Starting phenix.real_space_refine on Fri Oct 23 23:27:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n00_48771/10_2026/9n00_48771.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n00_48771/10_2026/9n00_48771.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9n00_48771/10_2026/9n00_48771.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n00_48771/10_2026/9n00_48771.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9n00_48771/10_2026/9n00_48771.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n00_48771/10_2026/9n00_48771.map" } resolution = 2.72 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= 0.004 sd= 0.154 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 2 5.49 5 Mg 1 5.21 5 S 47 5.16 5 C 7077 2.51 5 N 1991 2.21 5 O 2072 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11190 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 11162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1397, 11162 Classifications: {'peptide': 1397} Link IDs: {'PTRANS': 42, 'TRANS': 1354} Chain breaks: 5 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.42, per 1000 atoms: 0.22 Number of scatterers: 11190 At special positions: 0 Unit cell: (94.6, 149.468, 135.278, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 47 16.00 P 2 15.00 Mg 1 11.99 O 2072 8.00 N 1991 7.00 C 7077 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: 0.76 Conformation dependent library (CDL) restraints added in 534.9 milliseconds 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2656 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 4 sheets defined 74.9% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 13 through 29 removed outlier: 3.528A pdb=" N TRP A 22 " --> pdb=" O VAL A 18 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR A 25 " --> pdb=" O ASP A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 90 Processing helix chain 'A' and resid 103 through 115 removed outlier: 3.665A pdb=" N ALA A 107 " --> pdb=" O PHE A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 126 Processing helix chain 'A' and resid 127 through 145 removed outlier: 3.519A pdb=" N LYS A 143 " --> pdb=" O LYS A 139 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ILE A 144 " --> pdb=" O GLN A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 156 Processing helix chain 'A' and resid 164 through 178 removed outlier: 3.691A pdb=" N ASN A 178 " --> pdb=" O GLU A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 197 Processing helix chain 'A' and resid 216 through 226 Processing helix chain 'A' and resid 235 through 248 removed outlier: 3.558A pdb=" N ALA A 248 " --> pdb=" O SER A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 276 Processing helix chain 'A' and resid 290 through 309 removed outlier: 3.631A pdb=" N MET A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N THR A 308 " --> pdb=" O GLU A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 323 removed outlier: 3.862A pdb=" N ALA A 323 " --> pdb=" O ARG A 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 320 through 323' Processing helix chain 'A' and resid 339 through 348 Processing helix chain 'A' and resid 359 through 366 removed outlier: 3.521A pdb=" N LEU A 363 " --> pdb=" O SER A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 385 removed outlier: 3.852A pdb=" N ILE A 385 " --> pdb=" O ARG A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 402 Processing helix chain 'A' and resid 402 through 407 Processing helix chain 'A' and resid 424 through 433 removed outlier: 3.693A pdb=" N LEU A 428 " --> pdb=" O GLU A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 447 Processing helix chain 'A' and resid 449 through 464 removed outlier: 4.000A pdb=" N ARG A 462 " --> pdb=" O GLU A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 483 Processing helix chain 'A' and resid 490 through 508 Processing helix chain 'A' and resid 515 through 517 No H-bonds generated for 'chain 'A' and resid 515 through 517' Processing helix chain 'A' and resid 520 through 530 Processing helix chain 'A' and resid 546 through 560 removed outlier: 4.360A pdb=" N ASP A 550 " --> pdb=" O GLN A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 571 removed outlier: 3.573A pdb=" N GLY A 570 " --> pdb=" O