Starting phenix.real_space_refine on Wed Mar 4 08:59:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vf5_31947/03_2026/7vf5_31947.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vf5_31947/03_2026/7vf5_31947.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 { model { file = "/net/cci-nas-00/data/ceres_data/7vf5_31947/03_2026/7vf5_31947.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vf5_31947/03_2026/7vf5_31947.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vf5_31947/03_2026/7vf5_31947.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vf5_31947/03_2026/7vf5_31947.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.085 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 73 5.16 5 C 7760 2.51 5 N 2076 2.21 5 O 2404 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12313 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 9325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1188, 9325 Classifications: {'peptide': 1188} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 1141} Chain breaks: 3 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: 2.44, per 1000 atoms: 0.20 Number of scatterers: 12313 At special positions: 0 Unit cell: (104.96, 111.52, 144.32, 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 73 16.00 O 2404 8.00 N 2076 7.00 C 7760 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 574.0 milliseconds 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2996 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 3 sheets defined 76.8% alpha, 0.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 357 through 369 Processing helix chain 'A' and resid 373 through 392 removed outlier: 4.251A pdb=" N GLY A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ALA A 381 " --> pdb=" O GLY A 377 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS A 384 " --> pdb=" O GLU A 380 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP A 390 " --> pdb=" O THR A 386 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR A 392 " --> pdb=" O LEU A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 405 Processing helix chain 'A' and resid 406 through 421 removed outlier: 4.530A pdb=" N ILE A 412 " --> pdb=" O PRO A 408 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N LYS A 413 " --> pdb=" O SER A 409 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N SER A 416 " --> pdb=" O ILE A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 440 Processing helix chain 'A' and resid 440 through 445 removed outlier: 3.687A pdb=" N ALA A 444 " --> pdb=" O ASN A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 468 removed outlier: 3.553A pdb=" N GLU A 468 " --> pdb=" O SER A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 480 removed outlier: 4.215A pdb=" N GLY A 473 " --> pdb=" O CYS A 469 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A 480 " --> pdb=" O GLY A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 491 removed outlier: 4.016A pdb=" N GLU A 488 " --> pdb=" O SER A 484 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU A 489 " --> pdb=" O GLY A 485 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE A 491 " --> pdb=" O PHE A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 513 removed outlier: 3.598A pdb=" N LYS A 500 " --> pdb=" O SER A 496 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN A 502 " --> pdb=" O SER A 498 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N MET A 513 " --> pdb=" O SER A 509 " (cutoff:3.500A) 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 577 removed outlier: 3.635A pdb=" N THR A 577 " --> pdb=" O LEU A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 640 removed outlier: 3.925A pdb=" N LEU A 627 " --> pdb=" O GLU A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 645 Processing helix chain 'A' and resid 668 through 679 removed outlier: 3.815A pdb=" N ARG A 674 " --> pdb=" O PRO A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 689 Processing helix chain 'A' and resid 691 through 697 removed outlier: 4.012A pdb=" N HIS A 697 " --> pdb=" O VAL A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 714 removed outlier: 4.032A pdb=" N LEU A 701 " --> pdb=" O HIS A 697 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN A 702 " --> pdb=" O PRO A 698 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER A 714 " --> pdb=" O PHE A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 724 Processing helix chain 'A' and resid 724 through 746 removed outlier: 3.738A pdb=" N LEU A 730 " --> pdb=" O GLU A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 750 Processing helix chain 'A' and resid 756 through 780 removed outlier: 3.592A pdb=" N PHE A 778 " --> pdb=" O LEU A 774 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG A 780 " --> pdb=" O SER A 776 " (cutoff:3.500A) 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 832 removed outlier: 3.609A pdb=" N LEU A 828 " --> pdb=" O SER A 824 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR A 832 " --> pdb=" O LEU A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 862 Processing helix chain 'A' and resid 865 through 882 removed outlier: 3.743A pdb=" N GLU A 869 " --> pdb=" O VAL A 865 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLN A 870 " --> pdb=" O GLN A 866 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ALA A 873 " --> pdb=" O GLU A 869 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N SER A 874 " --> pdb=" O GLN A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 895 removed outlier: 3.761A pdb=" N GLU A 890 " --> pdb=" O ALA A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 906 No H-bonds generated for 'chain 'A' and resid 904 