb=" N LEU A 536 " --> pdb=" O ARG A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 558 Processing helix chain 'A' and resid 559 through 568 removed outlier: 4.171A pdb=" N LEU A 565 " --> pdb=" O ILE A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 590 Processing helix chain 'A' and resid 631 through 644 Processing helix chain 'A' and resid 781 through 783 No H-bonds generated for 'chain 'A' and resid 781 through 783' Processing helix chain 'A' and resid 785 through 789 removed outlier: 3.942A pdb=" N ALA A 789 " --> pdb=" O GLY A 786 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 824 No H-bonds generated for 'chain 'A' and resid 822 through 824' Processing helix chain 'A' and resid 825 through 846 Processing helix chain 'A' and resid 880 through 892 Processing helix chain 'A' and resid 976 through 981 removed outlier: 4.029A pdb=" N VAL A 980 " --> pdb=" O ARG A 976 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER A 981 " --> pdb=" O PRO A 977 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 976 through 981' Processing helix chain 'A' and resid 981 through 987 Processing helix chain 'A' and resid 1003 through 1005 No H-bonds generated for 'chain 'A' and resid 1003 through 1005' Processing helix chain 'A' and resid 1103 through 1112 Processing helix chain 'A' and resid 1124 through 1135 Processing helix chain 'A' and resid 1144 through 1156 Processing helix chain 'A' and resid 1165 through 1174 Processing helix chain 'A' and resid 1176 through 1182 Processing helix chain 'A' and resid 1211 through 1216 Processing helix chain 'A' and resid 1218 through 1231 removed outlier: 4.125A pdb=" N ALA A1222 " --> pdb=" O GLU A1218 " (cutoff:3.500A) Processing helix chain 'A' and resid 1242 through 1245 Processing helix chain 'A' and resid 1249 through 1263 Processing helix chain 'A' and resid 1274 through 1277 removed outlier: 3.977A pdb=" N GLY A1277 " --> pdb=" O GLY A1274 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1274 through 1277' Processing helix chain 'A' and resid 1337 through 1343 Processing helix chain 'A' and resid 1365 through 1373 removed outlier: 3.667A pdb=" N GLY A1373 " --> pdb=" O LYS A1369 " (cutoff:3.500A) Processing helix chain 'A' and resid 1387 through 1397 Processing helix chain 'A' and resid 1404 through 1408 Processing helix chain 'A' and resid 1452 through 1456 removed outlier: 3.700A pdb=" N VAL A1455 " --> pdb=" O PRO A1452 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR A1456 " --> pdb=" O THR A1453 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1452 through 1456' Processing helix chain 'A' and resid 1477 through 1485 Processing helix chain 'A' and resid 1496 through 1506 Processing helix chain 'A' and resid 1509 through 1525 Processing sheet with id=AA1, first strand: chain 'A' and resid 347 through 348 Processing sheet with id=AA2, first strand: chain 'A' and resid 456 through 457 removed outlier: 5.070A pdb=" N VAL A 428 " --> pdb=" O ASN A 395 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ASN A 395 " --> pdb=" O VAL A 428 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N THR A 430 " --> pdb=" O LEU A 393 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N LEU A 393 " --> pdb=" O THR A 430 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N ILE A 476 " --> pdb=" O LEU A 487 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU A 467 " --> pdb=" O SER A 475 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 629 through 630 Processing sheet with id=AA4, first strand: chain 'A' and resid 712 through 713 removed outlier: 3.947A pdb=" N GLN A 729 " --> pdb=" O ASP A 713 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 718 through 719 removed outlier: 4.443A pdb=" N GLY A 718 " --> pdb=" O LEU A 726 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N MET A 762 " --> pdb=" O TYR A 727 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ILE A 756 " --> pdb=" O LEU A 777 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N HIS A 773 " --> pdb=" O GLU A 760 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N MET A 762 " --> pdb=" O MET A 771 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N MET A 771 " --> pdb=" O MET A 762 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N GLU A 799 " --> pdb=" O PHE A 776 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N GLN A 778 " --> pdb=" O THR A 797 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N THR A 797 " --> pdb=" O GLN A 778 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N LEU A 794 " --> pdb=" O SER A 856 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N TYR A 858 " --> pdb=" O LEU A 794 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N LEU A 796 " --> pdb=" O TYR A 858 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N GLU A 815 " --> pdb=" O CYS A 854 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N