Starting phenix.real_space_refine on Thu Jul 31 16:25:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vf2_31946/07_2025/7vf2_31946.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vf2_31946/07_2025/7vf2_31946.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vf2_31946/07_2025/7vf2_31946.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vf2_31946/07_2025/7vf2_31946.map" model { file = "/net/cci-nas-00/data/ceres_data/7vf2_31946/07_2025/7vf2_31946.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vf2_31946/07_2025/7vf2_31946.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.070 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: 4 Type Number sf(0) Gaussians S 83 5.16 5 C 8551 2.51 5 N 2301 2.21 5 O 2630 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 76 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13565 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1196, 9390 Classifications: {'peptide': 1196} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 1149} Chain breaks: 2 Chain: "B" Number of atoms: 1187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1187 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 8, 'TRANS': 143} Chain: "C" Number of atoms: 1494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1494 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 3, 'TRANS': 180} Chain: "D" Number of atoms: 1494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1494 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 3, 'TRANS': 180} Time building chain proxies: 8.82, per 1000 atoms: 0.65 Number of scatterers: 13565 At special positions: 0 Unit cell: (112.34, 115.62, 150.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 83 16.00 O 2630 8.00 N 2301 7.00 C 8551 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.64 Conformation dependent library (CDL) restraints added in 1.9 seconds 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3300 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 3 sheets defined 74.5% alpha, 0.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'A' and resid 357 through 369 Processing helix chain 'A' and resid 374 through 390 removed outlier: 3.899A pdb=" N ALA A 378 " --> pdb=" O GLU A 374 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA A 381 " --> pdb=" O GLY A 377 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS A 384 " --> pdb=" O GLU A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 405 Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 413 through 421 Processing helix chain 'A' and resid 426 through 439 Processing helix chain 'A' and resid 440 through 445 Processing helix chain 'A' and resid 451 through 468 removed outlier: 3.570A pdb=" N GLN A 455 " --> pdb=" O LEU A 451 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU A 456 " --> pdb=" O ASN A 452 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU A 468 " --> pdb=" O SER A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 480 removed outlier: 3.878A pdb=" N GLY A 473 " --> pdb=" O CYS A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 490 removed outlier: 4.083A pdb=" N GLU A 488 " --> pdb=" O SER A 484 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU A 489 " --> pdb=" O GLY A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 511 Processing helix chain 'A' and resid 513 through 522 Processing helix chain 'A' and resid 529 through 539 Processing helix chain 'A' and resid 543 through 579 removed outlier: 3.688A pdb=" N LYS A 556 " --> pdb=" O ALA A 552 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER A 579 " --> pdb=" O GLU A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 640 Processing helix chain 'A' and resid 640 through 645 Processing helix chain 'A' and resid 668 through 679 removed outlier: 4.074A pdb=" N ARG A 674 " --> pdb=" O PRO A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 691 Processing helix chain 'A' and resid 691 through 697 removed outlier: 3.963A pdb=" N HIS A 697 " --> pdb=" O VAL A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 712 removed outlier: 3.766A pdb=" N LEU A 701 " --> pdb=" O HIS A 697 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL A 707 " --> pdb=" O ALA A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 724 removed outlier: 3.681A pdb=" N MET A 722 " --> pdb=" O LEU A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 746 removed outlier: 3.962A pdb=" N PHE A 738 " --> pdb=" O ALA A 734 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLU A 743 " --> pdb=" O TYR A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 776 Processing helix chain 'A' and resid 789 through 801 Processing helix chain 'A' and resid 802 through 804 No H-bonds generated for 'chain 'A' and resid 802 through 804' Processing helix chain 'A' and resid 805 through 816 Processing helix chain 'A' and resid 822 through 833 Processing helix chain 'A' and resid 845 through 862 removed outlier: 3.652A pdb=" N ASN A 849 " --> pdb=" O SER A 845 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL A 859 " --> pdb=" O ILE A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 882 removed outlier: 3.934A pdb=" N GLU A 869 " --> pdb=" O VAL A 865 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLN A 870 " --> pdb=" O GLN A 866 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N HIS A 871 " --> pdb=" O MET A 867 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N ALA A 873 " --> pdb=" O GLU A 869 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N SER A 874 " --> pdb=" O GLN A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 896 Processing helix chain 'A' and resid 897 through 899 No H-bonds generated for 'chain 'A' and resid 897 through 899' Processing helix chain 'A' and resid 907 through 918 Processing helix chain 'A' and resid 928 through 940 removed outlier: 4.078A pdb=" N THR A 932 " --> pdb=" O VAL A 928 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU A 937 " --> pdb=" O ALA A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 966 removed outlier: 3.775A pdb=" N VAL A 960 " --> pdb=" O TRP A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 989 removed outlier: 3.512A pdb=" N ILE A 973 " --> pdb=" O MET A 969 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N VAL A 975 " --> pdb=" O THR A 971 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N GLN A 985 " --> pdb=" O SER A 981 " (cutoff:3.500A) Proline residue: A 986 - end of helix Processing helix chain 'A' and resid 995 through 1021 Processing helix chain 'A' and resid 1032 through 1045 removed outlier: 3.962A pdb=" N THR A1039 " --> pdb=" O SER A1035 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N MET A1042 " --> pdb=" O VAL A1038 " (cutoff:3.500A) Processing helix chain 'A' and resid 1054 through 1070 Processing helix chain 'A' and resid 1076 through 1080 Processing helix chain 'A' and resid 1082 through 1087 Processing helix chain 'A' and resid 1089 through 1100 Processing