through 906' Processing helix chain 'A' and resid 907 through 918 Processing helix chain 'A' and resid 928 through 941 removed outlier: 4.234A pdb=" N THR A 932 " --> pdb=" O VAL A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 966 removed outlier: 3.587A pdb=" N LEU A 958 " --> pdb=" O LEU A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 983 removed outlier: 3.867A pdb=" N VAL A 975 " --> pdb=" O THR A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 989 removed outlier: 3.682A pdb=" N ARG A 988 " --> pdb=" O THR A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1019 removed outlier: 3.844A pdb=" N GLU A1019 " --> pdb=" O THR A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1032 through 1046 removed outlier: 4.198A pdb=" N THR A1039 " --> pdb=" O SER A1035 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N MET A1042 " --> pdb=" O VAL A1038 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N SER A1046 " --> pdb=" O MET A1042 " (cutoff:3.500A) Processing helix chain 'A' and resid 1054 through 1070 removed outlier: 3.954A pdb=" N LYS A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE A1060 " --> pdb=" O ASP A1056 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN A1061 " --> pdb=" O GLU A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1082 through 1087 Processing helix chain 'A' and resid 1091 through 1100 Processing helix chain 'A' and resid 1105 through 1107 No H-bonds generated for 'chain 'A' and resid 1105 through 1107' Processing helix chain 'A' and resid 1108 through 1120 removed outlier: 3.695A pdb=" N GLU A1118 " --> pdb=" O ILE A1114 " (cutoff:3.500A) Processing helix chain 'A' and resid 1133 through 1153 removed outlier: 3.600A pdb=" N ILE A1137 " --> pdb=" O GLU A1133 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL A1153 " --> pdb=" O MET A1149 " (cutoff:3.500A) Processing helix chain 'A' and resid 1154 through 1165 removed outlier: 3.699A pdb=" N GLU A1160 " --> pdb=" O LYS A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1170 through 1184 removed outlier: 3.628A pdb=" N VAL A1182 " --> pdb=" O ARG A1178 " (cutoff:3.500A) Processing helix chain 'A' and resid 1188 through 1208 removed outlier: 3.850A pdb=" N ILE A1195 " --> pdb=" O THR A1191 " (cutoff:3.500A) Processing helix chain 'A' and resid 1219 through 1234 Processing helix chain 'A' and resid 1235 through 1247 Processing helix chain 'A' and resid 1253 through 1269 Processing helix chain 'A' and resid 1275 through 1292 removed outlier: 4.024A pdb=" N GLU A1281 " --> pdb=" O GLN A1277 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N TYR A1282 " --> pdb=" O GLN A1278 " (cutoff:3.500A) Processing helix chain 'A' and resid 1308 through 1313 Processing helix chain 'A' and resid 1314 through 1316 No H-bonds generated for 'chain 'A' and resid 1314 through 1316' Processing helix chain 'A' and resid 1319 through 1336 Processing helix chain 'A' and resid 1340 through 1355 removed outlier: 3.631A pdb=" N LEU A1344 " --> pdb=" O SER A1340 " (cutoff:3.500A) Processing helix chain 'A' and resid 1357 through 1371 removed outlier: 3.837A pdb=" N ARG A1369 " --> pdb=" O LYS A1365 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LYS A1370 " --> pdb=" O SER A1366 " (cutoff:3.500A) Processing helix chain 'A' and resid 1373 through 1385 removed outlier: 3.502A pdb=" N THR A1385 " --> pdb=" O ARG A1381 " (cutoff:3.500A) Processing helix chain 'A' and resid 1390 through 1404 removed outlier: 3.652A pdb=" N ALA A1394 " --> pdb=" O THR A1390 " (cutoff:3.500A) Processing helix chain 'A' and resid 1434 through 1442 Processing helix chain 'A' and resid 1447 through 1462 removed outlier: 3.606A pdb=" N LEU A1459 " --> pdb=" O GLU A1455 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL A1460 " --> pdb=" O LEU A1456 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A1461 " --> pdb=" O GLU A1457 " (cutoff:3.500A) Processing helix chain 'A' and resid 1467 through 1486 removed outlier: 4.009A pdb=" N ASP A1471 " --> pdb=" O ASP A1467 " (cutoff:3.500A) Processing helix chain 'A' and resid 1507 through 1514 Processing helix chain 'A' and resid 1554 through 1559 removed outlier: 4.304A pdb=" N LYS A1558 " --> pdb=" O GLU A1554 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N CYS A1559 " --> pdb=" O LEU A1555 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1554 through 1559' Processing helix chain 'A' and resid 1565 through 1572 removed outlier: 4.131A pdb=" N LEU A1569 " --> pdb=" O LEU A1565 " (cutoff:3.500A) 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 176 Processing helix chain 'C' and resid 176 through 244 Processing helix chain 'C' and resid 245 through 247 No H-bonds generated for 'chain 'C' and resid 245 through 247' Processing helix chain 'D' and resid 65 through 98 removed outlier: 4.200A pdb=" N SER D 69 " --> pdb=" O GLN D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 145 Processing helix chain 'D' and resid 148 through 176 removed outlier: 3.561A pdb=" N SER D 176 " --> pdb=" O GLY D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 247 removed outlier: 3.835A pdb=" N GLU D 184 " --> pdb=" O ILE D 180 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N GLN D 245 " --> pdb=" O GLN D 241 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA D 246 " --> pdb=" O GLN D 242 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER D 247 " --> pdb=" O GLN D 243 " (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: 5.904A 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 838 hydrogen bonds defined for protein. 