SER A 856 " --> pdb=" O GLU A 815 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 808 through 812 removed outlier: 3.717A pdb=" N GLY A 810 " --> pdb=" O THR A 744 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ALA A 742 " --> pdb=" O ALA A 812 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA A 755 " --> pdb=" O LEU A 745 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ILE A 756 " --> pdb=" O LEU A 777 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N HIS A 773 " --> pdb=" O GLU A 760 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N MET A 762 " --> pdb=" O MET A 771 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N MET A 771 " --> pdb=" O MET A 762 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N GLU A 799 " --> pdb=" O PHE A 776 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N GLN A 778 " --> pdb=" O THR A 797 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N THR A 797 " --> pdb=" O GLN A 778 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N LEU A 794 " --> pdb=" O SER A 856 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N TYR A 858 " --> pdb=" O LEU A 794 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N LEU A 796 " --> pdb=" O TYR A 858 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU A1238 " --> pdb=" O GLY A1194 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N THR A1095 " --> pdb=" O TRP A1119 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N ILE A1121 " --> pdb=" O THR A1095 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ASP A1097 " --> pdb=" O ILE A1121 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 896 through 897 removed outlier: 3.768A pdb=" N LYS A 896 " --> pdb=" O PHE A 905 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 992 through 995 removed outlier: 7.176A pdb=" N LEU A 993 " --> pdb=" O LEU A1036 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N PHE A1038 " --> pdb=" O LEU A 993 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N PHE A 995 " --> pdb=" O PHE A1038 " (cutoff:3.500A) removed outlier: 9.045A pdb=" N PHE A1032 " --> pdb=" O LYS A1010 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N GLU A1012 " --> pdb=" O PHE A1032 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N CYS A1034 " --> pdb=" O GLU A1012 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ARG A1014 " --> pdb=" O CYS A1034 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N LEU A1036 " --> pdb=" O ARG A1014 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N TYR A 918 " --> pdb=" O GLU A1008 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N LYS A1010 " --> pdb=" O PHE A 916 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N PHE A 916 " --> pdb=" O LYS A1010 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N LEU A 951 " --> pdb=" O ARG A 972 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ARG A 972 " --> pdb=" O LEU A 951 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU A 953 " --> pdb=" O LYS A 970 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 992 through 995 removed outlier: 7.176A pdb=" N LEU A 993 " --> pdb=" O LEU A1036 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N PHE A1038 " --> pdb=" O LEU A 993 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N PHE A 995 " --> pdb=" O PHE A1038 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP A1039 " --> pdb=" O SER A1044 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER A1044 " --> pdb=" O ASP A1039 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1312 through 1314 Processing sheet with id=AB2, first strand: chain 'A' and resid 1356 through 1357 Processing sheet with id=AB3, first strand: chain 'A' and resid 1412 through 1414 287 hydrogen bonds defined for protein. 804 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.42 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2677 1.35 - 1.46: 1962 1.46 - 1.58: 3746 1.58 - 1.70: 0 1.70 - 1.82: 65 Bond restraints: 8450 Sorted by residual: bond pdb=" CB ASP A 833 " pdb=" CG ASP A 833 " ideal model delta sigma weight residual 1.516 1.546 -0.030 2.50e-02 1.60e+03 1.43e+00 bond pdb=" CB PRO A 548 " pdb=" CG PRO A 548 " ideal model delta sigma weight residual 1.492 1.545 -0.053 5.00e-02 4.00e+02 1.11e+00 bond pdb=" CG PRO A 412 " pdb=" CD PRO A 412 " ideal model delta sigma weight residual 1.503 1.538 -0.035 3.40e-02 8.65e+02 1.09e+00 bond pdb=" CA ASP A 547 " pdb=" CB ASP A 547 " ideal model delta sigma weight residual 1.519 1.537 -0.017 1.73e-02 3.34e+03 9.97e-01 bond pdb=" N GLU A 752 " pdb=" CA GLU A 752 " ideal model delta sigma weight residual 1.457 1.470 -0.012 1.29e-02 6.01e+03 9.13e-01 ... (remaining 8445 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 11277 2.16 - 4.32: 120 4.32 - 6.49: 14 6.49 - 8.65: 4 8.65 - 10.81: 1 Bond angle restraints: 11416 Sorted by residual: angle pdb=" CB MET A 736 " pdb=" CG