Starting phenix.real_space_refine on Sat Mar 7 07:20:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mop_23925/03_2026/7mop_23925.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mop_23925/03_2026/7mop_23925.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mop_23925/03_2026/7mop_23925.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mop_23925/03_2026/7mop_23925.map" model { file = "/net/cci-nas-00/data/ceres_data/7mop_23925/03_2026/7mop_23925.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mop_23925/03_2026/7mop_23925.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 S 122 5.16 5 C 12355 2.51 5 N 3325 2.21 5 O 3566 1.98 5 H 19681 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 181 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39049 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 38929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2445, 38929 Classifications: {'peptide': 2445} Link IDs: {'PTRANS': 104, 'TRANS': 2340} Chain breaks: 30 Chain: "B" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 120 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Time building chain proxies: 5.76, per 1000 atoms: 0.15 Number of scatterers: 39049 At special positions: 0 Unit cell: (135.3, 124.575, 169.95, 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) S 122 16.00 O 3566 8.00 N 3325 7.00 C 12355 6.00 H 19681 1.00 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: 3.42 Conformation dependent library (CDL) restraints added in 1.1 seconds 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4692 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 10 sheets defined 74.0% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 17 through 27 Processing helix chain 'A' and resid 32 through 39 Processing helix chain 'A' and resid 55 through 69 Processing helix chain 'A' and resid 89 through 104 removed outlier: 3.824A pdb=" N LEU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 123 Processing helix chain 'A' and resid 127 through 145 removed outlier: 3.596A pdb=" N VAL A 131 " --> pdb=" O ASP A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 168 Processing helix chain 'A' and resid 171 through 176 Processing helix chain 'A' and resid 185 through 189 removed outlier: 3.787A pdb=" N MET A 188 " --> pdb=" O ASP A 185 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N MET A 189 " --> pdb=" O LEU A 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 185 through 189' Processing helix chain 'A' and resid 235 through 247 Processing helix chain 'A' and resid 253 through 267 removed outlier: 4.202A pdb=" N LEU A 257 " --> pdb=" O LYS A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 290 Processing helix chain 'A' and resid 302 through 314 removed outlier: 4.213A pdb=" N ILE A 306 " --> pdb=" O TYR A 302 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLU A 307 " --> pdb=" O ASN A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 336 Processing helix chain 'A' and resid 343 through 351 Processing helix chain 'A' and resid 357 through 372 Processing helix chain 'A' and resid 379 through 395 Processing helix chain 'A' and resid 396 through 406 Processing helix chain 'A' and resid 407 through 419 removed outlier: 4.154A pdb=" N ALA A 411 " --> pdb=" O GLY A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 441 Processing helix chain 'A' and resid 444 through 450 Processing helix chain 'A' and resid 451 through 471 removed outlier: 3.754A pdb=" N LYS A 469 " --> pdb=" O ASP A 465 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLU A 470 " --> pdb=" O LEU A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 520 Processing helix chain 'A' and resid 527 through 531 Processing helix chain 'A' and resid 535 through 546 removed outlier: 3.518A pdb=" N SER A 539 " --> pdb=" O SER A 535 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N HIS A 542 " --> pdb=" O THR A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 569 Processing helix chain 'A' and resid 572 through 579 Processing helix chain 'A' and resid 580 through 590 Processing helix chain 'A' and resid 597 through 612 Proline residue: A 605 - end of helix Processing helix chain 'A' and resid 615 through 624 removed outlier: 3.752A pdb=" N CYS A 624 " --> pdb=" O SER A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 631 removed outlier: 3.717A pdb=" N ARG A 629 " --> pdb=" O GLN A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 638 removed outlier: 3.533A pdb=" N SER A 636 " --> pdb=" O VAL A 633 " (cutoff:3.500A) Proline residue: A 637 - end of helix Processing helix chain 'A' and resid 639 through 644 Processing helix chain 'A' and resid 653 through 670 Processing helix chain 'A' and resid 673 through 694 Processing helix chain 'A' and resid 765 through 782 Processing helix chain 'A' and resid 787 through 796 Processing helix chain 'A' and resid 798 through 805 removed outlier: 3.746A pdb=" N ILE A 805 " --> pdb=" O PRO A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 808 No H-bonds generated for 'chain 'A' and resid 806 through 808' Processing helix chain 'A' and resid 818 through 836 Processing helix chain 'A' and resid 838 through 853 Processing helix chain 'A' and resid 854 through 859 Proline residue: A 857 - end of helix No H-bonds generated for 'chain 'A' and resid 854 through 859' Processing helix chain 'A' and resid 868 through 876 removed outlier: 3.633A pdb=" N CYS A 876 " --> pdb=" O ARG A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 882 through 886 removed outlier: 3.555A pdb=" N LEU A 885 " --> pdb=" O ASP A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 911 removed outlier: 3.529A pdb=" N MET A 905 " --> pdb=" O ALA A 901 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N HIS A 908 " --> pdb=" O MET A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 926 Processing helix chain 'A' and resid 927 through 956 Processing helix chain 'A' and resid 967 through 975 removed outlier: 3.746A pdb=" N LYS A 973 " --> pdb=" O ALA A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 1042 through 1076 Proline residue: A1051 - end of helix Processing helix chain 'A' and resid 1097 through 1115 Processing helix chain 'A' and resid 1124 through 1143 removed outlier: 3.525A pdb=" N SER A1139 " --> pdb=" O VAL A1135 " (cutoff:3.500A) Proline residue: A1140 - end of helix Processing helix chain 'A' and resid 1150 through 1160 Processing helix chain 'A' and resid 1162 through 1176 Processing helix chain 'A' and resid 1181 through 1186 removed outlier: 4.131A pdb=" N LEU A1186 " --> pdb=" O VAL A1182 " (cutoff:3.500A) Processing helix chain 'A' and resid 1194 through 1211 removed outlier: 3.588A pdb=" N LYS A1208 " --> pdb=" O MET A1204 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN A1211 " --> pdb=" O GLU A1207 " (cutoff:3.500A) Processing helix chain 'A' and resid 1211 through 1216 Processing helix chain 'A' and resid 1237 through 1255 removed outlier: 3.789A pdb=" N THR A1251 " --> pdb=" O LYS A1247 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N CYS A1252 " --> pdb=" O ALA A1248 " (cutoff:3.500A) Processing helix chain 'A' and resid 1266 through 1294 Proline residue: A1285 - end of helix Processing helix chain 'A' and resid 1417 through 1427 Processing helix chain 'A' and resid 1432 through 1443 removed outlier: 3.722A pdb=" N LEU A1436 " --> pdb=" O GLU A1432 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS A1437 " --> pdb=" O GLN A1433 