helix chain 'A' and resid 1108 through 1120 removed outlier: 3.949A pdb=" N GLU A1118 " --> pdb=" O ILE A1114 " (cutoff:3.500A) Processing helix chain 'A' and resid 1133 through 1152 removed outlier: 3.513A pdb=" N ILE A1137 " --> pdb=" O GLU A1133 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG A1144 " --> pdb=" O ALA A1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 1154 through 1165 removed outlier: 3.801A pdb=" N GLU A1160 " --> pdb=" O LYS A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1170 through 1184 removed outlier: 3.935A pdb=" N VAL A1182 " --> pdb=" O ARG A1178 " (cutoff:3.500A) Processing helix chain 'A' and resid 1188 through 1208 Processing helix chain 'A' and resid 1219 through 1234 Processing helix chain 'A' and resid 1235 through 1247 removed outlier: 3.584A pdb=" N LEU A1245 " --> pdb=" O ALA A1241 " (cutoff:3.500A) Processing helix chain 'A' and resid 1253 through 1268 removed outlier: 3.670A pdb=" N ALA A1257 " --> pdb=" O ASP A1253 " (cutoff:3.500A) Processing helix chain 'A' and resid 1275 through 1291 removed outlier: 4.401A pdb=" N GLU A1281 " --> pdb=" O GLN A1277 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TYR A1282 " --> pdb=" O GLN A1278 " (cutoff:3.500A) Processing helix chain 'A' and resid 1308 through 1314 removed outlier: 3.601A pdb=" N SER A1314 " --> pdb=" O LEU A1310 " (cutoff:3.500A) Processing helix chain 'A' and resid 1319 through 1336 removed outlier: 3.687A pdb=" N SER A1325 " --> pdb=" O GLU A1321 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU A1334 " --> pdb=" O LEU A1330 " (cutoff:3.500A) Processing helix chain 'A' and resid 1340 through 1355 removed outlier: 3.601A pdb=" N LEU A1344 " --> pdb=" O SER A1340 " (cutoff:3.500A) Processing helix chain 'A' and resid 1357 through 1369 Processing helix chain 'A' and resid 1373 through 1385 Processing helix chain 'A' and resid 1390 through 1406 Processing helix chain 'A' and resid 1434 through 1443 Processing helix chain 'A' and resid 1447 through 1461 Processing helix chain 'A' and resid 1468 through 1486 removed outlier: 3.556A pdb=" N SER A1472 " --> pdb=" O ASP A1468 " (cutoff:3.500A) Processing helix chain 'A' and resid 1507 through 1514 Processing helix chain 'A' and resid 1525 through 1530 Processing helix chain 'A' and resid 1554 through 1559 removed outlier: 4.388A pdb=" N LYS A1558 " --> pdb=" O GLU A1554 " (cutoff:3.500A) Processing helix chain 'A' and resid 1565 through 1575 removed outlier: 3.868A pdb=" N PHE A1573 " --> pdb=" O LEU A1569 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU A1574 " --> pdb=" O GLU A1570 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER A1575 " --> pdb=" O ARG A1571 " (cutoff:3.500A) Processing helix chain 'B' and resid 1517 through 1521 removed outlier: 4.200A pdb=" N LYS B1520 " --> pdb=" O ALA B1517 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE B1521 " --> pdb=" O LEU B1518 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1517 through 1521' Processing helix chain 'B' and resid 1522 through 1531 Processing helix chain 'B' and resid 1533 through 1538 removed outlier: 3.762A pdb=" N GLY B1538 " --> pdb=" O LYS B1534 " (cutoff:3.500A) Processing helix chain 'B' and resid 1538 through 1551 Processing helix chain 'B' and resid 1555 through 1561 Processing helix chain 'B' and resid 1567 through 1583 Processing helix chain 'B' and resid 1596 through 1608 Processing helix chain 'B' and resid 1626 through 1643 Processing helix chain 'C' and resid 65 through 98 Processing helix chain 'C' and resid 102 through 112 Processing helix chain 'C' and resid 114 through 146 Processing helix chain 'C' and resid 151 through 175 Processing helix chain 'C' and resid 176 through 243 Processing helix chain 'D' and resid 66 through 100 Processing helix chain 'D' and resid 104 through 109 Processing helix chain 'D' and resid 114 through 145 removed outlier: 3.604A pdb=" N SER D 143 " --> pdb=" O GLN D 139 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA D 144 " --> pdb=" O ASN D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 178 removed outlier: 3.634A pdb=" N GLN D 169 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN D 174 " --> pdb=" O GLU D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 244 removed outlier: 3.790A pdb=" N GLU D 203 " --> pdb=" O SER D 199 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 657 through 658 Processing sheet with id=AA2, first strand: chain 'A' and resid 1126 through 1128 removed outlier: 6.178A pdb=" N MET A1126 " --> pdb=" O VAL A1519 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 1549 through 1551 902 hydrogen bonds defined for protein. 2688 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: 4.56 Time building geometry restraints manager: 4.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2859 1.33 - 1.45: 2695 1.45 - 1.57: 8074 1.57 - 1.69: 0 1.69 - 1.81: 132 Bond restraints: 13760 Sorted by residual: bond pdb=" C GLN A 647 " pdb=" N GLN A 648 " ideal model delta sigma weight residual 1.330 1.283 0.047 1.47e-02 4.63e+03 1.03e+01 bond pdb=" N ARG B1512 " pdb=" CA ARG B1512 " ideal model delta sigma weight residual 1.453 1.489 -0.036 1.31e-02 5.83e+03 7.72e+00 bond pdb=" N LYS C 146 " pdb=" CA LYS C 146 " ideal model delta sigma weight residual 1.455 1.489 -0.033 1.25e-02 6.40e+03 7.07e+00 bond pdb=" C TRP C 145 " pdb=" N LYS C 146 " ideal model delta sigma weight residual 1.333 1.366 -0.034 1.36e-02 5.41e+03 6.08e+00 bond pdb=" N GLU D 141 " pdb=" CA GLU D 141 " ideal model delta sigma weight residual 1.459 1.489 -0.031 1.28e-02 6.10e+03 5.73e+00 ... (remaining 13755 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 18136 2.06 - 4.13: 389 4.13 - 6.19: 48 6.19 - 8.25: 7 8.25 - 10.32: 2 Bond angle restraints: 18582 Sorted by residual: angle pdb=" N ILE A1541 " pdb=" CA ILE A1541 " pdb=" C ILE A1541 " ideal model delta sigma weight residual 113.47 105.93 7.54 1.01e+00 9.80e-01 5.58e+01 angle pdb=" N VAL A1274 " pdb=" CA VAL A1274 " pdb=" C VAL A1274 " ideal model delta sigma weight residual 113.42 107.22 6.20 1.17e+00 7.31e-01 2.81e+01 angle pdb=" CA GLU B1513 " pdb=" C GLU B1513 " pdb=" N PRO B1514 " ideal model delta sigma weight residual 118.75 123.54 -4.79 9.70e-01 1.06e+00 2.44e+01 angle pdb=" N ALA A 783 " pdb=" CA ALA A 783 " pdb=" C ALA A 783 " ideal model delta sigma weight residual 113.38 107.55 5.83 1.23e+00 6.61e-01 2.24e+01 angle pdb=" N SER A1444 " pdb=" CA SER A1444 " pdb=" C SER A1444 " ideal model delta sigma weight residual 114.75 109.41 5.34 1.26e+00 6.30e-01 1.80e+01 ... (remaining 18577 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 7715 17.96 - 35.92: 661 35.92 - 53.88: 124 53.88 - 71.84: 42 71.84 - 89.80: 39 Dihedral angle restraints: 8581 sinusoidal: 3540 harmonic: 5041 Sorted by residual: dihedral pdb=" CA HIS A1463 " pdb=" C HIS A1463 " pdb=" N SER A1464 " pdb=" CA SER A1464 " ideal model delta harmonic sigma weight