MET A 736 " pdb=" SD MET A 736 " ideal model delta sigma weight residual 112.70 123.51 -10.81 3.00e+00 1.11e-01 1.30e+01 angle pdb=" N HIS A 592 " pdb=" CA HIS A 592 " pdb=" C HIS A 592 " ideal model delta sigma weight residual 114.56 110.98 3.58 1.27e+00 6.20e-01 7.96e+00 angle pdb=" CB MET A 413 " pdb=" CG MET A 413 " pdb=" SD MET A 413 " ideal model delta sigma weight residual 112.70 120.97 -8.27 3.00e+00 1.11e-01 7.60e+00 angle pdb=" CA MET A 801 " pdb=" CB MET A 801 " pdb=" CG MET A 801 " ideal model delta sigma weight residual 114.10 119.33 -5.23 2.00e+00 2.50e-01 6.83e+00 angle pdb=" N ILE A 941 " pdb=" CA ILE A 941 " pdb=" C ILE A 941 " ideal model delta sigma weight residual 113.42 110.38 3.04 1.17e+00 7.31e-01 6.75e+00 ... (remaining 11411 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 4268 17.49 - 34.98: 604 34.98 - 52.48: 173 52.48 - 69.97: 32 69.97 - 87.46: 7 Dihedral angle restraints: 5084 sinusoidal: 2091 harmonic: 2993 Sorted by residual: dihedral pdb=" CA ARG A 479 " pdb=" C ARG A 479 " pdb=" N THR A 480 " pdb=" CA THR A 480 " ideal model delta harmonic sigma weight residual 180.00 160.85 19.15 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA LEU A 607 " pdb=" C LEU A 607 " pdb=" N ASN A 608 " pdb=" CA ASN A 608 " ideal model delta harmonic sigma weight residual 180.00 160.86 19.14 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA TYR A1264 " pdb=" C TYR A1264 " pdb=" N GLN A1265 " pdb=" CA GLN A1265 " ideal model delta harmonic sigma weight residual 180.00 162.06 17.94 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 5081 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 844 0.034 - 0.068: 260 0.068 - 0.102: 87 0.102 - 0.136: 38 0.136 - 0.169: 4 Chirality restraints: 1233 Sorted by residual: chirality pdb=" CA ILE A 466 " pdb=" N ILE A 466 " pdb=" C ILE A 466 " pdb=" CB ILE A 466 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.18e-01 chirality pdb=" CA VAL A1508 " pdb=" N VAL A1508 " pdb=" C VAL A1508 " pdb=" CB VAL A1508 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.28e-01 chirality pdb=" CA ILE A 476 " pdb=" N ILE A 476 " pdb=" C ILE A 476 " pdb=" CB ILE A 476 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.02e-01 ... (remaining 1230 not shown) Planarity restraints: 1467 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 547 " -0.062 5.00e-02 4.00e+02 9.29e-02 1.38e+01 pdb=" N PRO A 548 " 0.161 5.00e-02 4.00e+02 pdb=" CA PRO A 548 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO A 548 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 610 " 0.043 5.00e-02 4.00e+02 6.55e-02 6.86e+00 pdb=" N PRO A 611 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 611 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 611 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 499 " -0.033 5.00e-02 4.00e+02 4.97e-02 3.96e+00 pdb=" N PRO A 500 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 500 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 500 " -0.028 5.00e-02 4.00e+02 ... (remaining 1464 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1565 2.77 - 3.30: 7709 3.30 - 3.84: 13519 3.84 - 4.37: 15446 4.37 - 4.90: 27151 Nonbonded interactions: 65390 Sorted by model distance: nonbonded pdb=" OG SER A1365 " pdb=" OE1 GLN A1368 " model vdw 2.239 3.040 nonbonded pdb=" OG SER A 765 " pdb=" OD1 ASP A 767 " model vdw 2.288 3.040 nonbonded pdb=" O SER A 818 " pdb=" OG SER A 818 " model vdw 2.296 3.040 nonbonded pdb=" OH TYR A1359 " pdb=" OD2 ASP A1489 " model vdw 2.298 3.040 nonbonded pdb=" OD2 ASP A1097 " pdb=" OG SER A1106 " model vdw 2.307 3.040 ... (remaining 65385 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 0.620 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.140 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 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 : 0.002 0.053 8454 Z= 0.108 Angle : 0.540 10.810 11419 Z= 0.277 Chirality : 0.041 0.169 1233 Planarity : 0.005 0.093 1467 Dihedral : 17.507 87.460 3152 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.00 % Allowed : 30.32 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.27), residues: 1014 helix: 1.23 (0.32), residues: 287 sheet: 0.02 (0.45), residues: 139 loop : -0.51 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 391 TYR 0.011 0.001 TYR A 554 PHE 0.008 0.001 PHE A 579 TRP 0.009 0.001 TRP A 436 HIS 0.002 0.000 HIS A 773 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 8450) covalent geometry : angle 0.54008 (11416) hydrogen bonds : bond 0.15820 ( 278) hydrogen bonds : angle 6.48148 ( 804) metal coordination : bond 0.00111 ( 4) metal coordination : angle 0.59603 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.299 Fit side-chains revert: symmetry clash REVERT: A 391 ARG cc_start: 0.7409 (mmm160) cc_final: 0.7155 (mmp-170) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.1152 time to fit residues: 12.1928 Evaluate side-chains 76 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 GLN A1350 ASN ** A1503 GLN ** 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 = 0.3782 r_free = 0.3782 target = 0.138683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.087918 restraints weight = 11929.573| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 3.38 r_work: 0.2916 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.0700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8454 Z= 0.133 Angle : 0.512 7.194 11419 Z= 0.261 Chirality : 0.041 0.170 1233 Planarity : 0.005 0.062 1467 Dihedral : 3.813 24.388 1118 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.23 % Allowed : 27.09 % Favored : 70.