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR A1438 " --> pdb=" O ASP A1434 " (cutoff:3.500A) Processing helix chain 'A' and resid 1443 through 1454 Processing helix chain 'A' and resid 1457 through 1472 removed outlier: 3.567A pdb=" N ASP A1463 " --> pdb=" O TYR A1459 " (cutoff:3.500A) Processing helix chain 'A' and resid 1473 through 1498 removed outlier: 3.640A pdb=" N MET A1479 " --> pdb=" O ASP A1475 " (cutoff:3.500A) Processing helix chain 'A' and resid 1510 through 1520 removed outlier: 3.570A pdb=" N ILE A1514 " --> pdb=" O VAL A1510 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ALA A1518 " --> pdb=" O ILE A1514 " (cutoff:3.500A) Processing helix chain 'A' and resid 1520 through 1540 removed outlier: 4.103A pdb=" N ALA A1527 " --> pdb=" O ALA A1523 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N THR A1528 " --> pdb=" O SER A1524 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LEU A1531 " --> pdb=" O ALA A1527 " (cutoff:3.500A) Processing helix chain 'A' and resid 1540 through 1551 Processing helix chain 'A' and resid 1552 through 1575 removed outlier: 3.551A pdb=" N GLN A1565 " --> pdb=" O LEU A1561 " (cutoff:3.500A) Proline residue: A1566 - end of helix Processing helix chain 'A' and resid 1582 through 1608 Processing helix chain 'A' and resid 1631 through 1644 Processing helix chain 'A' and resid 1751 through 1768 Processing helix chain 'A' and resid 1771 through 1786 Processing helix chain 'A' and resid 1788 through 1798 Processing helix chain 'A' and resid 1799 through 1807 removed outlier: 3.877A pdb=" N MET A1803 " --> pdb=" O LYS A1799 " (cutoff:3.500A) Processing helix chain 'A' and resid 1808 through 1812 removed outlier: 3.557A pdb=" N GLY A1812 " --> pdb=" O GLN A1809 " (cutoff:3.500A) Processing helix chain 'A' and resid 1815 through 1829 Processing helix chain 'A' and resid 1830 through 1848 Processing helix chain 'A' and resid 1862 through 1865 Processing helix chain 'A' and resid 1866 through 1874 removed outlier: 3.850A pdb=" N ARG A1872 " --> pdb=" O ASN A1868 " (cutoff:3.500A) Processing helix chain 'A' and resid 1874 through 1881 Processing helix chain 'A' and resid 1881 through 1892 Processing helix chain 'A' and resid 1907 through 1917 Processing helix chain 'A' and resid 1939 through 1953 removed outlier: 3.806A pdb=" N ASP A1948 " --> pdb=" O GLU A1944 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET A1949 " --> pdb=" O VAL A1945 " (cutoff:3.500A) Processing helix chain 'A' and resid 2067 through 2082 Processing helix chain 'A' and resid 2082 through 2092 removed outlier: 3.838A pdb=" N ALA A2086 " --> pdb=" O TYR A2082 " (cutoff:3.500A) Processing helix chain 'A' and resid 2107 through 2115 Processing helix chain 'A' and resid 2127 through 2142 Processing helix chain 'A' and resid 2148 through 2166 Processing helix chain 'A' and resid 2169 through 2188 Processing helix chain 'A' and resid 2211 through 2219 Processing helix chain 'A' and resid 2220 through 2227 Processing helix chain 'A' and resid 2228 through 2232 Processing helix chain 'A' and resid 2238 through 2259 removed outlier: 3.721A pdb=" N THR A2242 " --> pdb=" O ASN A2238 " (cutoff:3.500A) Proline residue: A2249 - end of helix Processing helix chain 'A' and resid 2646 through 2659 Processing helix chain 'A' and resid 2662 through 2696 removed outlier: 3.819A pdb=" N HIS A2677 " --> pdb=" O SER A2673 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N PHE A2680 " --> pdb=" O ASN A2676 " (cutoff:3.500A) Processing helix chain 'A' and resid 3182 through 3195 Processing helix chain 'A' and resid 3201 through 3213 Processing helix chain 'A' and resid 3215 through 3234 Processing helix chain 'A' and resid 3328 through 3346 Processing helix chain 'A' and resid 3388 through 3398 removed outlier: 3.733A pdb=" N MET A3398 " --> pdb=" O LYS A3394 " (cutoff:3.500A) Processing helix chain 'A' and resid 3430 through 3437 Processing helix chain 'A' and resid 3440 through 3446 removed outlier: 3.732A pdb=" N SER A3446 " --> pdb=" O VAL A3442 " (cutoff:3.500A) Processing helix chain 'A' and resid 3446 through 3462 removed outlier: 3.612A pdb=" N ILE A3462 " --> pdb=" O SER A3458 " (cutoff:3.500A) Processing helix chain 'A' and resid 3576 through 3589 removed outlier: 3.559A pdb=" N GLU A3586 " --> pdb=" O GLN A3582 " (cutoff:3.500A) Processing helix chain 'A' and resid 3595 through 3612 Processing helix chain 'A' and resid 3612 through 3650 removed outlier: 4.363A pdb=" N THR A3640 " --> pdb=" O LYS A3636 " (cutoff:3.500A) Processing helix chain 'A' and resid 3723 through 3725 No H-bonds generated for 'chain 'A' and resid 3723 through 3725' Processing helix chain 'A' and resid 3726 through 3731 Processing helix chain 'A' and resid 3734 through 3751 removed outlier: 3.684A pdb=" N ASP A3751 " --> pdb=" O ILE A3747 " (cutoff:3.500A) Processing helix chain 'A' and resid 3853 through 3870 Processing helix chain 'A' and resid 3873 through 3878 removed outlier: 4.053A pdb=" N VAL A3878 " --> pdb=" O ALA A3875 " (cutoff:3.500A) Processing helix chain 'A' and resid 3879 through 3890 Processing helix chain 'A' and resid 3954 through 3962 Processing helix chain 'A' and resid 3962 through 3973 Processing helix chain 'A' and resid 3980 through 3987 removed outlier: 3.505A pdb=" N ALA A3983 " --> pdb=" O GLY A3980 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL A3984 " --> pdb=" O PRO A3981 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A3985 " --> pdb=" O PHE A3982 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP A3987 " --> pdb=" O VAL A3984 " (cutoff:3.500A) Processing helix chain 'A' and resid 3988 through 3992 removed outlier: 3.827A pdb=" N VAL A3991 " --> pdb=" O TYR A3988 " (cutoff:3.500A) Processing helix chain 'A' and resid 3993 through 4002 Processing helix chain 'A' and resid 4025 through 4035 Processing helix chain 'A' and resid 4038 through 4043 Processing helix chain 'A' and resid 4057 through 4073 Processing helix chain 'A' and resid 4074 through 4079 removed outlier: 6.174A pdb=" N MET A4077 " --> pdb=" O PHE A4074 " (cutoff:3.500A) Processing helix chain 'A' and resid 4096 through 4100 removed outlier: 3.802A pdb=" N CYS A4099 " --> pdb=" O SER A4096 " (cutoff:3.500A) Processing helix chain 'A' and resid 4102 through 4121 Processing helix chain 'A' and resid 4129 through 4138 Processing helix chain 'A' and resid 4144 through 4150 removed outlier: 4.148A pdb=" N SER A4148 " --> pdb=" O THR A4144 " (cutoff:3.500A) Processing helix chain 'A' and resid 4150 through 4161 Processing helix chain 'A' and resid 4164 through 4168 Processing helix chain 'A' and resid 4202 through 4217 removed outlier: 3.692A pdb=" N HIS A4208 " --> pdb=" O LYS A4204 " (cutoff:3.500A) Processing helix chain 'A' and resid 4219 through 4232 Processing helix chain 'A' and resid 4235 through 4240 Processing helix chain 'A' and resid 4243 through 4252 removed outlier: 3.837A pdb=" N GLU A4248 " --> pdb=" O GLU A4244 " (cutoff:3.500A) Processing helix chain 'A' and resid 4258 through 4265 Processing helix chain 'A' and resid 4275 through 4288 Processing helix chain 'A' and resid 4289 through 4302 Processing helix chain 'A' and resid 4310 through 4313 Processing helix chain 'A' and resid 4340 through 4342 No H-bonds generated for 'chain 'A' and resid 4340 through 4342' Processing helix chain 'A' and resid 4352 through 4364 Processing sheet with id=AA1, first strand: chain 'A' and resid 698 through 699 removed outlier: 5.966A pdb=" N ILE A 698 " --> pdb=" O ILE A 764 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 1626 through 1629 Processing sheet with id=AA3, first strand: chain 'A' and resid 1893 through 1895 Processing sheet with id=AA4, first strand: chain 'A' and resid 3289 through 3290 Processing sheet with id=AA5, first strand: chain 'A' and resid 3301 through 3302 Processing sheet with id=AA6, first strand: chain 'A' and resid 4016 through 4021 removed outlier: 5.947A pdb=" N MET A4017 " --> pdb=" O TYR A4047 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N VAL A4049 " --> pdb=" O MET A4017 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N VAL A4019 " --> pdb=" O VAL A4049 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 4081 through 4082 Processing sheet with id=AA8, first strand: chain 'A' and resid 4175 through 4180 Processing sheet with id=AA9, first strand: chain 'A' and resid 4266 through 4268 removed outlier: 6.810A pdb=" N GLU A4267 " --> pdb=" O ILE A4325 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N ARG A4327 " --> pdb=" O GLU A4267 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 4315 through 4316 removed outlier: 3.740A pdb=" N GLY A4319 " --> pdb=" O GLY A4316 " (cutoff:3.500A) 1242 hydrogen bonds defined for protein. 3645 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: 11.68 Time building geometry restraints manager: 4.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.80 - 1.00: 19628 1.00 - 1.20: 53 1.20 - 1.41: 7748 1.41 - 1.61: 11776 1.61 - 1.81: 191 Bond restraints: 39396 Sorted by residual: bond pdb=" NE2 GLN A 275 " pdb="HE22 GLN A 275 " ideal model delta sigma weight residual 0.860 0.799 0.061 2.00e-02 2.50e+03 9.35e+00 bond pdb=" NE2 GLN A 278 " pdb="HE22 GLN A 278 " ideal model delta sigma weight residual 0.860 0.805 0.055 2.00e-02 2.50e+03 7.49e+00 bond pdb=" N PRO A1140 " pdb=" CD PRO A1140 " ideal model delta sigma weight residual 1.473 1.441 0.032 1.40e-02 5.10e+03 5.38e+00 bond pdb=" CG LEU A 186 " pdb=" CD2 LEU A 186 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.97e+00 bond pdb=" CA ALA A1597 " pdb=" C ALA A1597 " ideal model delta sigma weight residual 1.524 1.506 0.018 1.29e-02 6.01e+03 1.88e+00 ... (remaining 39391 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.31: 71369 5.31 - 10.62: 23 10.62 - 15.92: 1 15.92 - 21.23: 3 21.23 - 26.54: 3 Bond angle restraints: 71399 Sorted by residual: angle pdb=" CD GLN A 278 " pdb=" NE2 GLN A 278 " pdb="HE22 GLN A 278 " ideal model delta sigma weight residual 120.00 146.54 -26.54 3.00e+00 1.11e-01 7.83e+01 angle pdb="HE21 GLN A 278 " pdb=" NE2 GLN A 278 " pdb="HE22 GLN A 278 " ideal model delta sigma weight residual 120.00 93.69 26.31 3.00e+00 1.11e-01 7.69e+01 angle pdb=" CD GLN A 278 " pdb=" NE2 GLN A 278 " pdb="HE21 GLN A 278 " ideal model delta sigma weight residual 120.00 98.57 21.43 3.00e+00 1.11e-01 5.10e+01 angle pdb="HE21 GLN A 275 " pdb=" NE2 GLN A 275 " pdb="HE22 GLN A 275 " ideal model delta sigma weight residual 120.00 99.21 20.79 3.00e+00 1.11e-01 4.80e+01 angle pdb=" CD GLN A 275 " pdb=" NE2 GLN A 275 " pdb="HE22 GLN A 275 " ideal model delta sigma weight residual 120.00 140.53 -20.53 3.00e+00 1.11e-01 4.68e+01 ... (remaining 71394 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 16607 17.98 - 35.96: 1219 35.96 - 53.95: 428 53.95 - 71.93: 100 71.93 - 89.91: 23 Dihedral angle restraints: 18377 sinusoidal: 10185 harmonic: 8192 Sorted by residual: dihedral pdb=" CA GLU A2124 " pdb=" C GLU A2124 " pdb=" N ASP A2125 " pdb=" CA ASP A2125 " ideal model delta harmonic sigma weight residual 180.00 152.09 27.91 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA TRP A 54 " pdb=" C TRP A 54 " pdb=" N VAL A 55 " pdb=" CA VAL A 55 " ideal model delta harmonic sigma weight residual -180.00 -153.25 -26.75 0 5.00e+00 4.00e-02 2.86e+01 dihedral pdb=" CA ASP A1144 " pdb=" C ASP A1144 " pdb=" N GLU A1145 " pdb=" CA GLU A1145 " ideal model delta harmonic sigma weight residual 180.00 155.47 24.53 0 5.00e+00 4.00e-02 2.41e+01 ... (remaining 18374 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2820 0.073 - 0.145: 320 0.145 - 0.218: 12 0.218 - 0.291: 1 0.291 - 0.363: 1 Chirality restraints: 3154 Sorted by residual: chirality pdb=" CA ARG A 144 " pdb=" N ARG A 144 " pdb=" C ARG A 144 " pdb=" CB ARG A 144 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.30e+00 chirality pdb=" CB ILE A2513 " pdb=" CA ILE A2513 " pdb=" CG1 ILE A2513 " pdb=" CG2 ILE A2513 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA THR A 157 " pdb=" N THR A 157 " pdb=" C THR A 157 " pdb=" CB THR A 157 " both_signs ideal model delta sigma weight residual False 2.53 2.31 0.21 2.00e-01 2.50e+01 1.16e+00 ... (remaining 3151 not shown) Planarity restraints: 5677 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 275 " -0.059 2.00e-02 2.50e+03 9.56e-02 1.37e+02 pdb=" CD GLN A 275 " 0.019 2.00e-02 2.50e+03 pdb=" OE1 GLN A 275 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 GLN A 275 " 0.162 2.00e-02 2.50e+03 pdb="HE21 GLN A 275 " 0.033 2.00e-02 2.50e+03 pdb="HE22 GLN A 275 " -0.154 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 278 " 0.044 2.00e-02 2.50e+03 9.01e-02 1.22e+02 pdb=" CD GLN A 278 " 0.015 2.00e-02 2.50e+03 pdb=" OE1 GLN A 278 " -0.006 2.00e-02 2.50e+03 pdb=" NE2 GLN A 278 " -0.155 2.00e-02 2.50e+03 pdb="HE21 GLN A 278 " -0.042 2.00e-02 2.50e+03 pdb="HE22 GLN A 278 " 0.144 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A4200 " -0.025 2.00e-02 2.50e+03 5.09e-02 2.59e+01 pdb=" CD GLU A4200 " 0.088 2.00e-02 2.50e+03 pdb=" OE1 GLU A4200 " -0.032 2.00e-02 2.50e+03 pdb=" OE2 GLU A4200 " -0.031 2.00e-02 2.50e+03 ... (remaining 5674 not shown) Histogram of nonbonded interaction distances: 1.38 - 2.02: 445 2.02 - 2.67: 58296 2.67 - 3.31: 118823 3.31 - 3.96: 148162 3.96 - 4.60: 238143 Nonbonded interactions: 563869 Sorted by model distance: nonbonded pdb=" OD1 ASN A3967 " pdb=" H ASP A3993 " model vdw 1.377 2.450 nonbonded pdb=" O GLU A 181 " pdb=" HH TYR A 191 " model vdw 1.547 2.450 nonbonded pdb=" OE1 GLN A 368 " pdb=" HZ3 LYS A 414 " model vdw 1.556 2.450 nonbonded pdb=" O ARG A4334 " pdb=" HH TYR A4350 " model vdw 1.557 2.450 nonbonded pdb="HH11 ARG A4082 " pdb=" OD1 ASN A4094 " model vdw 1.567 2.450 ... (remaining 563864 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: 3.440 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: 0.260 Extract box with map and model: 0.660 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 36.810 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 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 : 0.006 0.062 19715 Z= 0.243 Angle : 0.795 11.667 26687 Z= 0.459 Chirality : 0.045 0.363 3154 Planarity : 0.007 0.051 3361 Dihedral : 14.721 89.911 7336 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.33 % Allowed : 10.17 % Favored : 88.50 % 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: -0.65 (0.17), residues: 2388 helix: -0.21 (0.12), residues: 1667 sheet: 0.63 (0.61), residues: 71 loop : -0.75 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.043 0.005 ARG A2255 TYR 0.045 0.004 TYR A4154 PHE 0.038 0.003 PHE A 141 TRP 0.042 0.003 TRP A1513 HIS 0.009 0.002 HIS A1151 Details of bonding type rmsd covalent geometry : bond 0.00567 (19715) covalent geometry : angle 0.79520 (26687) hydrogen bonds : bond 0.12504 ( 1242) hydrogen bonds : angle 6.07569 ( 3645) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 3997 is missing expected H atoms. Skipping. Evaluate side-chains 