residual 180.00 -156.51 -23.49 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA LYS A1251 " pdb=" C LYS A1251 " pdb=" N GLY A1252 " pdb=" CA GLY A1252 " ideal model delta harmonic sigma weight residual -180.00 -158.65 -21.35 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA LYS A1465 " pdb=" C LYS A1465 " pdb=" N ASP A1466 " pdb=" CA ASP A1466 " ideal model delta harmonic sigma weight residual -180.00 -158.75 -21.25 0 5.00e+00 4.00e-02 1.81e+01 ... (remaining 8578 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1579 0.041 - 0.081: 479 0.081 - 0.122: 110 0.122 - 0.162: 13 0.162 - 0.203: 5 Chirality restraints: 2186 Sorted by residual: chirality pdb=" CA GLU D 136 " pdb=" N GLU D 136 " pdb=" C GLU D 136 " pdb=" CB GLU D 136 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA ARG B1639 " pdb=" N ARG B1639 " pdb=" C ARG B1639 " pdb=" CB ARG B1639 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.84e-01 chirality pdb=" CA GLU B1513 " pdb=" N GLU B1513 " pdb=" C GLU B1513 " pdb=" CB GLU B1513 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.67e-01 ... (remaining 2183 not shown) Planarity restraints: 2386 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 669 " 0.036 5.00e-02 4.00e+02 5.39e-02 4.65e+00 pdb=" N PRO A 670 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 670 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 670 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 67 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.64e+00 pdb=" C GLN C 67 " 0.028 2.00e-02 2.50e+03 pdb=" O GLN C 67 " -0.011 2.00e-02 2.50e+03 pdb=" N GLU C 68 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR D 148 " 0.024 5.00e-02 4.00e+02 3.66e-02 2.14e+00 pdb=" N PRO D 149 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO D 149 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 149 " 0.021 5.00e-02 4.00e+02 ... (remaining 2383 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.66: 176 2.66 - 3.22: 13487 3.22 - 3.78: 21777 3.78 - 4.34: 29896 4.34 - 4.90: 48636 Nonbonded interactions: 113972 Sorted by model distance: nonbonded pdb=" OG1 THR C 148 " pdb=" OG SER C 151 " model vdw 2.095 3.040 nonbonded pdb=" OD2 ASP A1206 " pdb=" OG1 THR A1222 " model vdw 2.119 3.040 nonbonded pdb=" O ASP A 508 " pdb=" OG SER A 512 " model vdw 2.140 3.040 nonbonded pdb=" OE1 GLU A1311 " pdb=" OG SER A1503 " model vdw 2.160 3.040 nonbonded pdb=" O ILE A 511 " pdb=" OH TYR A 675 " model vdw 2.176 3.040 ... (remaining 113967 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 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } 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=0.00 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: 2.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 35.480 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13760 Z= 0.210 Angle : 0.729 10.315 18582 Z= 0.439 Chirality : 0.041 0.203 2186 Planarity : 0.004 0.054 2386 Dihedral : 15.876 89.804 5281 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.26 % Allowed : 3.82 % Favored : 95.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.17), residues: 1704 helix: -1.44 (0.13), residues: 1221 sheet: None (None), residues: 0 loop : -2.35 (0.25), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B1500 HIS 0.005 0.001 HIS A1376 PHE 0.012 0.001 PHE A1453 TYR 0.010 0.001 TYR D 193 ARG 0.002 0.000 ARG A1144 Details of bonding type rmsd hydrogen bonds : bond 0.12313 ( 902) hydrogen bonds : angle 5.67959 ( 2688) covalent geometry : bond 0.00449 (13760) covalent geometry : angle 0.72889 (18582) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 217 time to evaluate : 1.578 Fit side-chains REVERT: A 1217 GLN cc_start: 0.8072 (mm-40) cc_final: 0.7839 (tp40) REVERT: A 1259 ILE cc_start: 0.8804 (tp) cc_final: 0.8559 (tp) REVERT: A 1483 MET cc_start: 0.8347 (mpp) cc_final: 0.7976 (mpt) REVERT: B 1513 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7446 (tm-30) REVERT: B 1514 PRO cc_start: 0.8866 (Cg_exo) cc_final: 0.8394 (Cg_endo) REVERT: C 78 MET cc_start: 0.8123 (tpt) cc_final: 0.7902 (tpt) REVERT: C 233 ARG cc_start: 0.8674 (ttm170) cc_final: 0.8387 (mtt90) REVERT: D 78 MET cc_start: 0.8476 (ptm) cc_final: 0.8258 (pp-130) REVERT: D 236 LEU cc_start: 0.6454 (tt) cc_final: 0.6006 (mt) outliers start: 4 outliers final: 1 residues processed: 220 average time/residue: 1.3847 time to fit residues: 332.9253 Evaluate side-chains 140 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 138 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1513 GLU Chi-restraints excluded: chain C residue 94 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 9.9990 chunk 128 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 44 optimal weight: 0.6980 chunk 86 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 133 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 99 optimal weight: 8.9990 chunk 154 optimal weight: 9.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 GLN A 430 GLN A 455 GLN ** A 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 555 GLN A 558 HIS A 636 HIS ** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 766 GLN A 797 HIS A 823 GLN A 951 GLN A 962 GLN ** A1041 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1142 ASN ** A1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1152 HIS A1175 HIS A1261 GLN ** A1336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1357 HIS A1440 GLN A1463 HIS A1510 ASN C 74 ASN C 85 GLN C 137 GLN C 152 GLN C 219 GLN C 228 GLN D 118 ASN D 137 GLN D 174 GLN D 201 GLN D 240 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.145560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.095051 restraints weight = 20083.803| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.95 r_work: 0.3242 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 13760 Z= 0.202 Angle : 0.673 11.583 18582 Z= 0.334 Chirality : 0.041 0.165 2186 Planarity : 0.004 0.054 2386 Dihedral : 5.493 73.559 1816 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.26 % Allowed : 12.16 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.19), residues: 1704 helix: -0.15 (0.14), residues: 1224 sheet: None (None), residues: 0 loop : -1.84 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B1500 HIS 0.003 0.001 HIS A1363 PHE 0.015 0.002 PHE A1533 TYR 0.018 0.002 TYR D 239 ARG 0.007 0.001 ARG D 72 Details of bonding type rmsd hydrogen bonds : bond 0.03985 ( 902) hydrogen bonds : angle 4.38149 ( 2688) covalent geometry : bond 0.00485 (13760) covalent geometry : angle 0.67261 (18582) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 146 time to evaluate : 1.538 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 664 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7545 (pp20) REVERT: A 867 MET cc_start: 0.9191 (OUTLIER) cc_final: 0.7930 (ptp) REVERT: A 987 TRP cc_start: 0.8355 (t-100) cc_final: 0.8109 (t-100) REVERT: A 1217 GLN cc_start: 0.8243 (mm-40) cc_final: 0.7991 (tp40) REVERT: A 1402 ARG cc_start: 0.8094 (mtp85) cc_final: 0.7061 (mmt-90) REVERT: A 1483 MET cc_start: 0.8630 (mpp) cc_final: 0.7725 (mpt) REVERT: A 1524 MET cc_start: 0.8650 (tpp) cc_final: 0.8331 (tpp) REVERT: B 1513 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7538 (tp30) REVERT: B 1606 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.7724 (mp10) REVERT: C 68 GLU cc_start: 0.8949 (OUTLIER) cc_final: 0.8626 (tp30) REVERT: C 78 MET cc_start: 0.8003 (tpt) cc_final: 0.7743 (tpt) REVERT: C 136 GLU cc_start: 0.8353 (mm-30) cc_final: 0.8079 (mm-30) REVERT: C 241 GLN cc_start: 0.8796 (tm-30) cc_final: 0.8474 (tm-30) REVERT: D 72 ARG cc_start: 0.8493 (mtm110) cc_final: 0.8074 (mtm-85) REVERT: D 78 MET cc_start: 0.8827 (ptm) cc_final: 0.8418 (pp-130) REVERT: D 89 GLU cc_start: 0.8328 (tm-30) cc_final: 0.8081 (pp20) REVERT: D 236 LEU cc_start: 0.6114 (tt) cc_final: 0.5683 (mt) outliers start: 35 outliers final: 6 residues processed: 169 average time/residue: 1.2211 time to fit residues: 228.4054 Evaluate side-chains 140 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 1.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 664 GLU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain A residue 920 ASP Chi-restraints excluded: chain A residue 1111 SER Chi-restraints excluded: chain A residue 1330 LEU Chi-restraints excluded: chain B residue 1513 GLU Chi-restraints excluded: chain B residue 1539 SER Chi-restraints excluded: chain B residue 1606 GLN Chi-restraints excluded: chain C residue 68 GLU Chi-restraints excluded: chain D residue 92 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 149 optimal weight: 0.9980 chunk 107 optimal weight: 20.0000 chunk 109 optimal weight: 6.9990 chunk 37 optimal weight: 40.0000 chunk 25 optimal weight: 0.9980 chunk 141 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 139 optimal weight: 0.9980 chunk 4 optimal weight: 9.9990 chunk 101 optimal weight: 0.7980 chunk 56 optimal weight: 0.0000 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 789 HIS ** A1041 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1507 HIS C 95 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.147386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.098462 restraints weight = 20151.527| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.89 r_work: 0.3314 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13760 Z= 0.131 Angle : 0.582 9.589 18582 Z= 0.290 Chirality : 0.038 0.145 2186 Planarity : 0.004 0.051 2386 Dihedral : 5.063 62.781 1814 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.59 % Allowed : 13.84 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.20), residues: 1704 helix: 0.65 (0.14), residues: 1215 sheet: None (None), residues: 0 loop : -1.52 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B1500 HIS 0.003 0.001 HIS A1376 PHE 0.012 0.001 PHE A1533 TYR 0.012 0.001 TYR D 239 ARG 0.006 0.000 ARG C 72 Details of bonding type rmsd hydrogen bonds : bond 0.03524 ( 902) hydrogen bonds : angle 4.06736 ( 2688) covalent geometry : bond 0.00304 (13760) covalent geometry : angle 0.58197 (18582) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 142 time to evaluate : 1.435 Fit side-chains revert: symmetry clash REVERT: A 426 ASP cc_start: 0.7805 (t0) cc_final: 0.7036 (p0) REVERT: A 780 ARG cc_start: 0.7461 (mtm110) cc_final: 0.7255 (mtm110) REVERT: A 831 TYR cc_start: 0.8200 (t80) cc_final: 0.7952 (t80) REVERT: A 867 MET cc_start: 0.9106 (OUTLIER) cc_final: 0.7722 (ptp) REVERT: A 987 TRP cc_start: 0.8333 (t-100) cc_final: 0.8100 (t-100) REVERT: A 1217 GLN cc_start: 0.8251 (mm-40) cc_final: 0.8033 (tp40) REVERT: A 1259 ILE cc_start: 0.8696 (OUTLIER) cc_final: 0.8383 (tp) REVERT: A 1402 ARG cc_start: 0.8019 (mtp85) cc_final: 0.7033 (mmm-85) REVERT: A 1483 MET cc_start: 0.8626 (mpp) cc_final: 0.7721 (mpt) REVERT: B 1513 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7388 (tp30) REVERT: B 1514 PRO cc_start: 0.8948 (Cg_exo) cc_final: 0.8519 (Cg_endo) REVERT: B 1606 GLN cc_start: 0.8130 (OUTLIER) cc_final: 0.7681 (mp10) REVERT: C 136 GLU cc_start: 0.8376 (mm-30) cc_final: 0.8066 (mm-30) REVERT: C 241 GLN cc_start: 0.8723 (tm-30) cc_final: 0.8403 (tm-30) REVERT: D 78 MET cc_start: 0.8801 (ptm) cc_final: 0.8395 (pp-130) REVERT: D 89 GLU cc_start: 0.8383 (tm-30) cc_final: 0.8120 (pp20) REVERT: D 108 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8604 (tp) REVERT: D 163 MET cc_start: 0.8959 (ttp) cc_final: 0.8624 (tpp) REVERT: D 206 ASP cc_start: 0.8517 (m-30) cc_final: 0.8231 (m-30) REVERT: D 236 LEU cc_start: 0.6208 (tt) cc_final: 0.5807 (mt) outliers start: 40 outliers final: 7 residues processed: 168 average time/residue: 1.2100 time to fit residues: 225.0606 Evaluate side-chains 140 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 128 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 805 ASN Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain A residue 920 ASP Chi-restraints excluded: chain A residue 1111 SER Chi-restraints excluded: chain A residue 1259 ILE Chi-restraints excluded: chain A residue 1548 VAL Chi-restraints excluded: chain B residue 1513 GLU Chi-restraints excluded: chain B residue 1539 SER Chi-restraints excluded: chain B residue 1606 GLN Chi-restraints excluded: chain B residue 1608 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 108 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 118 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 chunk 13 optimal weight: 0.9980 chunk 104 optimal weight: 0.7980 chunk 103 optimal weight: 10.0000 chunk 38 optimal weight: 0.5980 chunk 126 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 985 GLN ** A1041 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.144777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.096860 restraints weight = 20059.401| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.76 r_work: 0.3281 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13760 Z= 0.156 Angle : 0.595 10.863 18582 Z= 0.291 Chirality : 0.039 0.152 2186 Planarity : 0.004 0.051 2386 Dihedral : 4.842 55.535 1814 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.78 % Allowed : 15.65 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.20), residues: 1704 helix: 0.91 (0.15), residues: 1222 sheet: None (None), residues: 0 loop : -1.30 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1532 HIS 0.003 0.001 HIS A1376 PHE 0.014 0.001 PHE A1573 TYR 0.018 0.001 TYR D 239 ARG 0.010 0.000 ARG B1551 Details of bonding type rmsd hydrogen bonds : bond 0.03442 ( 902) hydrogen bonds : angle 3.96362 ( 2688) covalent geometry : bond 0.00377 (13760) covalent geometry : angle 0.59455 (18582) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 142 time to evaluate : 1.