2505 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.82 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4058 1.34 - 1.46: 1213 1.46 - 1.57: 7101 1.57 - 1.69: 0 1.69 - 1.81: 117 Bond restraints: 12489 Sorted by residual: bond pdb=" CA LEU A1552 " pdb=" CB LEU A1552 " ideal model delta sigma weight residual 1.525 1.550 -0.026 1.47e-02 4.63e+03 3.04e+00 bond pdb=" C VAL A1033 " pdb=" N PRO A1034 " ideal model delta sigma weight residual 1.336 1.354 -0.018 1.20e-02 6.94e+03 2.28e+00 bond pdb=" CG GLU A 380 " pdb=" CD GLU A 380 " ideal model delta sigma weight residual 1.516 1.481 0.035 2.50e-02 1.60e+03 1.91e+00 bond pdb=" CD GLU A 380 " pdb=" OE1 GLU A 380 " ideal model delta sigma weight residual 1.249 1.223 0.026 1.90e-02 2.77e+03 1.80e+00 bond pdb=" CG1 ILE A 855 " pdb=" CD1 ILE A 855 " ideal model delta sigma weight residual 1.513 1.461 0.052 3.90e-02 6.57e+02 1.80e+00 ... (remaining 12484 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 16621 2.13 - 4.26: 211 4.26 - 6.39: 39 6.39 - 8.52: 4 8.52 - 10.66: 1 Bond angle restraints: 16876 Sorted by residual: angle pdb=" N ILE A 624 " pdb=" CA ILE A 624 " pdb=" C ILE A 624 " ideal model delta sigma weight residual 111.90 108.57 3.33 8.10e-01 1.52e+00 1.69e+01 angle pdb=" N GLU A 380 " pdb=" CA GLU A 380 " pdb=" CB GLU A 380 " ideal model delta sigma weight residual 110.39 116.98 -6.59 1.66e+00 3.63e-01 1.58e+01 angle pdb=" C ILE A 379 " pdb=" N GLU A 380 " pdb=" CA GLU A 380 " ideal model delta sigma weight residual 120.72 114.10 6.62 1.67e+00 3.59e-01 1.57e+01 angle pdb=" C PHE A1400 " pdb=" N MET A1401 " pdb=" CA MET A1401 " ideal model delta sigma weight residual 120.38 124.83 -4.45 1.37e+00 5.33e-01 1.05e+01 angle pdb=" N ILE D 180 " pdb=" CA ILE D 180 " pdb=" C ILE D 180 " ideal model delta sigma weight residual 112.80 109.13 3.67 1.15e+00 7.56e-01 1.02e+01 ... (remaining 16871 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 7047 17.95 - 35.89: 560 35.89 - 53.84: 116 53.84 - 71.78: 35 71.78 - 89.73: 11 Dihedral angle restraints: 7769 sinusoidal: 3193 harmonic: 4576 Sorted by residual: dihedral pdb=" CA GLN A1443 " pdb=" C GLN A1443 " pdb=" N SER A1444 " pdb=" CA SER A1444 " ideal model delta harmonic sigma weight residual 180.00 160.09 19.91 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA HIS A1463 " pdb=" C HIS A1463 " pdb=" N SER A1464 " pdb=" CA SER A1464 " ideal model delta harmonic sigma weight residual 180.00 161.81 18.19 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA SER A 965 " pdb=" C SER A 965 " pdb=" N ALA A 966 " pdb=" CA ALA A 966 " ideal model delta harmonic sigma weight residual 180.00 163.03 16.97 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 7766 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1474 0.043 - 0.086: 439 0.086 - 0.128: 69 0.128 - 0.171: 6 0.171 - 0.214: 3 Chirality restraints: 1991 Sorted by residual: chirality pdb=" CB ILE A1250 " pdb=" CA ILE A1250 " pdb=" CG1 ILE A1250 " pdb=" CG2 ILE A1250 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CG LEU A 689 " pdb=" CB LEU A 689 " pdb=" CD1 LEU A 689 " pdb=" CD2 LEU A 689 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.50e-01 chirality pdb=" CB VAL A 865 " pdb=" CA VAL A 865 " pdb=" CG1 VAL A 865 " pdb=" CG2 VAL A 865 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.87e-01 ... (remaining 1988 not shown) Planarity restraints: 2168 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 447 " 0.039 5.00e-02 4.00e+02 5.88e-02 5.53e+00 pdb=" N PRO A 448 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 448 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 448 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A1504 " -0.039 5.00e-02 4.00e+02 5.78e-02 5.35e+00 pdb=" N PRO A1505 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO A1505 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A1505 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 145 " -0.012 2.00e-02 2.50e+03 1.34e-02 4.46e+00 pdb=" CG TRP C 145 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP C 145 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP C 145 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 145 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 145 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 145 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 145 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 145 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP C 145 " 0.001 2.00e-02 2.50e+03 ... (remaining 2165 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 548 2.73 - 3.27: 13115 3.27 - 3.81: 20562 3.81 - 4.36: 24564 4.36 - 4.90: 42391 Nonbonded interactions: 101180 Sorted by model distance: nonbonded pdb=" O ILE A 449 " pdb=" OG SER C 220 " model vdw 2.182 3.040 nonbonded pdb=" OE2 GLU A 518 " pdb=" OH TYR A 560 " model vdw 2.213 3.040 nonbonded pdb=" O GLY D 126 " pdb=" NE2 GLN D 130 " model vdw 2.219 3.120 nonbonded pdb=" OG SER A1507 " pdb=" OD1 ASN A1510 " model vdw 2.220 3.040 nonbonded pdb=" O LEU A1459 " pdb=" OG SER A1464 " model vdw 2.233 3.040 ... (remaining 101175 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: 2.