427 residues out of total 2173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 398 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 563 THR cc_start: 0.8767 (OUTLIER) cc_final: 0.8512 (m) REVERT: A 1187 GLU cc_start: 0.6785 (tt0) cc_final: 0.6537 (tt0) REVERT: A 1787 ARG cc_start: 0.7623 (ttp-170) cc_final: 0.7421 (ttp80) REVERT: A 1930 LEU cc_start: 0.7882 (tt) cc_final: 0.7332 (mt) REVERT: A 2221 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8140 (tm) REVERT: A 3387 ASP cc_start: 0.5523 (OUTLIER) cc_final: 0.4821 (p0) REVERT: A 3854 ASP cc_start: 0.6998 (m-30) cc_final: 0.6567 (m-30) REVERT: A 3858 ASP cc_start: 0.6743 (m-30) cc_final: 0.6415 (m-30) REVERT: A 3955 PHE cc_start: 0.4507 (p90) cc_final: 0.3943 (p90) REVERT: A 4017 MET cc_start: 0.2108 (ttm) cc_final: 0.1702 (tmm) REVERT: A 4317 MET cc_start: 0.2700 (ttm) cc_final: 0.1924 (ttp) outliers start: 29 outliers final: 12 residues processed: 422 average time/residue: 0.3836 time to fit residues: 236.1678 Evaluate side-chains 234 residues out of total 2173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 219 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 563 THR Chi-restraints excluded: chain A residue 955 CYS Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain A residue 1442 THR Chi-restraints excluded: chain A residue 2150 VAL Chi-restraints excluded: chain A residue 2156 VAL Chi-restraints excluded: chain A residue 2221 LEU Chi-restraints excluded: chain A residue 2228 VAL Chi-restraints excluded: chain A residue 2235 SER Chi-restraints excluded: chain A residue 2646 THR Chi-restraints excluded: chain A residue 3346 VAL Chi-restraints excluded: chain A residue 3387 ASP Chi-restraints excluded: chain A residue 3615 THR Chi-restraints excluded: chain A residue 3747 ILE Chi-restraints excluded: chain A residue 4183 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 216 optimal weight: 8.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 235 optimal weight: 9.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 ASN A 278 GLN A 791 GLN A 923 ASN A 924 GLN ** A3302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3736 GLN A4324 GLN A4358 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.162014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.128880 restraints weight = 89704.135| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 2.04 r_work: 0.3459 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 19715 Z= 0.175 Angle : 0.616 6.325 26687 Z= 0.323 Chirality : 0.038 0.158 3154 Planarity : 0.005 0.052 3361 Dihedral : 5.228 48.749 2636 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.52 % Allowed : 12.06 % Favored : 86.42 % 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: 0.75 (0.17), residues: 2388 helix: 0.88 (0.12), residues: 1682 sheet: 0.35 (0.55), residues: 71 loop : -0.27 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 144 TYR 0.014 0.001 TYR A4047 PHE 0.021 0.002 PHE A 358 TRP 0.020 0.002 TRP A1513 HIS 0.013 0.001 HIS A 118 Details of bonding type rmsd covalent geometry : bond 0.00396 (19715) covalent geometry : angle 0.61572 (26687) hydrogen bonds : bond 0.04851 ( 1242) hydrogen bonds : angle 4.63833 ( 3645) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 3997 is missing expected H atoms. Skipping. Evaluate side-chains 260 residues out of total 2173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 227 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 ASP cc_start: 0.7208 (t0) cc_final: 0.6644 (t0) REVERT: A 1065 GLU cc_start: 0.8250 (tt0) cc_final: 0.7990 (mt-10) REVERT: A 1930 LEU cc_start: 0.7886 (tt) cc_final: 0.7460 (mt) REVERT: A 2104 GLU cc_start: 0.7017 (pm20) cc_final: 0.6778 (tp30) REVERT: A 2515 THR cc_start: 0.8129 (m) cc_final: 0.7800 (p) REVERT: A 3854 ASP cc_start: 0.7483 (m-30) cc_final: 0.7050 (m-30) REVERT: A 3858 ASP cc_start: 0.7553 (m-30) cc_final: 0.7169 (m-30) REVERT: A 3955 PHE cc_start: 0.5304 (p90) cc_final: 0.4674 (p90) REVERT: A 3957 ARG cc_start: 0.7553 (mmm-85) cc_final: 0.7047 (mmp-170) REVERT: A 4017 MET cc_start: 0.0803 (ttm) cc_final: 0.0560 (tmm) REVERT: A 4162 GLU cc_start: 0.2176 (OUTLIER) cc_final: 0.1583 (pt0) REVERT: A 4317 MET cc_start: 0.3234 (ttm) cc_final: 0.2277 (ttp) outliers start: 33 outliers final: 22 residues processed: 250 average time/residue: 0.3330 time to fit residues: 127.1500 Evaluate side-chains 215 residues out of total 2173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 192 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 764 ILE Chi-restraints excluded: chain A residue 787 ASP Chi-restraints excluded: chain A residue 868 SER Chi-restraints excluded: chain A residue 955 CYS Chi-restraints excluded: chain A residue 1042 MET Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain A residue 2150 VAL Chi-restraints excluded: chain A residue 2156 VAL Chi-restraints excluded: chain A residue 2238 ASN Chi-restraints excluded: chain A residue 2646 THR Chi-restraints excluded: chain A residue 3346 VAL Chi-restraints excluded: chain A residue 3615 THR Chi-restraints excluded: chain A residue 3619 VAL Chi-restraints excluded: chain A residue 3747 ILE Chi-restraints excluded: chain A residue 3961 THR Chi-restraints excluded: chain A residue 4162 GLU Chi-restraints excluded: chain A residue 4183 VAL Chi-restraints excluded: chain A residue 4254 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 76 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 211 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 190 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN A 368 GLN A1155 GLN ** A3325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3582 GLN A3736 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.156574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.121458 restraints weight = 90801.405| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.36 r_work: 0.3347 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 19715 Z= 0.238 Angle : 0.621 6.491 26687 Z= 0.326 Chirality : 0.039 0.155 3154 Planarity : 0.005 0.048 3361 Dihedral : 4.881 43.201 2628 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.75 % Allowed : 12.84 % Favored : 85.41 % 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: 0.93 (0.17), residues: 2388 helix: 1.07 (0.12), residues: 1692 sheet: -0.09 (0.54), residues: 75 loop : -0.34 (0.26), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A3444 TYR 0.021 0.002 TYR A 106 PHE 0.024 0.002 PHE A1592 TRP 0.015 0.002 TRP A1513 HIS 0.008 0.002 HIS A3325 Details of bonding type rmsd covalent geometry : bond 0.00553 (19715) covalent geometry : angle 0.62069 (26687) hydrogen bonds : bond 0.04867 ( 1242) hydrogen bonds : angle 4.47013 ( 3645) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 3997 is missing expected H atoms. Skipping. Evaluate side-chains 232 residues out of total 2173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 194 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 ASP cc_start: 0.8176 (m-30) cc_final: 0.7906 (m-30) REVERT: A 372 ASP cc_start: 0.7390 (t0) cc_final: 0.6927 (t0) REVERT: A 444 MET cc_start: 0.8066 (mmt) cc_final: 0.7751 (mmt) REVERT: A 882 ASP cc_start: 0.6969 (OUTLIER) cc_final: 0.6758 (m-30) REVERT: A 1647 THR cc_start: 0.8102 (p) cc_final: 0.7791 (t) REVERT: A 2104 GLU cc_start: 0.7170 (pm20) cc_final: 0.6846 (tp30) REVERT: A 2221 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8202 (tm) REVERT: A 2515 THR cc_start: 0.8098 (m) cc_final: 