GLU A 566 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU A 571 " --> pdb=" O PHE A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 576 No H-bonds generated for 'chain 'A' and resid 574 through 576' Processing helix chain 'A' and resid 577 through 590 removed outlier: 4.011A pdb=" N ILE A 581 " --> pdb=" O VAL A 577 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG A 582 " --> pdb=" O ARG A 578 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU A 590 " --> pdb=" O ALA A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 605 Processing helix chain 'A' and resid 609 through 622 Processing helix chain 'A' and resid 626 through 628 No H-bonds generated for 'chain 'A' and resid 626 through 628' Processing helix chain 'A' and resid 629 through 640 Processing helix chain 'A' and resid 640 through 651 Processing helix chain 'A' and resid 653 through 671 removed outlier: 4.371A pdb=" N VAL A 665 " --> pdb=" O ILE A 661 " (cutoff:3.500A) Proline residue: A 666 - end of helix Processing helix chain 'A' and resid 673 through 684 Processing helix chain 'A' and resid 685 through 688 Processing helix chain 'A' and resid 692 through 705 Processing helix chain 'A' and resid 709 through 722 removed outlier: 3.798A pdb=" N ILE A 713 " --> pdb=" O ASP A 709 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ASP A 715 " --> pdb=" O ASN A 711 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N GLN A 716 " --> pdb=" O GLY A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 731 removed outlier: 4.808A pdb=" N SER A 730 " --> pdb=" O GLU A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 740 Processing helix chain 'A' and resid 749 through 760 removed outlier: 3.723A pdb=" N VAL A 753 " --> pdb=" O PRO A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 774 Processing helix chain 'A' and resid 777 through 783 Processing helix chain 'A' and resid 786 through 790 removed outlier: 4.474A pdb=" N LEU A 790 " --> pdb=" O ASP A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 798 removed outlier: 3.817A pdb=" N PHE A 797 " --> pdb=" O GLN A 793 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY A 798 " --> pdb=" O PRO A 794 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 793 through 798' Processing helix chain 'A' and resid 803 through 812 Processing helix chain 'A' and resid 812 through 828 removed outlier: 3.743A pdb=" N LEU A 816 " --> pdb=" O SER A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 881 Processing helix chain 'A' and resid 882 through 884 No H-bonds generated for 'chain 'A' and resid 882 through 884' Processing helix chain 'A' and resid 885 through 897 removed outlier: 5.457A pdb=" N GLU A 893 " --> pdb=" O GLN A 889 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N ARG A 894 " --> pdb=" O LYS A 890 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 914 Processing helix chain 'A' and resid 915 through 917 No H-bonds generated for 'chain 'A' and resid 915 through 917' Processing helix chain 'A' and resid 918 through 928 Processing helix chain 'A' and resid 928 through 933 Processing helix chain 'A' and resid 936 through 948 Processing helix chain 'A' and resid 952 through 965 Processing helix chain 'A' and resid 975 through 987 removed outlier: 3.692A pdb=" N VAL A 985 " --> pdb=" O SER A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 990 through 994 Processing helix chain 'A' and resid 995 through 1009 Processing helix chain 'A' and resid 1067 through 1079 Processing helix chain 'A' and resid 1079 through 1090 Processing helix chain 'A' and resid 1091 through 1094 Processing helix chain 'A' and resid 1095 through 1114 removed outlier: 3.684A pdb=" N ASP A1100 " --> pdb=" O GLU A1096 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP A1101 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1131 through 1145 Processing helix chain 'A' and resid 1145 through 1150 removed outlier: 3.505A pdb=" N ARG A1150 " --> pdb=" O PRO A1146 " (cutoff:3.500A) Processing helix chain 'A' and resid 1152 through 1164 removed outlier: 3.659A pdb=" N ALA A1156 " --> pdb=" O ARG A1152 " (cutoff:3.500A) Processing helix chain 'A' and resid 1168 through 1181 removed outlier: 4.125A pdb=" N ASP A1181 " --> pdb=" O PHE A1177 