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 426 ASP cc_start: 0.7744 (t0) cc_final: 0.6920 (p0) REVERT: A 780 ARG cc_start: 0.7460 (mtm110) cc_final: 0.7200 (mtm110) REVERT: A 831 TYR cc_start: 0.8201 (t80) cc_final: 0.7921 (t80) REVERT: A 867 MET cc_start: 0.9154 (OUTLIER) cc_final: 0.7769 (ptp) REVERT: A 987 TRP cc_start: 0.8348 (t-100) cc_final: 0.8113 (t-100) REVERT: A 1259 ILE cc_start: 0.8668 (OUTLIER) cc_final: 0.8363 (tp) REVERT: A 1402 ARG cc_start: 0.7906 (mtp85) cc_final: 0.7059 (mmm-85) REVERT: A 1458 LYS cc_start: 0.8397 (tptt) cc_final: 0.8128 (tptt) REVERT: B 1513 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7372 (tp30) REVERT: B 1514 PRO cc_start: 0.8937 (Cg_exo) cc_final: 0.8516 (Cg_endo) REVERT: B 1606 GLN cc_start: 0.8110 (OUTLIER) cc_final: 0.7630 (mp10) REVERT: C 136 GLU cc_start: 0.8421 (mm-30) cc_final: 0.8113 (mm-30) REVERT: C 241 GLN cc_start: 0.8702 (tm-30) cc_final: 0.8376 (tm-30) REVERT: D 78 MET cc_start: 0.8828 (ptm) cc_final: 0.8406 (pp-130) REVERT: D 89 GLU cc_start: 0.8390 (tm-30) cc_final: 0.8145 (pp20) REVERT: D 108 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8578 (tp) REVERT: D 163 MET cc_start: 0.8958 (ttp) cc_final: 0.8604 (tpp) REVERT: D 206 ASP cc_start: 0.8494 (m-30) cc_final: 0.8219 (m-30) REVERT: D 236 LEU cc_start: 0.6100 (tt) cc_final: 0.5728 (mt) outliers start: 43 outliers final: 11 residues processed: 174 average time/residue: 1.2612 time to fit residues: 243.1152 Evaluate side-chains 149 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 805 ASN Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain A residue 920 ASP Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1111 SER Chi-restraints excluded: chain A residue 1259 ILE Chi-restraints excluded: chain A residue 1520 LEU Chi-restraints excluded: chain A residue 1548 VAL Chi-restraints excluded: chain B residue 1513 GLU Chi-restraints excluded: chain B residue 1539 SER Chi-restraints excluded: chain B residue 1606 GLN Chi-restraints excluded: chain B residue 1608 VAL Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 108 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 68 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 155 optimal weight: 0.6980 chunk 168 optimal weight: 0.8980 chunk 148 optimal weight: 1.9990 chunk 165 optimal weight: 0.9990 chunk 154 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 chunk 129 optimal weight: 0.9980 chunk 37 optimal weight: 30.0000 chunk 169 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 998 HIS ** A1041 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.147576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.097467 restraints weight = 20145.679| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.92 r_work: 0.3279 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13760 Z= 0.140 Angle : 0.577 10.822 18582 Z= 0.283 Chirality : 0.038 0.164 2186 Planarity : 0.003 0.050 2386 Dihedral : 4.666 49.797 1814 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.59 % Allowed : 17.08 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.20), residues: 1704 helix: 1.15 (0.15), residues: 1223 sheet: None (None), residues: 0 loop : -1.15 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1532 HIS 0.003 0.001 HIS A1376 PHE 0.012 0.001 PHE C 120 TYR 0.012 0.001 TYR D 239 ARG 0.006 0.000 ARG B1551 Details of bonding type rmsd hydrogen bonds : bond 0.03331 ( 902) hydrogen bonds : angle 3.86692 ( 2688) covalent geometry : bond 0.00336 (13760) covalent geometry : angle 0.57688 (18582) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 146 time to evaluate : 1.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 THR cc_start: 0.8152 (OUTLIER) cc_final: 0.7945 (t) REVERT: A 426 ASP cc_start: 0.7702 (t0) cc_final: 0.6921 (p0) REVERT: A 664 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.7711 (pp20) REVERT: A 780 ARG cc_start: 0.7497 (mtm110) cc_final: 0.7270 (mtm110) REVERT: A 831 TYR cc_start: 0.8227 (t80) cc_final: 0.7882 (t80) REVERT: A 867 MET cc_start: 0.9154 (OUTLIER) cc_final: 0.7739 (ptp) REVERT: A 987 TRP cc_start: 0.8364 (t-100) cc_final: 0.8151 (t-100) REVERT: A 1027 GLU cc_start: 0.8307 (pp20) cc_final: 0.8104 (pp20) REVERT: A 1259 ILE cc_start: 0.8698 (OUTLIER) cc_final: 0.8390 (tp) REVERT: A 1402 ARG cc_start: 0.7910 (mtp85) cc_final: 0.6959 (mmm-85) REVERT: A 1458 LYS cc_start: 0.8430 (tptt) cc_final: 0.8147 (tptt) REVERT: A 1483 MET cc_start: 0.8687 (mpp) cc_final: 0.7809 (mpt) REVERT: B 1606 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7652 (mp10) REVERT: C 136 GLU cc_start: 0.8417 (mm-30) cc_final: 0.8075 (mm-30) REVERT: C 241 GLN cc_start: 0.8668 (tm-30) cc_final: 0.8391 (tm-30) REVERT: D 78 MET cc_start: 0.8835 (ptm) cc_final: 0.8393 (pp-130) REVERT: D 89 GLU cc_start: 0.8424 (tm-30) cc_final: 0.8190 (pp20) REVERT: D 108 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8601 (tp) REVERT: D 163 MET cc_start: 0.8968 (ttp) cc_final: 0.8631 (tpp) REVERT: D 206 ASP cc_start: 0.8536 (m-30) cc_final: 0.8279 (m-30) REVERT: D 236 LEU cc_start: 0.6120 (tt) cc_final: 0.5738 (mt) outliers start: 40 outliers final: 16 residues processed: 175 average time/residue: 1.1840 time to fit residues: 229.2049 Evaluate side-chains 161 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 139 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 664 GLU Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 805 ASN Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 908 ILE Chi-restraints excluded: chain A residue 920 ASP Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1111 SER Chi-restraints excluded: chain A residue 1259 ILE Chi-restraints excluded: chain A residue 1316 SER Chi-restraints excluded: chain A residue 1520 LEU Chi-restraints excluded: chain A residue 1548 VAL Chi-restraints excluded: chain A residue 1549 LYS Chi-restraints excluded: chain B residue 1513 GLU Chi-restraints excluded: chain B residue 1539 SER Chi-restraints excluded: chain B residue 1606 GLN Chi-restraints excluded: chain B residue 1608 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 108 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 161 optimal weight: 10.0000 chunk 118 optimal weight: 0.2980 chunk 101 optimal weight: 0.8980 chunk 38 optimal weight: 0.0000 chunk 92 optimal weight: 4.9990 chunk 135 optimal weight: 3.9990 chunk 86 optimal weight: 0.5980 chunk 110 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1041 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1150 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 = 0.4086 r_free = 0.4086 target = 0.146223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.097394 restraints weight = 20161.563| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.88 r_work: 0.3266 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13760 Z= 0.117 Angle : 0.570 12.152 18582 Z= 0.277 Chirality : 0.037 0.169 2186 Planarity : 0.003 0.047 2386 Dihedral : 4.476 46.082 1814 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.78 % Allowed : 17.85 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.20), residues: 1704 helix: 1.36 (0.15), residues: 1228 