0.7814 (p) REVERT: A 4017 MET cc_start: 0.1140 (ttm) cc_final: 0.0788 (tmm) outliers start: 38 outliers final: 25 residues processed: 222 average time/residue: 0.3432 time to fit residues: 116.4467 Evaluate side-chains 198 residues out of total 2173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 171 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 764 ILE Chi-restraints excluded: chain A residue 787 ASP Chi-restraints excluded: chain A residue 882 ASP Chi-restraints excluded: chain A residue 1042 MET Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1180 VAL Chi-restraints excluded: chain A residue 1505 SER Chi-restraints excluded: chain A residue 1628 CYS Chi-restraints excluded: chain A residue 1636 SER Chi-restraints excluded: chain A residue 1924 LEU Chi-restraints excluded: chain A residue 2221 LEU Chi-restraints excluded: chain A residue 2235 SER Chi-restraints excluded: chain A residue 2646 THR Chi-restraints excluded: chain A residue 2672 VAL Chi-restraints excluded: chain A residue 3346 VAL Chi-restraints excluded: chain A residue 3619 VAL Chi-restraints excluded: chain A residue 3961 THR Chi-restraints excluded: chain A residue 4183 VAL Chi-restraints excluded: chain A residue 4351 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 55 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 235 optimal weight: 9.9990 chunk 51 optimal weight: 0.5980 chunk 240 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 152 optimal weight: 1.9990 chunk 210 optimal weight: 0.8980 chunk 193 optimal weight: 0.0060 chunk 212 optimal weight: 0.0050 chunk 31 optimal weight: 3.9990 overall best weight: 0.4810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN ** A3325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3736 GLN A4044 ASN A4245 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.160722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.127629 restraints weight = 89113.701| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 2.04 r_work: 0.3442 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 19715 Z= 0.109 Angle : 0.512 5.998 26687 Z= 0.262 Chirality : 0.035 0.134 3154 Planarity : 0.004 0.050 3361 Dihedral : 4.287 40.995 2621 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.20 % Allowed : 13.67 % Favored : 85.14 % 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: 1.67 (0.17), residues: 2388 helix: 1.68 (0.13), residues: 1678 sheet: -0.08 (0.54), residues: 75 loop : -0.18 (0.26), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A2175 TYR 0.012 0.001 TYR A1593 PHE 0.017 0.001 PHE A1198 TRP 0.015 0.001 TRP A1513 HIS 0.005 0.001 HIS A1163 Details of bonding type rmsd covalent geometry : bond 0.00237 (19715) covalent geometry : angle 0.51152 (26687) hydrogen bonds : bond 0.03920 ( 1242) hydrogen bonds : angle 4.13338 ( 3645) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 3997 is missing expected H atoms. Skipping. Evaluate side-chains 210 residues out of total 2173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 184 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 ASP cc_start: 0.7213 (t0) cc_final: 0.6899 (t0) REVERT: A 882 ASP cc_start: 0.6985 (OUTLIER) cc_final: 0.6770 (m-30) REVERT: A 1647 THR cc_start: 0.8204 (p) cc_final: 0.7977 (t) REVERT: A 2104 GLU cc_start: 0.7007 (pm20) cc_final: 0.6758 (tp30) REVERT: A 2515 THR cc_start: 0.8005 (m) cc_final: 0.7672 (p) REVERT: A 4017 MET cc_start: 0.1489 (ttm) cc_final: 0.1085 (ttp) REVERT: A 4042 MET cc_start: 0.5462 (mmm) cc_final: 0.5209 (mmm) outliers start: 26 outliers final: 17 residues processed: 204 average time/residue: 0.3288 time to fit residues: 103.5610 Evaluate side-chains 189 residues out of total 2173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 171 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 764 ILE Chi-restraints excluded: chain A residue 787 ASP Chi-restraints excluded: chain A residue 882 ASP Chi-restraints excluded: chain A residue 1042 MET Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1180 VAL Chi-restraints excluded: chain A residue 1435 GLU Chi-restraints excluded: chain A residue 1531 LEU Chi-restraints excluded: chain A residue 2250 LEU Chi-restraints excluded: chain A residue 3200 LEU Chi-restraints excluded: chain A residue 3346 VAL Chi-restraints excluded: chain A residue 3615 THR Chi-restraints excluded: chain A residue 3619 VAL Chi-restraints excluded: chain A residue 4183 VAL Chi-restraints excluded: chain A residue 4351 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 65 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 190 optimal weight: 4.9990 chunk 172 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 202 optimal weight: 5.9990 chunk 152 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 173 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3327 GLN A3736 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.156145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.122509 restraints weight = 89509.287| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 2.12 r_work: 0.3369 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 19715 Z= 0.237 Angle : 0.590 6.381 26687 Z= 0.309 Chirality : 0.039 0.147 3154 Planarity : 0.005 0.053 3361 Dihedral : 4.422 37.827 2620 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.12 % Allowed : 13.58 % Favored : 84.31 % 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: 1.33 (0.17), residues: 2388 helix: 1.43 (0.12), residues: 1693 sheet: -0.26 (0.56), residues: 75 loop : -0.36 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A3444 TYR 0.023 0.002 TYR A 106 PHE 0.026 0.002 PHE A1592 TRP 0.017 0.002 TRP A1513 HIS 0.007 0.001 HIS A 894 Details of bonding type rmsd covalent geometry : bond 0.00541 (19715) covalent geometry : angle 0.58974 (26687) hydrogen bonds : bond 0.04641 ( 1242) hydrogen bonds : angle 4.28227 ( 3645) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 3997 is missing expected H atoms. Skipping. Evaluate side-chains 220 residues out of total 2173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 174 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASP cc_start: 0.6334 (OUTLIER) cc_final: 0.5988 (t0) REVERT: A 372 ASP cc_start: 0.7369 (t0) cc_final: 0.6875 (t0) REVERT: A 882 ASP cc_start: 0.7045 (OUTLIER) cc_final: 0.6772 (m-30) REVERT: A 1099 ARG cc_start: 0.7951 (mtp180) cc_final: 0.7638 (mpt180) REVERT: A 1647 THR cc_start: 0.8280 (p) cc_final: 0.8055 (t) REVERT: A 2221 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8259 (tm) REVERT: A 2515 THR cc_start: 0.8136 (m) cc_final: 0.7788 (p) REVERT: A 2522 ARG cc_start: 0.6391 (OUTLIER) cc_final: 0.6110 (mmt180) REVERT: A 2656 LYS cc_start: 0.8507 (tttm) cc_final: 0.8302 (ttmm) REVERT: A 3290 MET cc_start: 0.7635 (ttm) cc_final: 0.7235 (ttp) REVERT: A 4017 MET cc_start: 0.1827 (ttm) cc_final: 0.1299 (ttp) REVERT: A 4317 MET cc_start: 0.3466 (ttm) cc_final: 0.2615 (ttp) outliers start: 46 outliers final: 31 residues processed: 210 average time/residue: 0.3458 time to fit residues: 111.6478 Evaluate side-chains 204 residues out of total 2173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 169 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 764 ILE Chi-restraints excluded: chain A residue 787 ASP Chi-restraints excluded: chain A residue 882 ASP Chi-restraints excluded: chain A residue 1042 MET Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1180 VAL Chi-restraints excluded: chain A residue 1435 GLU Chi-restraints