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1203 removed outlier: 3.519A pdb=" N LEU A1203 " --> pdb=" O LEU A1199 " (cutoff:3.500A) Processing helix chain 'A' and resid 1205 through 1224 removed outlier: 3.607A pdb=" N ALA A1223 " --> pdb=" O ASP A1219 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN A1224 " --> pdb=" O ASN A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1241 Processing helix chain 'A' and resid 1244 through 1262 removed outlier: 3.661A pdb=" N ARG A1248 " --> pdb=" O HIS A1244 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE A1251 " --> pdb=" O VAL A1247 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG A1254 " --> pdb=" O MET A1250 " (cutoff:3.500A) Proline residue: A1256 - end of helix removed outlier: 4.052A pdb=" N LYS A1261 " --> pdb=" O TYR A1257 " (cutoff:3.500A) Processing helix chain 'A' and resid 1262 through 1274 Processing helix chain 'A' and resid 1280 through 1292 removed outlier: 4.848A pdb=" N ARG A1286 " --> pdb=" O LYS A1282 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N CYS A1287 " --> pdb=" O ILE A1283 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU A1288 " --> pdb=" O ALA A1284 " (cutoff:3.500A) Processing helix chain 'A' and resid 1295 through 1309 Proline residue: A1301 - end of helix Processing helix chain 'A' and resid 1313 through 1328 removed outlier: 3.938A pdb=" N THR A1317 " --> pdb=" O LYS A1313 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TRP A1318 " --> pdb=" O ASP A1314 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N MET A1327 " --> pdb=" O ALA A1323 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR A1328 " --> pdb=" O LEU A1324 " (cutoff:3.500A) Processing helix chain 'A' and resid 1332 through 1344 Processing helix chain 'A' and resid 1345 through 1357 removed outlier: 3.624A pdb=" N TRP A1349 " --> pdb=" O THR A1345 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL A1355 " --> pdb=" O GLY A1351 " (cutoff:3.500A) Processing helix chain 'A' and resid 1358 through 1365 Processing helix chain 'A' and resid 1365 through 1378 Processing helix chain 'A' and resid 1380 through 1392 removed outlier: 3.934A pdb=" N GLY A1386 " --> pdb=" O ARG A1382 " (cutoff:3.500A) Processing helix chain 'A' and resid 1393 through 1396 Processing helix chain 'A' and resid 1405 through 1419 Processing helix chain 'A' and resid 1431 through 1440 Processing helix chain 'A' and resid 1443 through 1462 Processing helix chain 'A' and resid 1467 through 1469 No H-bonds generated for 'chain 'A' and resid 1467 through 1469' Processing helix chain 'A' and resid 1470 through 1491 removed outlier: 4.849A pdb=" N GLU A1488 " --> pdb=" O GLU A1484 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N SER A1489 " --> pdb=" O GLU A1485 " (cutoff:3.500A) Processing helix chain 'A' and resid 1492 through 1508 Processing helix chain 'A' and resid 1510 through 1521 removed outlier: 3.753A pdb=" N ALA A1514 " --> pdb=" O VAL A1510 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU A1521 " --> pdb=" O LEU A1517 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 157 through 161 removed outlier: 8.884A pdb=" N ASN A 158 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL A 95 " --> pdb=" O ASN A 158 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N VAL A 160 " --> pdb=" O VAL A 95 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N PHE A 97 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE A 56 " --> pdb=" O ASN A 94 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ARG A 96 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ALA A 58 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N TYR A 98 " --> pdb=" O ALA A 58 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLN A 60 " --> pdb=" O TYR A 98 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL A 48 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ILE A 35 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N GLY A 50 " --> pdb=" O GLN A 33 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 312 through 318 removed outlier: 3.774A pdb=" N ALA A 393 " --> pdb=" O ILE A 357 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 332 through 333 Processing sheet with id=AA4, first strand: chain 'A' and resid 512 through 513 666 hydrogen bonds defined for protein. 