sheet: None (None), residues: 0 loop : -0.97 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1532 HIS 0.003 0.001 HIS A1376 PHE 0.015 0.001 PHE A1573 TYR 0.023 0.001 TYR D 239 ARG 0.007 0.000 ARG D 162 Details of bonding type rmsd hydrogen bonds : bond 0.03187 ( 902) hydrogen bonds : angle 3.77228 ( 2688) covalent geometry : bond 0.00272 (13760) covalent geometry : angle 0.56998 (18582) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 155 time to evaluate : 1.589 Fit side-chains revert: symmetry clash REVERT: A 423 THR cc_start: 0.8071 (OUTLIER) cc_final: 0.7854 (t) REVERT: A 426 ASP cc_start: 0.7629 (t0) cc_final: 0.6883 (p0) REVERT: A 664 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7642 (pp20) REVERT: A 831 TYR cc_start: 0.8191 (t80) cc_final: 0.7816 (t80) REVERT: A 867 MET cc_start: 0.9130 (OUTLIER) cc_final: 0.7942 (ptp) REVERT: A 987 TRP cc_start: 0.8267 (t-100) cc_final: 0.8005 (t-100) REVERT: A 1027 GLU cc_start: 0.8346 (pp20) cc_final: 0.8107 (pp20) REVERT: A 1255 ARG cc_start: 0.7685 (OUTLIER) cc_final: 0.7409 (ptm-80) REVERT: A 1259 ILE cc_start: 0.8559 (OUTLIER) cc_final: 0.8287 (tp) REVERT: A 1402 ARG cc_start: 0.7843 (mtp85) cc_final: 0.6943 (mmm-85) REVERT: A 1458 LYS cc_start: 0.8436 (tptt) cc_final: 0.8160 (tptt) REVERT: A 1483 MET cc_start: 0.8690 (mpp) cc_final: 0.7848 (mpt) REVERT: B 1606 GLN cc_start: 0.7953 (OUTLIER) cc_final: 0.7733 (mp10) REVERT: C 136 GLU cc_start: 0.8459 (mm-30) cc_final: 0.8085 (mm-30) REVERT: C 233 ARG cc_start: 0.8659 (ttm170) cc_final: 0.8405 (mtt90) REVERT: C 241 GLN cc_start: 0.8642 (tm-30) cc_final: 0.8372 (tm-30) REVERT: D 78 MET cc_start: 0.8846 (ptm) cc_final: 0.8390 (pp-130) REVERT: D 89 GLU cc_start: 0.8435 (tm-30) cc_final: 0.8197 (pp20) REVERT: D 108 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8504 (tp) REVERT: D 163 MET cc_start: 0.8917 (ttp) cc_final: 0.8587 (tpp) REVERT: D 206 ASP cc_start: 0.8434 (m-30) cc_final: 0.8176 (m-30) REVERT: D 236 LEU cc_start: 0.6064 (tt) cc_final: 0.5687 (mt) outliers start: 43 outliers final: 14 residues processed: 183 average time/residue: 1.2198 time to fit residues: 246.1008 Evaluate side-chains 159 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 664 GLU Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 805 ASN Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain A residue 908 ILE Chi-restraints excluded: chain A residue 920 ASP Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1111 SER Chi-restraints excluded: chain A residue 1185 CYS Chi-restraints excluded: chain A residue 1255 ARG Chi-restraints excluded: chain A residue 1259 ILE Chi-restraints excluded: chain A residue 1316 SER Chi-restraints excluded: chain A residue 1520 LEU Chi-restraints excluded: chain A residue 1548 VAL Chi-restraints excluded: chain B residue 1539 SER Chi-restraints excluded: chain B residue 1606 GLN Chi-restraints excluded: chain B residue 1608 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 108 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 8 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 114 optimal weight: 0.7980 chunk 121 optimal weight: 8.9990 chunk 100 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 167 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1041 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1336 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.145620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.096721 restraints weight = 20249.288| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.87 r_work: 0.3254 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 13760 Z= 0.133 Angle : 0.583 13.758 18582 Z= 0.283 Chirality : 0.038 0.191 2186 Planarity : 0.003 0.046 2386 Dihedral : 4.201 18.448 1811 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.46 % Allowed : 18.95 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.20), residues: 1704 helix: 1.44 (0.15), residues: 1229 sheet: None (None), residues: 0 loop : -0.92 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1532 HIS 0.003 0.001 HIS A1363 PHE 0.012 0.001 PHE C 120 TYR 0.011 0.001 TYR A 914 ARG 0.011 0.000 ARG D 233 Details of bonding type rmsd hydrogen bonds : bond 0.03205 ( 902) hydrogen bonds : angle 3.72152 ( 2688) covalent geometry : bond 0.00321 (13760) covalent geometry : angle 0.58316 (18582) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 138 time to evaluate : 1.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 THR cc_start: 0.7984 (OUTLIER) cc_final: 0.7749 (t) REVERT: A 426 ASP cc_start: 0.7593 (t0) cc_final: 0.6835 (p0) REVERT: A 664 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.7680 (pp20) REVERT: A 831 TYR cc_start: 0.8217 (t80) cc_final: 0.7864 (t80) REVERT: A 867 MET cc_start: 0.9226 (OUTLIER) cc_final: 0.8067 (ptp) REVERT: A 902 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7593 (mtm110) REVERT: A 987 TRP cc_start: 0.8282 (t-100) cc_final: 0.8064 (t-100) REVERT: A 1027 GLU cc_start: 0.8342 (pp20) cc_final: 0.8101 (pp20) REVERT: A 1255 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.7399 (ptt90) REVERT: A 1402 ARG cc_start: 0.7820 (mtp85) cc_final: 0.7116 (mmm-85) REVERT: A 1458 LYS cc_start: 0.8464 (tptt) cc_final: 0.8173 (tptt) REVERT: B 1606 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7747 (mp10) REVERT: C 136 GLU cc_start: 0.8479 (mm-30) cc_final: 0.8054 (mm-30) REVERT: C 233 ARG cc_start: 0.8644 (ttm170) cc_final: 0.8400 (mtt90) REVERT: C 241 GLN cc_start: 0.8586 (tm-30) cc_final: 0.8340 (tm-30) REVERT: D 78 MET cc_start: 0.8838 (ptm) cc_final: 0.8379 (pp-130) REVERT: D 89 GLU cc_start: 0.8481 (tm-30) cc_final: 0.8227 (pp20) REVERT: D 108 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8516 (tp) REVERT: D 163 MET cc_start: 0.8951 (ttp) cc_final: 0.8581 (tpp) REVERT: D 206 ASP cc_start: 0.8449 (m-30) cc_final: 0.8203 (m-30) REVERT: D 236 LEU cc_start: 0.6092 (tt) cc_final: 0.5786 (tp) REVERT: D 239 TYR cc_start: 0.6304 (t80) cc_final: 0.5830 (t80) outliers start: 38 outliers final: 17 residues processed: 167 average time/residue: 1.2263 time to fit residues: 226.5071 Evaluate side-chains 159 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 664 GLU Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 805 ASN Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 902 ARG Chi-restraints excluded: chain A residue 908 ILE Chi-restraints excluded: chain A residue 920 ASP Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1111 SER Chi-restraints excluded: chain A residue 1185 CYS Chi-restraints excluded: chain A residue 1255 ARG Chi-restraints excluded: chain A residue 1316 SER Chi-restraints excluded: chain A residue 1520 LEU Chi-restraints excluded: chain A residue 1548 VAL Chi-restraints excluded: chain B residue 1518 LEU Chi-restraints excluded: chain B residue 1539 SER Chi-restraints excluded: chain B residue 1606 GLN Chi-restraints excluded: chain B residue 1608 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 