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.27), residues: 1014 helix: 1.51 (0.32), residues: 283 sheet: 0.06 (0.47), residues: 139 loop : -0.53 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 635 TYR 0.008 0.001 TYR A 757 PHE 0.008 0.001 PHE A 758 TRP 0.013 0.001 TRP A 484 HIS 0.003 0.001 HIS A 773 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 8450) covalent geometry : angle 0.51153 (11416) hydrogen bonds : bond 0.03627 ( 278) hydrogen bonds : angle 4.99127 ( 804) metal coordination : bond 0.00198 ( 4) metal coordination : angle 0.69371 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 347 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.7751 (mm) REVERT: A 391 ARG cc_start: 0.7576 (mmm160) cc_final: 0.7175 (mmm160) REVERT: A 436 TRP cc_start: 0.7417 (m-10) cc_final: 0.6640 (m100) REVERT: A 599 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8293 (tptp) outliers start: 20 outliers final: 5 residues processed: 102 average time/residue: 0.1035 time to fit residues: 14.2112 Evaluate side-chains 88 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 599 LYS Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1350 ASN Chi-restraints excluded: chain A residue 1413 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 61 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 6 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 22 optimal weight: 0.0980 chunk 3 optimal weight: 20.0000 chunk 1 optimal weight: 0.0270 chunk 32 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1503 GLN ** 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 = 0.3808 r_free = 0.3808 target = 0.142594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.092498 restraints weight = 11750.825| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 3.31 r_work: 0.2966 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.0866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8454 Z= 0.094 Angle : 0.486 5.907 11419 Z= 0.246 Chirality : 0.040 0.162 1233 Planarity : 0.004 0.050 1467 Dihedral : 3.714 22.819 1118 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.23 % Allowed : 29.32 % Favored : 69.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.27), residues: 1014 helix: 1.59 (0.31), residues: 284 sheet: 0.08 (0.47), residues: 139 loop : -0.46 (0.26), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 973 TYR 0.009 0.001 TYR A1025 PHE 0.009 0.001 PHE A 758 TRP 0.013 0.001 TRP A 484 HIS 0.002 0.000 HIS A1135 Details of bonding type rmsd covalent geometry : bond 0.00216 ( 8450) covalent geometry : angle 0.48576 (11416) hydrogen bonds : bond 0.03269 ( 278) hydrogen bonds : angle 4.71434 ( 804) metal coordination : bond 0.00057 ( 4) metal coordination : angle 0.44237 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.314 Fit side-chains revert: symmetry clash REVERT: A 347 ILE cc_start: 0.8608 (OUTLIER) cc_final: 0.7758 (mm) REVERT: A 391 ARG cc_start: 0.7557 (mmm160) cc_final: 0.7101 (mmm160) REVERT: A 436 TRP cc_start: 0.7679 (m-10) cc_final: 0.6925 (m100) REVERT: A 1276 TYR cc_start: 0.8802 (m-80) cc_final: 0.8596 (m-80) outliers start: 11 outliers final: 4 residues processed: 102 average time/residue: 0.0754 time to fit residues: 10.9455 Evaluate side-chains 89 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 84 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain A residue 1413 VAL Chi-restraints excluded: chain A residue 1414 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 24 optimal weight: 9.9990 chunk 84 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 90 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 71 optimal weight: 6.9990 chunk 6 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 HIS ** A1503 GLN ** 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 = 0.3776 r_free = 0.3776 target = 0.139658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.089461 restraints weight = 11970.586| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 3.31 r_work: 0.2923 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8454 Z= 0.180 Angle : 0.517 6.082 11419 Z= 0.262 Chirality : 0.041 0.161 1233 Planarity : 0.004 0.047 1467 Dihedral : 3.769 22.631 1118 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.79 % Allowed : 27.76 % Favored : 69.