excluded: chain A residue 1505 SER Chi-restraints excluded: chain A residue 1517 MET Chi-restraints excluded: chain A residue 1628 CYS Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain A residue 1672 THR Chi-restraints excluded: chain A residue 1924 LEU Chi-restraints excluded: chain A residue 2221 LEU Chi-restraints excluded: chain A residue 2522 ARG Chi-restraints excluded: chain A residue 2646 THR Chi-restraints excluded: chain A residue 2654 GLU Chi-restraints excluded: chain A residue 2672 VAL Chi-restraints excluded: chain A residue 3200 LEU Chi-restraints excluded: chain A residue 3346 VAL Chi-restraints excluded: chain A residue 3615 THR Chi-restraints excluded: chain A residue 3619 VAL Chi-restraints excluded: chain A residue 3961 THR Chi-restraints excluded: chain A residue 4069 ILE Chi-restraints excluded: chain A residue 4183 VAL Chi-restraints excluded: chain A residue 4351 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 109 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 159 optimal weight: 0.5980 chunk 168 optimal weight: 0.8980 chunk 220 optimal weight: 9.9990 chunk 223 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 182 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 166 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3736 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.158041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.124767 restraints weight = 89532.362| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.08 r_work: 0.3409 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19715 Z= 0.134 Angle : 0.517 5.673 26687 Z= 0.266 Chirality : 0.035 0.135 3154 Planarity : 0.004 0.051 3361 Dihedral : 4.228 35.948 2620 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.61 % Allowed : 13.90 % Favored : 84.49 % 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: 1.71 (0.17), residues: 2388 helix: 1.76 (0.12), residues: 1685 sheet: -0.13 (0.58), residues: 75 loop : -0.34 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A3444 TYR 0.012 0.001 TYR A1593 PHE 0.019 0.001 PHE A1198 TRP 0.017 0.001 TRP A1513 HIS 0.010 0.001 HIS A 450 Details of bonding type rmsd covalent geometry : bond 0.00305 (19715) covalent geometry : angle 0.51714 (26687) hydrogen bonds : bond 0.04049 ( 1242) hydrogen bonds : angle 4.09440 ( 3645) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 3997 is missing expected H atoms. Skipping. Evaluate side-chains 208 residues out of total 2173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 173 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASP cc_start: 0.6220 (OUTLIER) cc_final: 0.5949 (t0) REVERT: A 372 ASP cc_start: 0.7287 (t0) cc_final: 0.6952 (t0) REVERT: A 882 ASP cc_start: 0.6995 (OUTLIER) cc_final: 0.6701 (m-30) REVERT: A 1647 THR cc_start: 0.8253 (p) cc_final: 0.8036 (t) REVERT: A 2104 GLU cc_start: 0.7487 (pm20) cc_final: 0.7108 (tp30) REVERT: A 2228 VAL cc_start: 0.8538 (OUTLIER) cc_final: 0.8327 (t) REVERT: A 2515 THR cc_start: 0.8005 (m) cc_final: 0.7668 (p) REVERT: A 2522 ARG cc_start: 0.6214 (OUTLIER) cc_final: 0.5987 (mmt180) REVERT: A 2656 LYS cc_start: 0.8520 (tttm) cc_final: 0.8295 (ttmm) REVERT: A 3217 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.7896 (mp10) REVERT: A 4017 MET cc_start: 0.1840 (ttm) cc_final: 0.1241 (ttp) REVERT: A 4317 MET cc_start: 0.3466 (ttm) cc_final: 0.2577 (ttp) outliers start: 35 outliers final: 26 residues processed: 201 average time/residue: 0.3295 time to fit residues: 103.6402 Evaluate side-chains 197 residues out of total 2173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 166 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 764 ILE Chi-restraints excluded: chain A residue 787 ASP Chi-restraints excluded: chain A residue 882 ASP Chi-restraints excluded: chain A residue 1042 MET Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1180 VAL Chi-restraints excluded: chain A residue 1435 GLU Chi-restraints excluded: chain A residue 1531 LEU Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain A residue 2228 VAL Chi-restraints excluded: chain A residue 2250 LEU Chi-restraints excluded: chain A residue 2522 ARG Chi-restraints excluded: chain A residue 2646 THR Chi-restraints excluded: chain A residue 2654 GLU Chi-restraints excluded: chain A residue 3200 LEU Chi-restraints excluded: chain A residue 3217 GLN Chi-restraints excluded: chain A residue 3346 VAL Chi-restraints excluded: chain A residue 3615 THR Chi-restraints excluded: chain A residue 3619 VAL Chi-restraints excluded: chain A residue 3961 THR Chi-restraints excluded: chain A residue 3993 ASP Chi-restraints excluded: chain A residue 4069 ILE Chi-restraints excluded: chain A residue 4183 VAL Chi-restraints excluded: chain A residue 4351 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 220 optimal weight: 10.0000 chunk 118 optimal weight: 5.9990 chunk 173 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 231 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 145 optimal weight: 0.0670 chunk 238 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 overall best weight: 2.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3325 HIS ** 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 = 0.4027 r_free = 0.4027 target = 0.154711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.121105 restraints weight = 89539.652| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.13 r_work: 0.3342 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.4339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 19715 Z= 0.262 Angle : 0.608 6.065 26687 Z= 0.319 Chirality : 0.040 0.151 3154 Planarity : 0.005 0.050 3361 Dihedral : 4.468 32.877 2620 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.98 % Allowed : 14.31 % Favored : 83.71 % 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: 1.18 (0.17), residues: 2388 helix: 1.40 (0.12), residues: 1687 sheet: -0.26 (0.59), residues: 75 loop : -0.66 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A3444 TYR 0.016 0.002 TYR A4047 PHE 0.030 0.002 PHE A1592 TRP 0.017 0.002 TRP A1513 HIS 0.008 0.002 HIS A 260 Details of bonding type rmsd covalent geometry : bond 0.00606 (19715) covalent geometry : angle 0.60811 (26687) hydrogen bonds : bond 0.04754 ( 1242) hydrogen bonds : angle 4.32097 ( 3645) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 3997 is missing expected H atoms. Skipping. Evaluate side-chains 216 residues out of total 2173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 173 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASP cc_start: 0.6227 (OUTLIER) cc_final: 0.5950 (t0) REVERT: A 882 ASP cc_start: 0.7099 (OUTLIER) cc_final: 0.6766 (m-30) REVERT: A 1647 THR cc_start: 0.8296 (p) cc_final: 0.8051 (t) REVERT: A 2104 GLU cc_start: 0.7415 (pm20) cc_final: 0.7077 (tp30) REVERT: A 2156 VAL cc_start: 0.8798 (OUTLIER) cc_final: 0.8491 (t) REVERT: A 2221 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8210 (tm) REVERT: A 2228 VAL cc_start: 0.8630 (OUTLIER) cc_final: 0.8420 (t) REVERT: A 2515 THR cc_start: 0.8137 (m) cc_final: 0.7803 (p) REVERT: A 2522 ARG cc_start: 0.6296 (OUTLIER) cc_final: 0.5866 (mmt180) REVERT: A 2656 LYS cc_start: 0.8518 (tttm) cc_final: 0.8282 (ttmm) REVERT: A 3217 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7808 (mp10) REVERT: A 4162 GLU cc_start: 0.1965 (OUTLIER) cc_final: 0.1153 (pt0) REVERT: A 4317 MET cc_start: 0.3435 (ttm) cc_final: 0.2579 (ttp) outliers start: 43 outliers final: 29 residues