108 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 74 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 chunk 127 optimal weight: 8.9990 chunk 43 optimal weight: 0.3980 chunk 61 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 135 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1041 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1150 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 = 0.4076 r_free = 0.4076 target = 0.145155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.096030 restraints weight = 20277.279| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.89 r_work: 0.3242 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 13760 Z= 0.146 Angle : 0.597 14.155 18582 Z= 0.286 Chirality : 0.039 0.171 2186 Planarity : 0.003 0.046 2386 Dihedral : 4.182 18.572 1811 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.20 % Allowed : 19.53 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.20), residues: 1704 helix: 1.49 (0.15), residues: 1229 sheet: None (None), residues: 0 loop : -0.91 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1532 HIS 0.003 0.001 HIS A1363 PHE 0.023 0.001 PHE A1573 TYR 0.009 0.001 TYR A 739 ARG 0.011 0.000 ARG D 233 Details of bonding type rmsd hydrogen bonds : bond 0.03222 ( 902) hydrogen bonds : angle 3.70380 ( 2688) covalent geometry : bond 0.00354 (13760) covalent geometry : angle 0.59702 (18582) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 140 time to evaluate : 1.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 426 ASP cc_start: 0.7543 (t0) cc_final: 0.6829 (p0) REVERT: A 664 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.7667 (pp20) REVERT: A 831 TYR cc_start: 0.8179 (t80) cc_final: 0.7831 (t80) REVERT: A 867 MET cc_start: 0.9238 (OUTLIER) cc_final: 0.8052 (ptp) REVERT: A 902 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7612 (mtm110) REVERT: A 1027 GLU cc_start: 0.8372 (pp20) cc_final: 0.8110 (pp20) REVERT: A 1255 ARG cc_start: 0.7669 (OUTLIER) cc_final: 0.7297 (ptt90) REVERT: A 1259 ILE cc_start: 0.8565 (OUTLIER) cc_final: 0.8310 (tp) REVERT: A 1402 ARG cc_start: 0.7797 (mtp85) cc_final: 0.7135 (mmm-85) REVERT: A 1458 LYS cc_start: 0.8497 (tptt) cc_final: 0.8265 (tptt) REVERT: B 1606 GLN cc_start: 0.7981 (OUTLIER) cc_final: 0.7758 (mp10) REVERT: C 136 GLU cc_start: 0.8514 (mm-30) cc_final: 0.8114 (mm-30) REVERT: C 233 ARG cc_start: 0.8675 (ttm170) cc_final: 0.8426 (mtt90) REVERT: C 241 GLN cc_start: 0.8635 (tm-30) cc_final: 0.8404 (tm-30) REVERT: D 78 MET cc_start: 0.8847 (ptm) cc_final: 0.8384 (pp-130) REVERT: D 89 GLU cc_start: 0.8474 (tm-30) cc_final: 0.8221 (pp20) REVERT: D 108 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8530 (tp) REVERT: D 163 MET cc_start: 0.8948 (ttp) cc_final: 0.8580 (tpp) REVERT: D 206 ASP cc_start: 0.8452 (m-30) cc_final: 0.8206 (m-30) REVERT: D 236 LEU cc_start: 0.6095 (tt) cc_final: 0.5797 (tp) REVERT: D 239 TYR cc_start: 0.6403 (t80) cc_final: 0.5969 (t80) outliers start: 34 outliers final: 18 residues processed: 167 average time/residue: 1.2970 time to fit residues: 239.8573 Evaluate side-chains 159 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 2.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 664 GLU Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 805 ASN Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 902 ARG Chi-restraints excluded: chain A residue 908 ILE Chi-restraints excluded: chain A residue 920 ASP Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1111 SER Chi-restraints excluded: chain A residue 1185 CYS Chi-restraints excluded: chain A residue 1255 ARG Chi-restraints excluded: chain A residue 1259 ILE Chi-restraints excluded: chain A residue 1316 SER Chi-restraints excluded: chain A residue 1520 LEU Chi-restraints excluded: chain A residue 1548 VAL Chi-restraints excluded: chain B residue 1518 LEU Chi-restraints excluded: chain B residue 1539 SER Chi-restraints excluded: chain B residue 1606 GLN Chi-restraints excluded: chain B residue 1608 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 108 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 135 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 11 optimal weight: 0.0770 chunk 78 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 126 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 160 optimal weight: 5.9990 chunk 127 optimal weight: 0.9990 chunk 153 optimal weight: 6.9990 overall best weight: 0.7742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 713 GLN ** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1041 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.145825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.096934 restraints weight = 20045.744| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.86 r_work: 0.3255 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13760 Z= 0.129 Angle : 0.588 15.357 18582 Z= 0.282 Chirality : 0.038 0.172 2186 Planarity : 0.003 0.046 2386 Dihedral : 4.140 18.518 1811 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.88 % Allowed : 19.92 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.20), residues: 1704 helix: 1.59 (0.15), residues: 1228 sheet: None (None), residues: 0 loop : -0.88 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1532 HIS 0.003 0.001 HIS A1363 PHE 0.014 0.001 PHE C 120 TYR 0.009 0.001 TYR A 914 ARG 0.012 0.001 ARG A 780 Details of bonding type rmsd hydrogen bonds : bond 0.03177 ( 902) hydrogen bonds : angle 3.68162 ( 2688) covalent geometry : bond 0.00311 (13760) covalent geometry : angle 0.58780 (18582) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 137 time to evaluate : 1.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 426 ASP cc_start: 0.7447 (t0) cc_final: 0.6779 (p0) REVERT: A 664 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7695 (pp20) REVERT: A 831 TYR cc_start: 0.8208 (t80) cc_final: 0.7837 (t80) REVERT: A 867 MET cc_start: 0.9215 (OUTLIER) cc_final: 0.8014 (ptp) REVERT: A 902 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7606 (mtm110) REVERT: A 1027 GLU cc_start: 0.8358 (pp20) cc_final: 0.8093 (pp20) REVERT: A 1255 ARG cc_start: 0.7638 (OUTLIER) cc_final: 0.7291 (ptt90) REVERT: A 1259 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.8288 (tp) REVERT: A 1402 ARG cc_start: 0.7728 (mtp85) cc_final: 0.7000 (mmm-85) REVERT: A 1458 LYS cc_start: 0.8533 (tptt) cc_final: 0.8306 (tptt) REVERT: B 1606 GLN cc_start: 0.7904 (OUTLIER) cc_final: 0.7694 (mp10) REVERT: C 136 GLU cc_start: 0.8506 (mm-30) cc_final: 0.8101 (mm-30) REVERT: C 233 ARG cc_start: 0.8686 (ttm170) cc_final: 0.8439 (mtt90) REVERT: C 241 GLN cc_start: 0.8631 (tm-30) cc_final: 0.8375 (tm-30) REVERT: D 78 MET cc_start: 0.8817 (ptm) cc_final: 0.8355 (pp-130) REVERT: D 89 GLU cc_start: 0.8482 (tm-30) cc_final: 0.8229 (pp20) REVERT: D 108 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8533 (tp) REVERT: D 163 MET cc_start: 0.8947 (ttp) cc_final: 0.8611 (tpp) REVERT: D 206 ASP cc_start: 0.8434 (m-30) cc_final: 0.8189 (m-30) REVERT: D 236 LEU cc_start: 0.6086 (tt) cc_final: 0.5768 (tp) REVERT: D 239 TYR cc_start: 0.6407 (t80) cc_final: 0.5979 (t80) outliers start: 29 outliers final: 17 residues processed: 161 average time/residue: 1.2959 time to fit residues: 229.5716 Evaluate side-chains 156 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 664 GLU Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 805 ASN Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 902 ARG Chi-restraints excluded: chain A residue 908 ILE Chi-restraints excluded: chain A residue 920 ASP Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1111 SER Chi-restraints excluded: chain A residue 1185 CYS Chi-restraints excluded: chain A residue 1255 ARG Chi-restraints excluded: chain A residue 1259 ILE Chi-restraints excluded: chain A residue 1520 LEU Chi-restraints excluded: chain A residue 1548 VAL Chi-restraints excluded: chain B residue 1498 VAL Chi-restraints excluded: chain B residue 1518 LEU Chi-restraints excluded: chain B residue 1539 SER Chi-restraints excluded: chain B residue 1606 GLN Chi-restraints excluded: chain B residue 1608 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 108 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 124 optimal weight: 0.5980 chunk 110 optimal weight: 20.0000 chunk 96 optimal weight: 0.0020 chunk 9 optimal weight: 0.0270 chunk 167 optimal weight: 0.9990 chunk 118 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 104 optimal weight: 0.8980 chunk 125 optimal weight: 0.5980 chunk 115 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.4246 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 HIS ** A1041 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.147443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.098804 restraints weight = 20099.238| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.88 r_work: 0.3285 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13760 Z= 0.110 Angle : 0.581 15.538 18582 Z= 0.280 Chirality : 0.037 0.181 2186 Planarity : 0.004 0.066 2386 Dihedral : 4.039 18.070 1811 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.94 % Allowed : 19.92 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.21), residues: 1704 helix: 1.74 (0.15), residues: 1232 sheet: None (None), residues: 0 loop : -0.81 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 894 HIS 0.002 0.001 HIS A1363 PHE 0.023 0.001 PHE A1573 TYR 0.011 0.001 TYR A 914 ARG 0.014 0.001 ARG A 780 Details of bonding type rmsd hydrogen bonds : bond 0.03077 ( 902) hydrogen bonds : angle 3.63589 ( 2688) covalent geometry : bond 0.00256 (13760) covalent geometry : angle 0.58139 (18582) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 147 time to evaluate : 1.489 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 426 ASP cc_start: 0.7286 (t0) cc_final: 0.6640 (p0) REVERT: A 664 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7702 (pp20) REVERT: A 831 TYR cc_start: 0.8209 (t80) cc_final: 0.7864 (t80) REVERT: A 867 MET cc_start: 0.9183 (OUTLIER) cc_final: 0.7896 (ptp) REVERT: A 902 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7610 (mtm110) REVERT: A 1027 GLU cc_start: 0.8370 (pp20) cc_final: 0.8065 (pp20) REVERT: A 1255 ARG cc_start: 0.7581 (OUTLIER) cc_final: 0.7256 (ptt90) REVERT: A 1259 ILE cc_start: 0.8521 (OUTLIER) cc_final: 0.8267 (tp) REVERT: A 1402 ARG cc_start: 0.7697 (mtp85) cc_final: 0.6867 (mmm-85) REVERT: A 1458 LYS cc_start: 0.8533 (tptt) cc_final: 0.8312 (tptt) REVERT: A 1483 MET cc_start: 0.8658 (mpp) cc_final: 0.7740 (mpt) REVERT: A 1548 VAL cc_start: 0.7664 (OUTLIER) cc_final: 0.7463 (t) REVERT: C 72 ARG cc_start: 0.8368 (mtp85) cc_final: 0.7927 (ptm160) REVERT: C 136 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8080 (mm-30) REVERT: C 233 ARG cc_start: 0.8678 (ttm170) cc_final: 0.8441 (mtt90) REVERT: D 72 ARG cc_start: 0.8148 (mtm-85) cc_final: 0.7371 (tpp80) REVERT: D 78 MET cc_start: 0.8786 (ptm) cc_final: 0.8332 (pp-130) REVERT: D 89 GLU cc_start: 0.8462 (tm-30) cc_final: 0.8230 (pp20) REVERT: D 108 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8484 (tp) REVERT: D 163 MET cc_start: 0.8959 (ttp) cc_final: 0.8625 (tpp) REVERT: D 206 ASP cc_start: 0.8395 (m-30) cc_final: 0.8126 (m-30) REVERT: D 236 LEU cc_start: 0.6047 (tt) cc_final: 0.5714 (tp) REVERT: D 239 TYR cc_start: 0.6339 (t80) cc_final: 0.6014 (t80) outliers start: 30 outliers final: 15 residues processed: 171 average time/residue: 1.2205 time to fit residues: 230.5012 Evaluate side-chains 161 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 139 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 664 GLU Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 805 ASN Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 902 ARG Chi-restraints excluded: chain A residue 908 ILE Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1111 SER Chi-restraints excluded: chain A residue 1185 CYS Chi-restraints excluded: chain A residue 1255 ARG Chi-restraints excluded: chain A residue 1259 ILE Chi-restraints excluded: chain A residue 1316 SER Chi-restraints excluded: chain A residue 1520 LEU Chi-restraints excluded: chain A residue 1548 VAL Chi-restraints excluded: chain B residue 1498 VAL Chi-restraints excluded: chain B residue 1518 LEU Chi-restraints excluded: chain B residue 1539 SER Chi-restraints excluded: chain B residue 1608 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 108 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 115 optimal weight: 5.9990 chunk 75 optimal weight: 0.5980 chunk 24 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 chunk 139 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1041 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 240 GLN C 241 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.144590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.095382 restraints weight = 20207.968| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.88 r_work: 0.3236 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 13760 Z= 0.171 Angle : 0.627 16.103 18582 Z= 0.299 Chirality : 0.040 0.169 2186 Planarity : 0.004 0.045 2386 Dihedral : 4.102 18.599 1811 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.81 % Allowed : 20.50 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.21), residues: 1704 helix: 1.69 (0.15), residues: 1231 sheet: None (None), residues: 0 loop : -0.78 (0.30), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1532 HIS 0.003 0.001 HIS A1150 PHE 0.014 0.001 PHE D 120 TYR 0.018 0.001 TYR A 417 ARG 0.010 0.001 ARG A 780 Details of bonding type rmsd hydrogen bonds : bond 0.03249 ( 902) hydrogen bonds : angle 3.70725 ( 2688) covalent geometry : bond 0.00423 (13760) covalent geometry : angle 0.62688 (18582) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9204.52 seconds wall clock time: 157 minutes 59.95 seconds (9479.95 seconds total)