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.27), residues: 1014 helix: 1.54 (0.31), residues: 284 sheet: -0.11 (0.47), residues: 143 loop : -0.45 (0.26), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1393 TYR 0.013 0.001 TYR A 761 PHE 0.009 0.001 PHE A 974 TRP 0.013 0.001 TRP A 484 HIS 0.005 0.001 HIS A 773 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 8450) covalent geometry : angle 0.51747 (11416) hydrogen bonds : bond 0.03580 ( 278) hydrogen bonds : angle 4.61603 ( 804) metal coordination : bond 0.01122 ( 4) metal coordination : angle 0.27477 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 86 time to evaluate : 0.229 Fit side-chains revert: symmetry clash REVERT: A 347 ILE cc_start: 0.8676 (OUTLIER) cc_final: 0.7826 (mm) REVERT: A 391 ARG cc_start: 0.7498 (mmm160) cc_final: 0.6998 (mmm160) REVERT: A 436 TRP cc_start: 0.7887 (m-10) cc_final: 0.7134 (m100) REVERT: A 710 ILE cc_start: 0.8575 (OUTLIER) cc_final: 0.8310 (mm) outliers start: 25 outliers final: 14 residues processed: 109 average time/residue: 0.0766 time to fit residues: 12.0209 Evaluate side-chains 99 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 797 THR Chi-restraints excluded: chain A residue 861 GLU Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1278 VAL Chi-restraints excluded: chain A residue 1413 VAL Chi-restraints excluded: chain A residue 1414 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 37 optimal weight: 3.9990 chunk 23 optimal weight: 0.0170 chunk 91 optimal weight: 0.9980 chunk 86 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 101 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 overall best weight: 1.2020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 HIS A1350 ASN ** A1503 GLN ** 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 = 0.3788 r_free = 0.3788 target = 0.140919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.090521 restraints weight = 11973.797| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 3.35 r_work: 0.2936 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8454 Z= 0.134 Angle : 0.505 6.376 11419 Z= 0.253 Chirality : 0.041 0.151 1233 Planarity : 0.004 0.046 1467 Dihedral : 3.737 20.946 1118 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.23 % Allowed : 27.42 % Favored : 69.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.27), residues: 1014 helix: 1.58 (0.31), residues: 286 sheet: -0.20 (0.46), residues: 149 loop : -0.43 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 892 TYR 0.011 0.001 TYR A 761 PHE 0.009 0.001 PHE A 758 TRP 0.014 0.001 TRP A 484 HIS 0.003 0.000 HIS A 773 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 8450) covalent geometry : angle 0.50517 (11416) hydrogen bonds : bond 0.03345 ( 278) hydrogen bonds : angle 4.47765 ( 804) metal coordination : bond 0.00698 ( 4) metal coordination : angle 0.29688 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 85 time to evaluate : 0.209 Fit side-chains revert: symmetry clash REVERT: A 347 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.7804 (mm) REVERT: A 372 ASP cc_start: 0.8610 (t0) cc_final: 0.8367 (t0) REVERT: A 391 ARG cc_start: 0.7530 (mmm160) cc_final: 0.7213 (mmm160) REVERT: A 392 MET cc_start: 0.6493 (ppp) cc_final: 0.6203 (ppp) REVERT: A 422 ASN cc_start: 0.7272 (p0) cc_final: 0.6589 (p0) REVERT: A 436 TRP cc_start: 0.7963 (m-10) cc_final: 0.7215 (m100) REVERT: A 710 ILE cc_start: 0.8543 (OUTLIER) cc_final: 0.8277 (mm) REVERT: A 1419 ARG cc_start: 0.6159 (OUTLIER) cc_final: 0.5736 (ttp-170) outliers start: 29 outliers final: 21 residues processed: 110 average time/residue: 0.0863 time to fit residues: 13.2437 Evaluate side-chains 108 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 84 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 592 HIS Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 797 THR Chi-restraints excluded: chain A residue 861 GLU Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1278 VAL Chi-restraints excluded: chain A residue 1356 ASN Chi-restraints excluded: chain A residue 1413 VAL Chi-restraints excluded: chain A residue 1414 THR Chi-restraints excluded: chain A residue 1419 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 71 optimal weight: 4.9990 chunk 99 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 16 optimal weight: 20.0000 chunk 88 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 70 optimal weight: 0.0370 overall best weight: 0.7662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 HIS ** A1503 GLN ** 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 = 0.3795 r_free = 0.3795 target = 0.141216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.091619 restraints weight = 11719.073| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 3.28 r_work: 0.2959 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8454 Z= 0.106 Angle : 0.487 6.242 11419 Z= 0.245 Chirality : 0.040 0.162 1233 Planarity : 0.004 0.045 1467 Dihedral : 3.651 20.847 1118 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.23 % Allowed : 27.65 % Favored : 69.