1959 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: 2.11 Time building geometry restraints manager: 1.04 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: 3150 1.33 - 1.45: 2191 1.45 - 1.57: 5993 1.57 - 1.69: 3 1.69 - 1.82: 74 Bond restraints: 11411 Sorted by residual: bond pdb=" C4 ADP A1601 " pdb=" C5 ADP A1601 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.02e+01 bond pdb=" N ILE A 989 " pdb=" CA ILE A 989 " ideal model delta sigma weight residual 1.457 1.497 -0.040 9.00e-03 1.23e+04 2.00e+01 bond pdb=" C5 ADP A1601 " pdb=" C6 ADP A1601 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" CA ALA A 348 " pdb=" C ALA A 348 " ideal model delta sigma weight residual 1.522 1.470 0.052 1.38e-02 5.25e+03 1.40e+01 bond pdb=" CA TRP A1267 " pdb=" C TRP A1267 " ideal model delta sigma weight residual 1.523 1.473 0.050 1.37e-02 5.33e+03 1.32e+01 ... (remaining 11406 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.40: 14935 3.40 - 6.80: 486 6.80 - 10.20: 39 10.20 - 13.61: 2 13.61 - 17.01: 1 Bond angle restraints: 15463 Sorted by residual: angle pdb=" PA ADP A1601 " pdb=" O3A ADP A1601 " pdb=" PB ADP A1601 " ideal model delta sigma weight residual 120.50 137.51 -17.01 3.00e+00 1.11e-01 3.21e+01 angle pdb=" C ASP A 787 " pdb=" CA ASP A 787 " pdb=" CB ASP A 787 " ideal model delta sigma weight residual 115.79 109.88 5.91 1.19e+00 7.06e-01 2.47e+01 angle pdb=" C ARG A 738 " pdb=" N LEU A 739 " pdb=" CA LEU A 739 " ideal model delta sigma weight residual 120.28 113.22 7.06 1.44e+00 4.82e-01 2.41e+01 angle pdb=" CA THR A 949 " pdb=" C THR A 949 " pdb=" N PHE A 950 " ideal model delta sigma weight residual 118.14 124.44 -6.30 1.31e+00 5.83e-01 2.31e+01 angle pdb=" N ASP A 488 " pdb=" CA ASP A 488 " pdb=" C ASP A 488 " ideal model delta sigma weight residual 113.56 106.87 6.69 1.39e+00 5.18e-01 2.31e+01 ... (remaining 15458 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.16: 6579 23.16 - 46.33: 246 46.33 - 69.49: 23 69.49 - 92.65: 13 92.65 - 115.82: 1 Dihedral angle restraints: 6862 sinusoidal: 2786 harmonic: 4076 Sorted by residual: dihedral pdb=" C5' ADP A1601 " pdb=" O5' ADP A1601 " pdb=" PA ADP A1601 " pdb=" O2A ADP A1601 " ideal model delta sinusoidal sigma weight residual -60.00 -175.82 115.82 1 2.00e+01 2.50e-03 3.45e+01 dihedral pdb=" CA VAL A 44 " pdb=" C VAL A 44 " pdb=" N ASP A 45 " pdb=" CA ASP A 45 " ideal model delta harmonic sigma weight residual -180.00 -154.54 -25.46 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA TYR A1397 " pdb=" C TYR A1397 " pdb=" N LYS A1398 " pdb=" CA LYS A1398 " ideal model delta harmonic sigma weight residual 180.00 159.68 20.32 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 6859 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1138 0.074 - 0.148: 482 0.148 - 0.222: 91 0.222 - 0.296: 22 0.296 - 0.370: 2 Chirality restraints: 1735 Sorted by residual: chirality pdb=" CA HIS A 545 " pdb=" N HIS A 545 " pdb=" C HIS A 545 " pdb=" CB HIS A 545 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.42e+00 chirality pdb=" CB VAL A 731 " pdb=" CA VAL A 731 " pdb=" CG1 VAL A 731 " pdb=" CG2 VAL A 731 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CA GLN A 716 " pdb=" N GLN A 716 " pdb=" C GLN A 716 " pdb=" CB GLN A 716 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.12e+00 ... (remaining 1732 not shown) Planarity restraints: 1999 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A1328 " -0.021 2.00e-02 2.50e+03 4.28e-02 1.83e+01 pdb=" C THR A1328 " 0.074 2.00e-02 2.50e+03 pdb=" O THR A1328 " -0.028 2.00e-02 2.50e+03 pdb=" N GLN A1329 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 916 " -0.020 2.00e-02 2.50e+03 3.98e-02 1.58e+01 pdb=" C GLU A 916 " 0.069 2.00e-02 2.50e+03 pdb=" O GLU A 916 " -0.026 2.00e-02 2.50e+03 pdb=" N ALA A 917 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 748 " -0.065 5.00e-02 4.00e+02 9.81e-02 1.54e+01 pdb=" N PRO A 749 " 0.170 5.00e-02 4.00e+02 pdb=" CA PRO A 749 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 749 " -0.052 5.00e-02 4.00e+02 ... (remaining 1996 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 932 2.71 - 3.26: 11678 3.26 - 3.81: 17489 3.81 - 4.35: 21742 