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.050 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 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 : 0.003 0.055 12489 Z= 0.152 Angle : 0.637 10.656 16876 Z= 0.351 Chirality : 0.040 0.214 1991 Planarity : 0.004 0.059 2168 Dihedral : 14.392 89.727 4773 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.22), residues: 1544 helix: 1.01 (0.16), residues: 1128 sheet: None (None), residues: 0 loop : -1.31 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1268 TYR 0.013 0.001 TYR A 417 PHE 0.025 0.002 PHE A 738 TRP 0.036 0.002 TRP C 145 HIS 0.011 0.001 HIS A 797 Details of bonding type rmsd covalent geometry : bond 0.00336 (12489) covalent geometry : angle 0.63664 (16876) hydrogen bonds : bond 0.12456 ( 838) hydrogen bonds : angle 5.01615 ( 2505) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: C 109 ARG cc_start: 0.8619 (mtp-110) cc_final: 0.7845 (mtp180) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.5367 time to fit residues: 93.4734 Evaluate side-chains 101 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 30.0000 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.2980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.9980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 GLN A 542 GLN ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1463 HIS A1510 ASN D 130 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.193248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.129358 restraints weight = 13556.357| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 2.69 r_work: 0.3742 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.1093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12489 Z= 0.191 Angle : 0.639 9.241 16876 Z= 0.314 Chirality : 0.040 0.160 1991 Planarity : 0.004 0.057 2168 Dihedral : 4.394 19.385 1639 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.34 % Allowed : 8.03 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.21), residues: 1544 helix: 1.01 (0.15), residues: 1159 sheet: None (None), residues: 0 loop : -1.50 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1268 TYR 0.011 0.001 TYR A 850 PHE 0.015 0.002 PHE A1362 TRP 0.011 0.001 TRP A1532 HIS 0.005 0.001 HIS A 494 Details of bonding type rmsd covalent geometry : bond 0.00469 (12489) covalent geometry : angle 0.63872 (16876) hydrogen bonds : bond 0.04091 ( 838) hydrogen bonds : angle 3.98268 ( 2505) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 121 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 390 ASP cc_start: 0.8794 (t70) cc_final: 0.8370 (m-30) REVERT: A 488 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7434 (mm-30) REVERT: A 905 ILE cc_start: 0.8240 (OUTLIER) cc_final: 0.7777 (mp) REVERT: A 1083 GLU cc_start: 0.7329 (mp0) cc_final: 0.6947 (tp30) REVERT: A 1191 THR cc_start: 0.8779 (t) cc_final: 0.8284 (m) REVERT: C 109 ARG cc_start: 0.8123 (mtp-110) cc_final: 0.7445 (mtp180) outliers start: 33 outliers final: 9 residues processed: 141 average time/residue: 0.5406 time to fit residues: 83.5820 Evaluate side-chains 116 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 863 SER Chi-restraints excluded: chain A residue 905 ILE Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1294 ASP Chi-restraints excluded: chain A residue 1457 GLU Chi-restraints excluded: chain A residue 1511 LEU Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 163 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 121 optimal weight: 3.9990 chunk 2 optimal weight: 0.0060 chunk 25 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 143 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 49 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 ASN A 419 GLN ** A1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.193600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.131092 restraints weight = 13601.036| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 2.91 r_work: 0.3773 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12489 Z= 0.157 Angle : 0.584 9.735 16876 Z= 0.288 Chirality : 0.038 0.141 1991 Planarity : 0.004 0.056 2168 Dihedral : 4.270 18.331 1639 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.98 % Allowed : 10.44 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.22), residues: 1544 helix: 1.13 (0.15), residues: 1162 sheet: None (None), residues: 0 loop : -1.44 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1515 TYR 0.013 0.001 TYR A 850 PHE 0.014 0.001 PHE A1362 TRP 0.008 0.001 TRP A1532 HIS 0.004 0.001 HIS A 494 Details of bonding type rmsd covalent geometry : bond 0.00382 (12489) covalent geometry : angle 0.58410 (16876) hydrogen bonds : bond 0.03739 ( 838) hydrogen bonds : angle 3.82319 ( 2505) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 125 time to evaluate : 0.455 Fit side-chains revert: symmetry clash REVERT: A 390 ASP cc_start: 0.8770 (t70) cc_final: 0.8335 (m-30) REVERT: A 488 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7383 (mm-30) REVERT: A 513 MET cc_start: 0.7570 (mmm) cc_final: 0.7298 (mmm) REVERT: A 905 ILE cc_start: 0.8106 (OUTLIER) cc_final: 0.7623 (mp) REVERT: A 923 MET cc_start: 0.7786 (OUTLIER) cc_final: 0.7064 (mtm) REVERT: A 1083 GLU cc_start: 0.7309 (mp0) cc_final: 0.6852 (tp30) REVERT: A 1184 LEU cc_start: 0.8217 (tt) cc_final: 0.8004 (tt) REVERT: C 109 ARG cc_start: 0.8209 (mtp-110) cc_final: 0.7742 (mtp180) REVERT: D 87 MET cc_start: 0.7059 (OUTLIER) cc_final: 0.6807 (mmm) outliers start: 42 outliers final: 12 residues processed: 153 average time/residue: 0.4586 time to fit residues: 77.9735 Evaluate side-chains 124 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 575 GLU Chi-restraints excluded: chain A residue 863 SER Chi-restraints excluded: chain A residue 905 ILE Chi-restraints excluded: chain A residue 923 MET Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1042 MET Chi-restraints excluded: chain A residue 1294 ASP Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 163 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 46 optimal weight: 9.9990 chunk 74 optimal weight: 0.5980 chunk 32 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 8 optimal weight: 0.0570 chunk 121 optimal weight: 6.9990 chunk 16 optimal weight: 0.5980 chunk 96 optimal weight: 10.0000 chunk 102 