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.27), residues: 1014 helix: 1.76 (0.31), residues: 286 sheet: -0.15 (0.47), residues: 148 loop : -0.39 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 892 TYR 0.010 0.001 TYR A 761 PHE 0.009 0.001 PHE A 758 TRP 0.013 0.001 TRP A 484 HIS 0.002 0.000 HIS A 773 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 8450) covalent geometry : angle 0.48749 (11416) hydrogen bonds : bond 0.03100 ( 278) hydrogen bonds : angle 4.35502 ( 804) metal coordination : bond 0.00520 ( 4) metal coordination : angle 0.43885 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 92 time to evaluate : 0.225 Fit side-chains revert: symmetry clash REVERT: A 347 ILE cc_start: 0.8634 (OUTLIER) cc_final: 0.7782 (mm) REVERT: A 372 ASP cc_start: 0.8453 (t0) cc_final: 0.8164 (t0) REVERT: A 422 ASN cc_start: 0.7304 (p0) cc_final: 0.6587 (p0) REVERT: A 436 TRP cc_start: 0.8135 (m-10) cc_final: 0.7407 (m100) REVERT: A 465 MET cc_start: 0.8708 (ttp) cc_final: 0.8420 (ttm) REVERT: A 710 ILE cc_start: 0.8575 (OUTLIER) cc_final: 0.8299 (mm) REVERT: A 872 ASP cc_start: 0.8712 (m-30) cc_final: 0.8452 (m-30) REVERT: A 1419 ARG cc_start: 0.6201 (OUTLIER) cc_final: 0.5810 (ttp-170) outliers start: 29 outliers final: 21 residues processed: 118 average time/residue: 0.0737 time to fit residues: 12.2502 Evaluate side-chains 110 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 86 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 592 HIS Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 797 THR Chi-restraints excluded: chain A residue 861 GLU Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1278 VAL Chi-restraints excluded: chain A residue 1356 ASN Chi-restraints excluded: chain A residue 1413 VAL Chi-restraints excluded: chain A residue 1414 THR Chi-restraints excluded: chain A residue 1419 ARG Chi-restraints excluded: chain A residue 1461 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 1 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 23 optimal weight: 9.9990 chunk 96 optimal weight: 0.0870 chunk 78 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 36 optimal weight: 9.9990 chunk 71 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1503 GLN ** 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 = 0.3803 r_free = 0.3803 target = 0.142147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.091935 restraints weight = 11949.887| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 3.36 r_work: 0.2960 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8454 Z= 0.106 Angle : 0.493 7.032 11419 Z= 0.246 Chirality : 0.040 0.158 1233 Planarity : 0.004 0.045 1467 Dihedral : 3.626 20.338 1118 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.34 % Allowed : 27.54 % Favored : 69.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.27), residues: 1014 helix: 1.77 (0.31), residues: 286 sheet: -0.16 (0.47), residues: 148 loop : -0.39 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 892 TYR 0.010 0.001 TYR A 761 PHE 0.009 0.001 PHE A 758 TRP 0.014 0.001 TRP A 484 HIS 0.002 0.000 HIS A 773 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 8450) covalent geometry : angle 0.49288 (11416) hydrogen bonds : bond 0.03096 ( 278) hydrogen bonds : angle 4.33548 ( 804) metal coordination : bond 0.00438 ( 4) metal coordination : angle 0.50964 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 88 time to evaluate : 0.245 Fit side-chains revert: symmetry clash REVERT: A 347 ILE cc_start: 0.8600 (OUTLIER) cc_final: 0.7745 (mm) REVERT: A 372 ASP cc_start: 0.8518 (t0) cc_final: 0.8216 (t0) REVERT: A 391 ARG cc_start: 0.7386 (mmm160) cc_final: 0.7103 (mmm160) REVERT: A 392 MET cc_start: 0.6666 (ppp) cc_final: 0.6393 (ppp) REVERT: A 422 ASN cc_start: 0.7263 (p0) cc_final: 0.6812 (p0) REVERT: A 436 TRP cc_start: 0.8144 (m-10) cc_final: 0.7397 (m100) REVERT: A 710 ILE cc_start: 0.8631 (OUTLIER) cc_final: 0.8359 (mm) REVERT: A 872 ASP cc_start: 0.8711 (m-30) cc_final: 0.8448 (m-30) outliers start: 30 outliers final: 24 residues processed: 114 average time/residue: 0.0797 time to fit residues: 12.8074 Evaluate side-chains 109 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 83 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 592 HIS Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 797 THR Chi-restraints excluded: chain A residue 861 GLU Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 1034 CYS Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1278 VAL Chi-restraints excluded: chain A residue 1356 ASN Chi-restraints excluded: chain A residue 1413 VAL Chi-restraints