4.35 - 4.90: 36138 Nonbonded interactions: 87979 Sorted by model distance: nonbonded pdb=" OG SER A 885 " pdb=" OD1 ASN A 886 " model vdw 2.164 3.040 nonbonded pdb=" O THR A1108 " pdb=" ND1 HIS A1112 " model vdw 2.212 3.120 nonbonded pdb=" O ASP A 78 " pdb=" OD1 ASP A 81 " model vdw 2.217 3.040 nonbonded pdb=" O ILE A 439 " pdb=" NH1 ARG A 444 " model vdw 2.226 3.120 nonbonded pdb=" CD1 LEU A 615 " pdb=" OE1 GLU A1521 " model vdw 2.230 3.460 ... (remaining 87974 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.430 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.090 Find NCS groups from input model: 0.050 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:9.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6702 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 : 0.017 0.120 11411 Z= 0.777 Angle : 1.368 17.007 15463 Z= 0.842 Chirality : 0.081 0.370 1735 Planarity : 0.009 0.122 1999 Dihedral : 12.435 115.818 4206 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.08 % Allowed : 1.59 % Favored : 98.33 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.21), residues: 1385 helix: 0.40 (0.16), residues: 897 sheet: 0.48 (0.61), residues: 65 loop : -0.62 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.002 ARG A 251 TYR 0.061 0.004 TYR A 648 PHE 0.039 0.004 PHE A1416 TRP 0.055 0.006 TRP A 887 HIS 0.025 0.004 HIS A 514 Details of bonding type rmsd/Z covalent geometry : bond 0.01702 / 0.78 (11411) covalent geometry : angle 1.36769 / 0.84 (15463) hydrogen bonds : bond 0.20364 / 13.49 ( 666) hydrogen bonds : angle 6.48495 / 4.79 ( 1959) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 183 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 ASP cc_start: 0.6802 (m-30) cc_final: 0.6588 (m-30) REVERT: A 506 LYS cc_start: 0.7769 (ttpp) cc_final: 0.7542 (tttm) REVERT: A 654 ILE cc_start: 0.7828 (tp) cc_final: 0.7298 (tp) REVERT: A 682 HIS cc_start: 0.6434 (m-70) cc_final: 0.5930 (t70) REVERT: A 1286 ARG cc_start: 0.7018 (mmm-85) cc_final: 0.6754 (mmt-90) REVERT: A 1338 ASN cc_start: 0.7380 (m110) cc_final: 0.7134 (m-40) REVERT: A 1357 THR cc_start: 0.8161 (m) cc_final: 0.7939 (p) REVERT: A 1366 ARG cc_start: 0.6697 (mtp-110) cc_final: 0.6259 (ttm-80) outliers start: 1 outliers final: 0 residues processed: 184 average time/residue: 0.6904 time to fit residues: 135.3769 Evaluate side-chains 114 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 55] chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 40.0000 chunk 55 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 373 GLN A 492 ASN A 689 ASN A 806 GLN A 884 HIS A1164 HIS A1468 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.238701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.196686 restraints weight = 12167.209| |-----------------------------------------------------------------------------| r_work (start): 0.4117 rms_B_bonded: 2.45 r_work: 0.3807 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work: 0.3752 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11411 Z= 0.161 Angle : 0.656 11.693 15463 Z= 0.346 Chirality : 0.042 0.149 1735 Planarity : 0.005 0.058 1999 Dihedral : 5.967 115.976 1536 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.51 % Allowed : 7.44 % Favored : 90.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.22), residues: 1385 helix: 1.36 (0.16), residues: 937 sheet: 0.86 (0.59), residues: 64 loop : -0.38 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 277 TYR 0.023 0.002 TYR A 648 PHE 0.014 0.002 PHE A 610 TRP 0.017 0.002 TRP A1435 HIS 0.010 0.001 HIS A 514 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.16 (11411) covalent geometry : angle 0.65620 / 0.35 (15463) hydrogen bonds : bond 0.05926 / 3.89 ( 666) hydrogen bonds : angle 4.57398 / 3.37 ( 1959) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 123 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 MET cc_start: 0.8273 (mtp) cc_final: 0.7874 (mtt) REVERT: A 220 ARG cc_start: 0.8522 (mtt180) cc_final: 0.8302 (mtt90) REVERT: A 1315 LEU cc_start: 0.8367 (mm) cc_final: 0.8127 (mt) REVERT: A 1316 GLU cc_start: 0.8328 (tt0) cc_final: 0.8108 (tt0) REVERT: A 1338 ASN cc_start: 0.7981 (m110) cc_final: 0.7777 (m-40) REVERT: A 1382 ARG cc_start: 0.7602 (OUTLIER) cc_final: 