optimal weight: 6.9990 chunk 20 optimal weight: 0.6980 chunk 124 optimal weight: 6.9990 overall best weight: 0.7900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 814 HIS ** A1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.194483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.129984 restraints weight = 13489.220| |-----------------------------------------------------------------------------| r_work (start): 0.3987 rms_B_bonded: 2.70 r_work: 0.3747 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12489 Z= 0.145 Angle : 0.582 10.215 16876 Z= 0.282 Chirality : 0.038 0.135 1991 Planarity : 0.004 0.058 2168 Dihedral : 4.178 19.056 1639 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.77 % Allowed : 12.50 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.22), residues: 1544 helix: 1.26 (0.15), residues: 1162 sheet: None (None), residues: 0 loop : -1.44 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1515 TYR 0.011 0.001 TYR A1518 PHE 0.017 0.001 PHE A1362 TRP 0.007 0.001 TRP A1532 HIS 0.010 0.001 HIS A 494 Details of bonding type rmsd covalent geometry : bond 0.00351 (12489) covalent geometry : angle 0.58237 (16876) hydrogen bonds : bond 0.03555 ( 838) hydrogen bonds : angle 3.69664 ( 2505) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 122 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 390 ASP cc_start: 0.8792 (t70) cc_final: 0.8331 (m-30) REVERT: A 488 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7466 (mm-30) REVERT: A 513 MET cc_start: 0.7606 (mmm) cc_final: 0.7349 (mmm) REVERT: A 867 MET cc_start: 0.7711 (OUTLIER) cc_final: 0.6207 (pmt) REVERT: A 903 PHE cc_start: 0.8202 (OUTLIER) cc_final: 0.7640 (t80) REVERT: A 923 MET cc_start: 0.7810 (OUTLIER) cc_final: 0.7054 (mtm) REVERT: A 1184 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7935 (tt) REVERT: A 1191 THR cc_start: 0.8704 (t) cc_final: 0.8197 (m) REVERT: A 1397 PHE cc_start: 0.6714 (t80) cc_final: 0.6497 (t80) REVERT: A 1570 GLU cc_start: 0.4610 (OUTLIER) cc_final: 0.4323 (tm-30) REVERT: C 109 ARG cc_start: 0.8107 (mtp-110) cc_final: 0.7424 (mtp180) REVERT: C 195 GLU cc_start: 0.6457 (OUTLIER) cc_final: 0.5768 (mp0) REVERT: C 225 LEU cc_start: 0.6639 (OUTLIER) cc_final: 0.6406 (mm) outliers start: 39 outliers final: 16 residues processed: 143 average time/residue: 0.5110 time to fit residues: 80.5478 Evaluate side-chains 134 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 863 SER Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain A residue 903 PHE Chi-restraints excluded: chain A residue 923 MET Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1042 MET Chi-restraints excluded: chain A residue 1184 LEU Chi-restraints excluded: chain A residue 1294 ASP Chi-restraints excluded: chain A residue 1299 LEU Chi-restraints excluded: chain A residue 1362 PHE Chi-restraints excluded: chain A residue 1457 GLU Chi-restraints excluded: chain A residue 1511 LEU Chi-restraints excluded: chain A residue 1570 GLU Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 163 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 83 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 153 optimal weight: 10.0000 chunk 64 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 146 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 906 ASN ** A1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.211759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.134007 restraints weight = 14073.631| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 2.97 r_work: 0.3718 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12489 Z= 0.183 Angle : 0.603 10.610 16876 Z= 0.293 Chirality : 0.039 0.127 1991 Planarity : 0.004 0.058 2168 Dihedral : 4.238 19.029 1639 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.05 % Allowed : 14.13 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.22), residues: 1544 helix: 1.17 (0.15), residues: 1167 sheet: None (None), residues: 0 loop : -1.47 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 665 TYR 0.012 0.001 TYR A1359 PHE 0.016 0.002 PHE A1362 TRP 0.010 0.001 TRP C 145 HIS 0.007 0.001 HIS A 494 Details of bonding type rmsd covalent geometry : bond 0.00455 (12489) covalent geometry : angle 0.60302 (16876) hydrogen bonds : bond 0.03638 ( 838) hydrogen bonds : angle 3.73559 ( 2505) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 114 time to evaluate : 0.484 Fit side-chains revert: symmetry clash REVERT: A 390 ASP cc_start: 0.8754 (t70) cc_final: 0.8288 (m-30) REVERT: A 488 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7545 (mm-30) REVERT: A 513 MET cc_start: 0.7703 (mmm) cc_final: 0.7382 (mmm) REVERT: A 867 MET cc_start: 0.7748 (OUTLIER) cc_final: 0.6265 (pmt) REVERT: A 880 LYS cc_start: 0.8027 (ttpp) cc_final: 0.7633 (mtpm) REVERT: A 923 MET cc_start: 0.7939 (OUTLIER) cc_final: 0.7166 (mtm) REVERT: A 1397 PHE cc_start: 0.6816 (t80) cc_final: 0.6610 (t80) REVERT: A 1570 GLU cc_start: 0.4743 (OUTLIER) cc_final: 0.4428 (tm-30) REVERT: C 109 ARG cc_start: 0.8142 (mtp-110) cc_final: 0.7467 (mtp180) REVERT: C 195 GLU cc_start: 0.6533 (OUTLIER) cc_final: 0.5883 (mp0) outliers start: 43 outliers final: 16 residues processed: 145 average time/residue: 0.5057 time to fit residues: 80.7856 Evaluate side-chains 127 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 863 SER Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain A residue 903 PHE Chi-restraints excluded: chain A residue 923 MET Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1042 MET Chi-restraints excluded: chain A residue 1294 ASP Chi-restraints excluded: chain A residue 1299 LEU Chi-restraints excluded: chain A residue 1511 LEU Chi-restraints excluded: chain A residue 1570 GLU Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 163 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 92 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 chunk 51 optimal weight: 0.0050 chunk 19 optimal weight: 0.3980 chunk 97 optimal weight: 0.9980 chunk 105 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 56 optimal weight: 0.1980 chunk 65 optimal weight: 0.2980 overall best weight: 0.