excluded: chain A residue 1414 THR Chi-restraints excluded: chain A residue 1461 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 80 optimal weight: 0.0570 chunk 30 optimal weight: 8.9990 chunk 79 optimal weight: 0.8980 chunk 11 optimal weight: 0.1980 chunk 94 optimal weight: 0.0170 chunk 102 optimal weight: 0.6980 chunk 14 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 101 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 HIS ** A1503 GLN ** 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 = 0.3815 r_free = 0.3815 target = 0.143082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.093678 restraints weight = 11747.925| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 3.29 r_work: 0.2985 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8454 Z= 0.088 Angle : 0.500 7.865 11419 Z= 0.247 Chirality : 0.042 0.392 1233 Planarity : 0.004 0.044 1467 Dihedral : 3.625 19.538 1118 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.56 % Allowed : 28.09 % Favored : 69.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.27), residues: 1014 helix: 1.88 (0.31), residues: 286 sheet: -0.08 (0.48), residues: 142 loop : -0.42 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 486 TYR 0.009 0.001 TYR A1025 PHE 0.021 0.001 PHE A 579 TRP 0.016 0.001 TRP A 484 HIS 0.002 0.000 HIS A 394 Details of bonding type rmsd covalent geometry : bond 0.00202 ( 8450) covalent geometry : angle 0.50028 (11416) hydrogen bonds : bond 0.02844 ( 278) hydrogen bonds : angle 4.27614 ( 804) metal coordination : bond 0.00085 ( 4) metal coordination : angle 0.53460 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: A 347 ILE cc_start: 0.8540 (OUTLIER) cc_final: 0.7687 (mm) REVERT: A 372 ASP cc_start: 0.8502 (t0) cc_final: 0.8244 (t0) REVERT: A 392 MET cc_start: 0.6577 (ppp) cc_final: 0.6360 (ppp) REVERT: A 395 ASN cc_start: 0.8674 (m-40) cc_final: 0.8428 (t0) REVERT: A 422 ASN cc_start: 0.7006 (p0) cc_final: 0.6375 (p0) REVERT: A 436 TRP cc_start: 0.8200 (m-10) cc_final: 0.7469 (m100) REVERT: A 485 TYR cc_start: 0.7913 (m-80) cc_final: 0.7393 (m-80) REVERT: A 710 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8385 (mm) REVERT: A 872 ASP cc_start: 0.8723 (m-30) cc_final: 0.8461 (m-30) REVERT: A 1419 ARG cc_start: 0.6194 (OUTLIER) cc_final: 0.5807 (ttp80) REVERT: A 1480 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7551 (mt-10) outliers start: 23 outliers final: 18 residues processed: 106 average time/residue: 0.0908 time to fit residues: 13.4358 Evaluate side-chains 103 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 592 HIS Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 861 GLU Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 1034 CYS Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain A residue 1278 VAL Chi-restraints excluded: chain A residue 1356 ASN Chi-restraints excluded: chain A residue 1413 VAL Chi-restraints excluded: chain A residue 1414 THR Chi-restraints excluded: chain A residue 1419 ARG Chi-restraints excluded: chain A residue 1461 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 45 optimal weight: 0.0980 chunk 20 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 8 optimal weight: 30.0000 chunk 83 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 HIS ** A1503 GLN ** 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 = 0.3777 r_free = 0.3777 target = 0.139345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.088542 restraints weight = 11824.417| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 3.36 r_work: 0.2898 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8454 Z= 0.168 Angle : 0.542 8.521 11419 Z= 0.267 Chirality : 0.042 0.326 1233 Planarity : 0.004 0.045 1467 Dihedral : 3.711 20.300 1118 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.79 % Allowed : 27.76 % Favored : 69.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.27), residues: 1014 helix: 1.75 (0.31), residues: 286 sheet: -0.13 (0.48), residues: 143 loop : -0.44 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 391 TYR 0.012 0.001 TYR A1025 PHE 0.010 0.001 PHE A1235 TRP 0.019 0.001 TRP A 396 HIS 0.004 0.001 HIS A 394 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 8450) covalent geometry : angle 0.54203 (11416) hydrogen bonds : bond 0.03343 ( 278) hydrogen bonds : angle 4.39636 ( 804) metal coordination : bond 0.01004 ( 4) metal coordination : angle 0.66176 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 85 time to evaluate : 0.214 Fit side-chains REVERT: A 347 ILE cc_start: 0.8558 (OUTLIER) cc_final: 0.7709 (mm) REVERT: A 391 ARG cc_start: 0.7590 (mmm160) cc_final: 0.6947 (mmm160) REVERT: A 392 MET cc_start: 0.6567 (ppp) cc_final: 0.6282 (ppp) REVERT: A 422 ASN cc_start: 0.7141 (p0) cc_final: 0.6928 (p0) REVERT: A 436 TRP cc_start: 0.8233 (m-10) cc_final: 0.7544 (m100) REVERT: A 485 TYR cc_start: 0.7915 (m-80) cc_final: 0.7419 (m-80) REVERT: A 710 ILE cc_start: 0.8602 (OUTLIER) cc_final: 0.8362 (mm) REVERT: A 801 MET cc_start: 0.7532 (tmm) cc_final: 0.7286 (tmm) REVERT: A 872 ASP cc_start: 0.8706 (m-30) cc_final: 0.8460 (m-30) outliers start: 25 outliers final: 17 residues processed: 106 average time/residue: 0.0827 time to fit residues: 12.2996 Evaluate side-chains 102 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 861 GLU Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 1034 CYS Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1278 VAL Chi-restraints excluded: chain A residue 1413 VAL Chi-restraints excluded: chain A residue 1414 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 43 optimal weight: 0.0470 chunk 17 optimal weight: 8.9990 chunk 6 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 89 optimal weight: 0.0570 chunk 85 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1503 GLN ** 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 = 0.3790 r_free = 0.3790 target = 0.140492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.089945 restraints weight = 11786.780| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 3.39 r_work: 0.2939 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 8454 Z= 0.097 Angle : 0.523 9.980 11419 Z= 0.258 Chirality : 0.041 0.157 1233 Planarity : 0.004 0.045 1467 Dihedral : 3.651 19.658 1118 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.01 % Allowed : 28.54 % Favored : 69.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.27), residues: 1014 helix: 1.84 (0.31), residues: 286 sheet: -0.15 (0.48), residues: 142 loop : -0.43 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 590 TYR 0.010 0.001 TYR A1025 PHE 0.009 0.001 PHE A 758 TRP 0.015 0.001 TRP A 484 HIS 0.007 0.001 HIS A 592 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 8450) covalent geometry : angle 0.52304 (11416) hydrogen bonds : bond 0.03043 ( 278) hydrogen bonds : angle 4.34029 ( 804) metal coordination : bond 0.00254 ( 4) metal coordination : angle 0.66407 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.291 Fit side-chains REVERT: A 347 ILE cc_start: 0.8562 (OUTLIER) cc_final: 0.7695 (mm) REVERT: A 372 ASP cc_start: 0.8471 (t0) cc_final: 0.8187 (t0) REVERT: A 391 ARG cc_start: 0.7576 (mmm160) cc_final: 0.7085 (mmm160) REVERT: A 392 MET cc_start: 0.6653 (ppp) cc_final: 0.6268 (ppp) REVERT: A 395 ASN cc_start: 0.8731 (m-40) cc_final: 0.8438 (t0) REVERT: A 422 ASN cc_start: 0.6864 (p0) cc_final: 0.6520 (p0) REVERT: A 436 TRP cc_start: 0.8267 (m-10) cc_final: 0.7584 (m100) REVERT: A 485 TYR cc_start: 0.7920 (m-80) cc_final: 0.7564 (m-80) REVERT: A 710 ILE cc_start: 0.8609 (OUTLIER) cc_final: 0.8361 (mm) REVERT: A 872 ASP cc_start: 0.8706 (m-30) cc_final: 0.8440 (m-30) outliers start: 18 outliers final: 15 residues processed: 98 average time/residue: 0.0816 time to fit residues: 11.2787 Evaluate side-chains 98 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 861 GLU Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 1034 CYS Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain A residue 1278 VAL Chi-restraints excluded: chain A residue 1413 VAL Chi-restraints excluded: chain A residue 1414 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 30 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 94 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 75 optimal weight: 0.0370 chunk 57 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 chunk 90 optimal weight: 0.6980 chunk 15 optimal weight: 7.9990 chunk 52 optimal weight: 0.5980 chunk 20 optimal weight: 10.0000 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1250 GLN ** A1503 GLN ** 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 = 0.3802 r_free = 0.3802 target = 0.141394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.090435 restraints weight = 11958.250| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 3.46 r_work: 0.2951 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8454 Z= 0.096 Angle : 0.531 10.223 11419 Z= 0.260 Chirality : 0.041 0.169 1233 Planarity : 0.004 0.045 1467 Dihedral : 3.640 19.506 1118 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.56 % Allowed : 27.65 % Favored : 69.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.27), residues: 1014 helix: 1.89 (0.31), residues: 286 sheet: -0.16 (0.48), residues: 142 loop : -0.39 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 886 TYR 0.010 0.001 TYR A1025 PHE 0.022 0.001 PHE A 579 TRP 0.058 0.002 TRP A 396 HIS 0.003 0.000 HIS A 592 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 8450) covalent geometry : angle 0.53103 (11416) hydrogen bonds : bond 0.02946 ( 278) hydrogen bonds : angle 4.32940 ( 804) metal coordination : bond 0.00152 ( 4) metal coordination : angle 0.78169 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2055.95 seconds wall clock time: 35 minutes 49.33 seconds (2149.33 seconds total)