processed: 209 average time/residue: 0.3351 time to fit residues: 108.7071 Evaluate side-chains 199 residues out of total 2173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 162 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 764 ILE Chi-restraints excluded: chain A residue 787 ASP Chi-restraints excluded: chain A residue 882 ASP Chi-restraints excluded: chain A residue 1042 MET Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1180 VAL Chi-restraints excluded: chain A residue 1435 GLU Chi-restraints excluded: chain A residue 1505 SER Chi-restraints excluded: chain A residue 1628 CYS Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain A residue 2150 VAL Chi-restraints excluded: chain A residue 2156 VAL Chi-restraints excluded: chain A residue 2188 GLU Chi-restraints excluded: chain A residue 2221 LEU Chi-restraints excluded: chain A residue 2228 VAL Chi-restraints excluded: chain A residue 2235 SER Chi-restraints excluded: chain A residue 2250 LEU Chi-restraints excluded: chain A residue 2522 ARG Chi-restraints excluded: chain A residue 2646 THR Chi-restraints excluded: chain A residue 2654 GLU Chi-restraints excluded: chain A residue 2672 VAL Chi-restraints excluded: chain A residue 3200 LEU Chi-restraints excluded: chain A residue 3217 GLN Chi-restraints excluded: chain A residue 3346 VAL Chi-restraints excluded: chain A residue 3615 THR Chi-restraints excluded: chain A residue 3619 VAL Chi-restraints excluded: chain A residue 3961 THR Chi-restraints excluded: chain A residue 4162 GLU Chi-restraints excluded: chain A residue 4183 VAL Chi-restraints excluded: chain A residue 4351 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 123 optimal weight: 10.0000 chunk 92 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 150 optimal weight: 0.6980 chunk 206 optimal weight: 0.9990 chunk 181 optimal weight: 4.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3327 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.156393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.123060 restraints weight = 89347.715| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.08 r_work: 0.3375 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.4456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19715 Z= 0.157 Angle : 0.529 6.091 26687 Z= 0.275 Chirality : 0.036 0.135 3154 Planarity : 0.004 0.050 3361 Dihedral : 4.266 30.938 2620 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.61 % Allowed : 14.54 % Favored : 83.85 % 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: 1.57 (0.17), residues: 2388 helix: 1.71 (0.12), residues: 1680 sheet: -0.10 (0.61), residues: 75 loop : -0.54 (0.25), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A3444 TYR 0.012 0.001 TYR A1593 PHE 0.020 0.001 PHE A1198 TRP 0.018 0.001 TRP A1513 HIS 0.005 0.001 HIS A1789 Details of bonding type rmsd covalent geometry : bond 0.00361 (19715) covalent geometry : angle 0.52871 (26687) hydrogen bonds : bond 0.04172 ( 1242) hydrogen bonds : angle 4.11877 ( 3645) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 3997 is missing expected H atoms. Skipping. Evaluate side-chains 206 residues out of total 2173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 171 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 GLU cc_start: 0.7716 (mm-30) cc_final: 0.6915 (pm20) REVERT: A 372 ASP cc_start: 0.7443 (t0) cc_final: 0.6943 (t0) REVERT: A 882 ASP cc_start: 0.7156 (OUTLIER) cc_final: 0.6837 (m-30) REVERT: A 1647 THR cc_start: 0.8315 (p) cc_final: 0.8097 (t) REVERT: A 2104 GLU cc_start: 0.7364 (pm20) cc_final: 0.7040 (tp30) REVERT: A 2156 VAL cc_start: 0.8734 (OUTLIER) cc_final: 0.8438 (t) REVERT: A 2515 THR cc_start: 0.8022 (m) cc_final: 0.7699 (p) REVERT: A 2522 ARG cc_start: 0.6186 (OUTLIER) cc_final: 0.5856 (mmt180) REVERT: A 2656 LYS cc_start: 0.8508 (tttm) cc_final: 0.8271 (ttmm) REVERT: A 3217 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7866 (mp10) REVERT: A 3600 ASP cc_start: 0.7210 (m-30) cc_final: 0.6941 (m-30) REVERT: A 4317 MET cc_start: 0.3487 (ttm) cc_final: 0.2565 (ttp) outliers start: 35 outliers final: 28 residues processed: 200 average time/residue: 0.3267 time to fit residues: 101.7019 Evaluate side-chains 200 residues out of total 2173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 168 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 764 ILE Chi-restraints excluded: chain A residue 787 ASP Chi-restraints excluded: chain A residue 882 ASP Chi-restraints excluded: chain A residue 1042 MET Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1180 VAL Chi-restraints excluded: chain A residue 1435 GLU Chi-restraints excluded: chain A residue 1531 LEU Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain A residue 1672 THR Chi-restraints excluded: chain A residue 2156 VAL Chi-restraints excluded: chain A residue 2235 SER Chi-restraints excluded: chain A residue 2250 LEU Chi-restraints excluded: chain A residue 2522 ARG Chi-restraints excluded: chain A residue 2646 THR Chi-restraints excluded: chain A residue 2654 GLU Chi-restraints excluded: chain A residue 2672 VAL Chi-restraints excluded: chain A residue 3200 LEU Chi-restraints excluded: chain A residue 3217 GLN Chi-restraints excluded: chain A residue 3346 VAL Chi-restraints excluded: chain A residue 3615 THR Chi-restraints excluded: chain A residue 3619 VAL Chi-restraints excluded: chain A residue 3961 THR Chi-restraints excluded: chain A residue 3993 ASP Chi-restraints excluded: chain A residue 4183 VAL Chi-restraints excluded: chain A residue 4351 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 89 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 193 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 233 optimal weight: 7.9990 chunk 99 optimal weight: 0.2980 chunk 88 optimal weight: 0.7980 chunk 160 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3325 HIS ** 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 = 0.4059 r_free = 0.4059 target = 0.157400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.124085 restraints weight = 89721.806| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.13 r_work: 0.3407 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.4529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19715 Z= 0.132 Angle : 0.505 6.436 26687 Z= 0.260 Chirality : 0.035 0.139 3154 Planarity : 0.004 0.052 3361 Dihedral : 4.084 28.721 2620 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.70 % Allowed : 14.31 % Favored : 83.99 % 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: 1.90 (0.17), residues: 2388 helix: 1.94 (0.13), residues: 1687 sheet: -0.01 (0.61), residues: 75 loop : -0.43 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A3444 TYR 0.011 0.001 TYR A1593 PHE 0.019 0.001 PHE A1198 TRP 0.020 0.001 TRP A1513 HIS 0.005 0.001 HIS A1789 Details of bonding type rmsd covalent geometry : bond 0.00301 (19715) covalent geometry : angle 0.50479 (26687) hydrogen bonds : bond 0.03919 ( 1242) hydrogen bonds : angle 3.99511 ( 3645) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 3997 is missing expected H atoms. Skipping. Evaluate side-chains 205 residues out of total 2173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 168 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 GLU cc_start: 0.7663 (mm-30) cc_final: 0.6872 (pm20) REVERT: A 372 ASP cc_start: 0.7376 (t0) cc_final: 0.6868 (t0) REVERT: A 882 ASP cc_start: 0.7093 (OUTLIER) cc_final: 0.6789 (m-30) REVERT: A 2104 GLU cc_start: 0.7294 (pm20) cc_final: 0.7003 (tp30) REVERT: A 2221 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8241 (tm) REVERT: A 2515 THR cc_start: 0.7950 (m) cc_final: 0.7638 (p) REVERT: A 2522 ARG cc_start: 0.6094 (OUTLIER) cc_final: 0.5814 (mmt180) REVERT: A 2656 LYS cc_start: 0.8494 (tttm) cc_final: 0.8264 (ttmm) REVERT: A 3217 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7803 (mp10) REVERT: A 3290 MET cc_start: 0.7321 (ttp) cc_final: 0.7086 (ttp) REVERT: A 4077 MET cc_start: 0.5373 (tmm) cc_final: 0.5086 (tmm) REVERT: A 4317 MET cc_start: 0.3426 (ttm) cc_final: 0.2477 (ttp) outliers start: 37 outliers final: 30 residues processed: 199 average time/residue: 0.3298 time to fit residues: 101.9116 Evaluate side-chains 198 residues out of total 2173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 164 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 764 ILE Chi-restraints excluded: chain A residue 787 ASP Chi-restraints excluded: chain A residue 882 ASP Chi-restraints excluded: chain A residue 1042 MET Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1180 VAL Chi-restraints excluded: chain A residue 1435 GLU Chi-restraints excluded: chain A residue 1505 SER Chi-restraints excluded: chain A residue 1531 LEU Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain A residue 1672 THR Chi-restraints excluded: chain A residue 2221 LEU Chi-restraints excluded: chain A residue 2235 SER Chi-restraints excluded: chain A residue 2250 LEU Chi-restraints excluded: chain A residue 2522 ARG Chi-restraints excluded: chain A residue 2646 THR Chi-restraints excluded: chain A residue 2654 GLU Chi-restraints excluded: chain A residue 3200 LEU Chi-restraints excluded: chain A residue 3217 GLN Chi-restraints excluded: chain A residue 3346 VAL Chi-restraints excluded: chain A residue 3615 THR Chi-restraints excluded: chain A residue 3619 VAL Chi-restraints excluded: chain A residue 3961 THR Chi-restraints excluded: chain A residue 4183 VAL Chi-restraints excluded: chain A residue 4210 VAL Chi-restraints excluded: chain A residue 4351 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 98 optimal weight: 1.9990 chunk 217 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 158 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 104 optimal weight: 0.6980 chunk 205 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 126 optimal weight: 0.3980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 ASN ** A 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4208 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.158453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.125732 restraints weight = 89429.624| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.00 r_work: 0.3413 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.4597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 19715 Z= 0.109 Angle : 0.486 6.170 26687 Z= 0.249 Chirality : 0.034 0.136 3154 Planarity : 0.004 0.048 3361 Dihedral : 3.928 26.519 2620 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.47 % Allowed : 14.63 % Favored : 83.89 % 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: 2.20 (0.17), residues: 2388 helix: 2.17 (0.13), residues: 1688 sheet: 0.10 (0.63), residues: 75 loop : -0.32 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A3444 TYR 0.013 0.001 TYR A4231 PHE 0.016 0.001 PHE A1198 TRP 0.021 0.001 TRP A1513 HIS 0.005 0.001 HIS A1789 Details of bonding type rmsd covalent geometry : bond 0.00243 (19715) covalent geometry : angle 0.48561 (26687) hydrogen bonds : bond 0.03682 ( 1242) hydrogen bonds : angle 3.88362 ( 3645) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 3997 is missing expected H atoms. Skipping. Evaluate side-chains 199 residues out of total 2173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 167 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 GLU cc_start: 0.7688 (mm-30) cc_final: 0.6930 (tp30) REVERT: A 372 ASP cc_start: 0.7283 (t0) cc_final: 0.6762 (t0) REVERT: A 882 ASP cc_start: 0.7189 (OUTLIER) cc_final: 0.6887 (m-30) REVERT: A 2104 GLU cc_start: 0.7258 (pm20) cc_final: 0.6921 (tp30) REVERT: A 2221 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8236 (tm) REVERT: A 2515 THR cc_start: 0.7888 (m) cc_final: 0.7578 (p) REVERT: A 2522 ARG cc_start: 0.6055 (OUTLIER) cc_final: 0.5812 (mmt180) REVERT: A 2656 LYS cc_start: 0.8506 (tttm) cc_final: 0.8270 (ttmm) REVERT: A 3290 MET cc_start: 0.7230 (ttp) cc_final: 0.6972 (ttp) REVERT: A 4317 MET cc_start: 0.3386 (ttm) cc_final: 0.2415 (ttp) outliers start: 32 outliers final: 26 residues processed: 195 average time/residue: 0.3285 time to fit residues: 100.4704 Evaluate side-chains 192 residues out of total 2173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 163 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain A residue 764 ILE Chi-restraints excluded: chain A residue 787 ASP Chi-restraints excluded: chain A residue 882 ASP Chi-restraints excluded: chain A residue 1042 MET Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1180 VAL Chi-restraints excluded: chain A residue 1435 GLU Chi-restraints excluded: chain A residue 1505 SER Chi-restraints excluded: chain A residue 1531 LEU Chi-restraints excluded: chain A residue 1628 CYS Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain A residue 1672 THR Chi-restraints excluded: chain A residue 2221 LEU Chi-restraints excluded: chain A residue 2235 SER Chi-restraints excluded: chain A residue 2522 ARG Chi-restraints excluded: chain A residue 2646 THR Chi-restraints excluded: chain A residue 2654 GLU Chi-restraints excluded: chain A residue 3200 LEU Chi-restraints excluded: chain A residue 3615 THR Chi-restraints excluded: chain A residue 3619 VAL Chi-restraints excluded: chain A residue 4183 VAL Chi-restraints excluded: chain A residue 4210 VAL Chi-restraints excluded: chain A residue 4351 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 129 optimal weight: 0.0670 chunk 207 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 43 optimal weight: 0.0870 chunk 25 optimal weight: 3.9990 chunk 174 optimal weight: 7.9990 chunk 216 optimal weight: 8.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.2302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3325 HIS ** 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 = 0.4060 r_free = 0.4060 target = 0.157369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.123984 restraints weight = 89565.618| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.14 r_work: 0.3404 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.4670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19715 Z= 0.144 Angle : 0.504 6.135 26687 Z= 0.260 Chirality : 0.035 0.151 3154 Planarity : 0.004 0.051 3361 Dihedral : 3.910 25.817 2619 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.38 % Allowed : 14.82 % Favored : 83.80 % 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: 2.15 (0.17), residues: 2388 helix: 2.15 (0.13), residues: 1687 sheet: 0.10 (0.64), residues: 75 loop : -0.41 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A3444 TYR 0.011 0.001 TYR A1593 PHE 0.021 0.001 PHE A1592 TRP 0.018 0.001 TRP A1513 HIS 0.005 0.001 HIS A 894 Details of bonding type rmsd covalent geometry : bond 0.00330 (19715) covalent geometry : angle 0.50399 (26687) hydrogen bonds : bond 0.03855 ( 1242) hydrogen bonds : angle 3.92382 ( 3645) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9918.99 seconds wall clock time: 168 minutes 34.40 seconds (10114.40 seconds total)