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1175 HIS ** A1293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.196416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.131951 restraints weight = 13556.209| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 2.71 r_work: 0.3787 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12489 Z= 0.114 Angle : 0.567 11.614 16876 Z= 0.275 Chirality : 0.036 0.130 1991 Planarity : 0.004 0.059 2168 Dihedral : 4.049 17.603 1639 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.06 % Allowed : 16.26 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.22), residues: 1544 helix: 1.45 (0.16), residues: 1165 sheet: None (None), residues: 0 loop : -1.41 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1268 TYR 0.011 0.001 TYR A 560 PHE 0.015 0.001 PHE A 504 TRP 0.009 0.001 TRP C 145 HIS 0.007 0.001 HIS A 494 Details of bonding type rmsd covalent geometry : bond 0.00260 (12489) covalent geometry : angle 0.56719 (16876) hydrogen bonds : bond 0.03340 ( 838) hydrogen bonds : angle 3.58382 ( 2505) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 121 time to evaluate : 0.421 Fit side-chains REVERT: A 336 MET cc_start: 0.3410 (tmm) cc_final: 0.2919 (tpt) REVERT: A 390 ASP cc_start: 0.8758 (t70) cc_final: 0.8306 (m-30) REVERT: A 488 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7441 (mm-30) REVERT: A 513 MET cc_start: 0.7516 (mmm) cc_final: 0.7258 (mmm) REVERT: A 656 MET cc_start: 0.8037 (tpp) cc_final: 0.7724 (tpt) REVERT: A 880 LYS cc_start: 0.8004 (ttpp) cc_final: 0.7642 (mtpm) REVERT: A 903 PHE cc_start: 0.8156 (OUTLIER) cc_final: 0.7518 (t80) REVERT: A 906 ASN cc_start: 0.7386 (t0) cc_final: 0.7185 (m-40) REVERT: A 923 MET cc_start: 0.7780 (OUTLIER) cc_final: 0.6942 (mtm) REVERT: A 997 LEU cc_start: 0.6859 (OUTLIER) cc_final: 0.6588 (tp) REVERT: A 1083 GLU cc_start: 0.7302 (mp0) cc_final: 0.6945 (tp30) REVERT: A 1191 THR cc_start: 0.8706 (t) cc_final: 0.8173 (m) REVERT: C 109 ARG cc_start: 0.8124 (mtp-110) cc_final: 0.7478 (mtp180) REVERT: C 195 GLU cc_start: 0.6322 (OUTLIER) cc_final: 0.5678 (mp0) REVERT: D 218 MET cc_start: 0.7348 (OUTLIER) cc_final: 0.7121 (mtt) outliers start: 29 outliers final: 11 residues processed: 141 average time/residue: 0.4916 time to fit residues: 76.7427 Evaluate side-chains 127 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 863 SER Chi-restraints excluded: chain A residue 903 PHE Chi-restraints excluded: chain A residue 923 MET Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1294 ASP Chi-restraints excluded: chain A residue 1299 LEU Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 218 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 97 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 90 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 68 optimal weight: 0.3980 chunk 9 optimal weight: 5.9990 chunk 108 optimal weight: 7.9990 chunk 86 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.195238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.130451 restraints weight = 13505.945| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 2.70 r_work: 0.3779 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12489 Z= 0.139 Angle : 0.586 11.939 16876 Z= 0.283 Chirality : 0.037 0.121 1991 Planarity : 0.004 0.060 2168 Dihedral : 4.051 18.723 1639 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.20 % Allowed : 16.69 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.22), residues: 1544 helix: 1.45 (0.15), residues: 1168 sheet: None (None), residues: 0 loop : -1.38 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 173 TYR 0.018 0.001 TYR A 341 PHE 0.018 0.001 PHE A1362 TRP 0.012 0.001 TRP C 145 HIS 0.006 0.001 HIS A 494 Details of bonding type rmsd covalent geometry : bond 0.00337 (12489) covalent geometry : angle 0.58621 (16876) hydrogen bonds : bond 0.03377 ( 838) hydrogen bonds : angle 3.55147 ( 2505) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 120 time to evaluate : 0.477 Fit side-chains revert: symmetry clash REVERT: A 336 MET cc_start: 0.3403 (tmm) cc_final: 0.3152 (tpt) REVERT: A 390 ASP cc_start: 0.8730 (t70) cc_final: 0.8154 (m-30) REVERT: A 393 ARG cc_start: 0.8028 (ttm-80) cc_final: 0.7530 (ttt90) REVERT: A 488 GLU cc_start: 0.7713 (mm-30) cc_final: 0.7452 (mm-30) REVERT: A 513 MET cc_start: 0.7522 (mmm) cc_final: 0.7219 (mmm) REVERT: A 656 MET cc_start: 0.8034 (tpp) cc_final: 0.7723 (tpt) REVERT: A 880 LYS cc_start: 0.8007 (ttpp) cc_final: 0.7657 (mtpm) REVERT: A 903 PHE cc_start: 0.8206 (OUTLIER) cc_final: 0.7581 (t80) REVERT: A 906 ASN cc_start: 0.7421 (t0) cc_final: 0.7204 (m-40) REVERT: A 923 MET cc_start: 0.7785 (OUTLIER) cc_final: 0.6983 (mtm) REVERT: A 997 LEU cc_start: 0.7025 (OUTLIER) cc_final: 0.6746 (tp) REVERT: A 1083 GLU cc_start: 0.7289 (mp0) cc_final: 0.6951 (tp30) REVERT: A 1191 THR cc_start: 0.8701 (t) cc_final: 0.8201 (m) REVERT: A 1311 GLU cc_start: 0.7404 (mm-30) cc_final: 0.6968 (tm-30) REVERT: A 1361 LEU cc_start: 0.7034 (OUTLIER) cc_final: 0.6489 (tt) REVERT: C 109 ARG cc_start: 0.8137 (mtp-110) cc_final: 0.7513 (mtp180) REVERT: C 195 GLU cc_start: 0.6347 (OUTLIER) cc_final: 0.5682 (mp0) REVERT: D 84 GLU cc_start: 0.8204 (tp30) cc_final: 0.7478 (tt0) outliers start: 31 outliers final: 15 residues processed: 143 average time/residue: 0.5118 time to fit residues: 80.5425 Evaluate side-chains 134 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 863 SER Chi-restraints excluded: chain A residue 903 PHE Chi-restraints excluded: chain A residue 923 MET Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 998 HIS Chi-restraints excluded: chain A residue 1361 LEU Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 241 GLN Chi-restraints excluded: chain D residue 90 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 68 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 chunk 150 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 chunk 106 optimal weight: 7.9990 chunk 137 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.213860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.132743 restraints weight = 14029.918| |-----------------------------------------------------------------------------| r_work (start): 0.3924 rms_B_bonded: 2.99 r_work: 0.3705 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 12489 Z= 0.212 Angle : 0.654 13.318 16876 Z= 0.312 Chirality : 0.040 0.126 1991 Planarity : 0.004 0.059 2168 Dihedral : 4.234 19.418 1639 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.20 % Allowed : 17.19 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.22), residues: 1544 helix: 1.20 (0.15), residues: 1171 sheet: None (None), residues: 0 loop : -1.38 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1268 TYR 0.029 0.002 TYR A 341 PHE 0.037 0.002 PHE A1362 TRP 0.007 0.001 TRP A1532 HIS 0.006 0.001 HIS A 494 Details of bonding type rmsd covalent geometry : bond 0.00532 (12489) covalent geometry : angle 0.65429 (16876) hydrogen bonds : bond 0.03658 ( 838) hydrogen bonds : angle 3.71308 ( 2505) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 107 time to evaluate : 0.504 Fit side-chains REVERT: A 390 ASP cc_start: 0.8767 (t70) cc_final: 0.8360 (t0) REVERT: A 393 ARG cc_start: 0.8082 (ttm-80) cc_final: 0.7616 (ttt90) REVERT: A 488 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7576 (mm-30) REVERT: A 513 MET cc_start: 0.7758 (mmm) cc_final: 0.7403 (mmm) REVERT: A 779 GLN cc_start: 0.7429 (mm-40) cc_final: 0.7167 (mt0) REVERT: A 880 LYS cc_start: 0.8002 (ttpp) cc_final: 0.7623 (mtpm) REVERT: A 906 ASN cc_start: 0.7521 (t0) cc_final: 0.7272 (m-40) REVERT: A 923 MET cc_start: 0.8005 (OUTLIER) cc_final: 0.7148 (mtm) REVERT: A 1083 GLU cc_start: 0.7301 (mp0) cc_final: 0.6942 (tp30) REVERT: A 1311 GLU cc_start: 0.7445 (mm-30) cc_final: 0.6991 (tm-30) REVERT: A 1361 LEU cc_start: 0.7021 (OUTLIER) cc_final: 0.6518 (tt) REVERT: A 1457 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7685 (pm20) REVERT: C 109 ARG cc_start: 0.8130 (mtp-110) cc_final: 0.7528 (mtp180) outliers start: 31 outliers final: 15 residues processed: 129 average time/residue: 0.5225 time to fit residues: 74.1498 Evaluate side-chains 123 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 863 SER Chi-restraints excluded: chain A residue 903 PHE Chi-restraints excluded: chain A residue 923 MET Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1103 LEU Chi-restraints excluded: chain A residue 1294 ASP Chi-restraints excluded: chain A residue 1361 LEU Chi-restraints excluded: chain A residue 1457 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 142 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 149 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 81 optimal weight: 0.5980 chunk 133 optimal weight: 0.9980 chunk 146 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 152 optimal weight: 5.9990 chunk 136 optimal weight: 10.0000 chunk 101 optimal weight: 4.9990 chunk 47 optimal weight: 0.0470 chunk 90 optimal weight: 2.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.216631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.136310 restraints weight = 13981.665| |-----------------------------------------------------------------------------| r_work (start): 0.3957 rms_B_bonded: 2.98 r_work: 0.3739 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12489 Z= 0.134 Angle : 0.601 13.511 16876 Z= 0.286 Chirality : 0.038 0.120 1991 Planarity : 0.004 0.061 2168 Dihedral : 4.145 18.630 1639 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.06 % Allowed : 17.12 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.22), residues: 1544 helix: 1.37 (0.15), residues: 1171 sheet: None (None), residues: 0 loop : -1.34 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 173 TYR 0.024 0.001 TYR A 341 PHE 0.021 0.001 PHE A1397 TRP 0.008 0.001 TRP A1532 HIS 0.006 0.001 HIS A 494 Details of bonding type rmsd covalent geometry : bond 0.00322 (12489) covalent geometry : angle 0.60079 (16876) hydrogen bonds : bond 0.03405 ( 838) hydrogen bonds : angle 3.61418 ( 2505) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 110 time to evaluate : 0.468 Fit side-chains revert: symmetry clash REVERT: A 390 ASP cc_start: 0.8745 (t70) cc_final: 0.8288 (t0) REVERT: A 393 ARG cc_start: 0.8028 (ttm-80) cc_final: 0.7542 (ttt90) REVERT: A 488 GLU cc_start: 0.7747 (mm-30) cc_final: 0.7521 (mm-30) REVERT: A 513 MET cc_start: 0.7571 (mmm) cc_final: 0.7243 (mmm) REVERT: A 638 MET cc_start: 0.8383 (mtp) cc_final: 0.8126 (mtm) REVERT: A 656 MET cc_start: 0.8036 (tpp) cc_final: 0.7720 (tpt) REVERT: A 738 PHE cc_start: 0.6820 (m-80) cc_final: 0.5934 (m-80) REVERT: A 880 LYS cc_start: 0.7974 (ttpp) cc_final: 0.7592 (mtpm) REVERT: A 906 ASN cc_start: 0.7479 (t0) cc_final: 0.7249 (m-40) REVERT: A 923 MET cc_start: 0.7839 (OUTLIER) cc_final: 0.7023 (mtm) REVERT: A 997 LEU cc_start: 0.6937 (OUTLIER) cc_final: 0.6684 (tp) REVERT: A 1083 GLU cc_start: 0.7282 (mp0) cc_final: 0.6960 (tp30) REVERT: A 1311 GLU cc_start: 0.7409 (mm-30) cc_final: 0.6967 (tm-30) REVERT: A 1361 LEU cc_start: 0.7004 (OUTLIER) cc_final: 0.6473 (tt) REVERT: A 1457 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7702 (pm20) REVERT: C 109 ARG cc_start: 0.8098 (mtp-110) cc_final: 0.7504 (mtp180) REVERT: D 84 GLU cc_start: 0.8160 (tp30) cc_final: 0.7435 (tt0) REVERT: D 87 MET cc_start: 0.7034 (mmm) cc_final: 0.6809 (mmm) outliers start: 29 outliers final: 14 residues processed: 131 average time/residue: 0.5066 time to fit residues: 73.6099 Evaluate side-chains 124 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 863 SER Chi-restraints excluded: chain A residue 903 PHE Chi-restraints excluded: chain A residue 921 ASN Chi-restraints excluded: chain A residue 923 MET Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1103 LEU Chi-restraints excluded: chain A residue 1361 LEU Chi-restraints excluded: chain A residue 1457 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 241 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 49 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 120 optimal weight: 0.9980 chunk 116 optimal weight: 4.9990 chunk 146 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.216390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.136014 restraints weight = 14029.065| |-----------------------------------------------------------------------------| r_work (start): 0.3954 rms_B_bonded: 2.99 r_work: 0.3736 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12489 Z= 0.145 Angle : 0.618 14.053 16876 Z= 0.291 Chirality : 0.038 0.123 1991 Planarity : 0.004 0.060 2168 Dihedral : 4.113 18.465 1639 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.56 % Allowed : 17.90 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.22), residues: 1544 helix: 1.43 (0.15), residues: 1166 sheet: None (None), residues: 0 loop : -1.32 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 173 TYR 0.024 0.001 TYR A 341 PHE 0.042 0.001 PHE A1362 TRP 0.007 0.001 TRP A1532 HIS 0.006 0.001 HIS A 494 Details of bonding type rmsd covalent geometry : bond 0.00354 (12489) covalent geometry : angle 0.61799 (16876) hydrogen bonds : bond 0.03411 ( 838) hydrogen bonds : angle 3.57888 ( 2505) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.472 Fit side-chains revert: symmetry clash REVERT: A 336 MET cc_start: 0.4049 (tmm) cc_final: 0.3421 (tpt) REVERT: A 390 ASP cc_start: 0.8742 (t70) cc_final: 0.8292 (t0) REVERT: A 393 ARG cc_start: 0.8038 (ttm-80) cc_final: 0.7548 (ttt90) REVERT: A 488 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7533 (mm-30) REVERT: A 513 MET cc_start: 0.7584 (mmm) cc_final: 0.7261 (mmm) REVERT: A 656 MET cc_start: 0.8065 (tpp) cc_final: 0.7749 (tpt) REVERT: A 738 PHE cc_start: 0.6820 (m-80) cc_final: 0.5923 (m-80) REVERT: A 880 LYS cc_start: 0.7968 (ttpp) cc_final: 0.7601 (mtpm) REVERT: A 906 ASN cc_start: 0.7490 (t0) cc_final: 0.7288 (m-40) REVERT: A 923 MET cc_start: 0.7850 (OUTLIER) cc_final: 0.7040 (mtm) REVERT: A 1083 GLU cc_start: 0.7281 (mp0) cc_final: 0.6970 (tp30) REVERT: A 1311 GLU cc_start: 0.7452 (mm-30) cc_final: 0.6910 (tm-30) REVERT: A 1361 LEU cc_start: 0.7003 (OUTLIER) cc_final: 0.6480 (tt) REVERT: A 1457 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7706 (pm20) REVERT: C 87 MET cc_start: 0.5887 (tpp) cc_final: 0.5661 (mmp) REVERT: C 109 ARG cc_start: 0.8077 (mtp-110) cc_final: 0.7493 (mtp180) REVERT: D 84 GLU cc_start: 0.8177 (tp30) cc_final: 0.7438 (tt0) outliers start: 22 outliers final: 14 residues processed: 125 average time/residue: 0.5088 time to fit residues: 70.0567 Evaluate side-chains 123 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 863 SER Chi-restraints excluded: chain A residue 903 PHE Chi-restraints excluded: chain A residue 921 ASN Chi-restraints excluded: chain A residue 923 MET Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1103 LEU Chi-restraints excluded: chain A residue 1361 LEU Chi-restraints excluded: chain A residue 1457 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 241 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 139 optimal weight: 9.9990 chunk 131 optimal weight: 0.9990 chunk 100 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 105 optimal weight: 8.9990 chunk 124 optimal weight: 4.9990 chunk 151 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 22 optimal weight: 0.5980 chunk 86 optimal weight: 0.7980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.213522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.132628 restraints weight = 13993.109| |-----------------------------------------------------------------------------| r_work (start): 0.3921 rms_B_bonded: 2.97 r_work: 0.3701 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12489 Z= 0.209 Angle : 0.668 14.132 16876 Z= 0.317 Chirality : 0.040 0.147 1991 Planarity : 0.004 0.060 2168 Dihedral : 4.271 19.499 1639 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.49 % Allowed : 18.11 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.21), residues: 1544 helix: 1.25 (0.15), residues: 1162 sheet: None (None), residues: 0 loop : -1.33 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 173 TYR 0.028 0.002 TYR A 341 PHE 0.017 0.002 PHE A1362 TRP 0.008 0.001 TRP C 145 HIS 0.006 0.001 HIS A 494 Details of bonding type rmsd covalent geometry : bond 0.00524 (12489) covalent geometry : angle 0.66800 (16876) hydrogen bonds : bond 0.03655 ( 838) hydrogen bonds : angle 3.72318 ( 2505) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3441.13 seconds wall clock time: 59 minutes 41.83 seconds (3581.83 seconds total)