0.6850 (ptm160) REVERT: A 1469 ASN cc_start: 0.8149 (OUTLIER) cc_final: 0.7942 (t0) outliers start: 30 outliers final: 8 residues processed: 142 average time/residue: 0.5861 time to fit residues: 89.6707 Evaluate side-chains 110 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 1367 GLU Chi-restraints excluded: chain A residue 1382 ARG Chi-restraints excluded: chain A residue 1401 VAL Chi-restraints excluded: chain A residue 1406 ILE Chi-restraints excluded: chain A residue 1461 SER Chi-restraints excluded: chain A residue 1469 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: [124, 24, 23, 12, 104, 52, 63, 60, 0, 18, 55] chunk 124 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 12 optimal weight: 8.9990 chunk 104 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 60 optimal weight: 0.4980 chunk 0 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 332 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.238314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.198746 restraints weight = 12117.377| |-----------------------------------------------------------------------------| r_work (start): 0.4134 rms_B_bonded: 2.21 r_work: 0.3851 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3806 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11411 Z= 0.137 Angle : 0.576 11.081 15463 Z= 0.298 Chirality : 0.040 0.183 1735 Planarity : 0.004 0.043 1999 Dihedral : 5.776 111.670 1536 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.42 % Allowed : 9.69 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.22), residues: 1385 helix: 1.48 (0.17), residues: 939 sheet: 0.91 (0.59), residues: 64 loop : -0.31 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1366 TYR 0.022 0.002 TYR A 648 PHE 0.015 0.001 PHE A 610 TRP 0.016 0.001 TRP A1516 HIS 0.008 0.001 HIS A 514 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (11411) covalent geometry : angle 0.57576 / 0.30 (15463) hydrogen bonds : bond 0.05043 / 3.32 ( 666) hydrogen bonds : angle 4.27632 / 3.13 ( 1959) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 100 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLN cc_start: 0.7389 (OUTLIER) cc_final: 0.7163 (mp-120) REVERT: A 192 MET cc_start: 0.8254 (mtp) cc_final: 0.7833 (mtt) REVERT: A 516 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.7705 (mmp80) REVERT: A 1253 ARG cc_start: 0.7713 (ttp-110) cc_final: 0.7489 (ttp80) REVERT: A 1316 GLU cc_start: 0.8309 (tt0) cc_final: 0.8086 (tt0) REVERT: A 1382 ARG cc_start: 0.7507 (OUTLIER) cc_final: 0.6846 (ptm160) outliers start: 29 outliers final: 13 residues processed: 117 average time/residue: 0.6576 time to fit residues: 82.3569 Evaluate side-chains 113 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 516 ARG Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 821 GLU Chi-restraints excluded: chain A residue 931 MET Chi-restraints excluded: chain A residue 1367 GLU Chi-restraints excluded: chain A residue 1382 ARG Chi-restraints excluded: chain A residue 1401 VAL Chi-restraints excluded: chain A residue 1511 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: [66, 131, 32, 80, 120, 59, 128, 65, 43, 57, 67] chunk 66 optimal weight: 1.9990 chunk 131 optimal weight: 0.0050 chunk 32 optimal weight: 3.9990 chunk 80 optimal weight: 20.0000 chunk 120 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 overall best weight: 1.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 101 ASN A 332 GLN ** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 565 ASN A1136 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.234249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.195819 restraints weight = 12163.585| |-----------------------------------------------------------------------------| r_work (start): 0.4112 rms_B_bonded: 1.68 r_work: 0.3754 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3697 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11411 Z= 0.161 Angle : 0.597 11.219 15463 Z= 0.305 Chirality : 0.041 0.146 1735 Planarity : 0.004 0.040 1999 Dihedral : 5.819 106.271 1536 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.34 % Allowed : 10.36 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.22), residues: 1385 helix: 1.45 (0.17), residues: 940 sheet: 0.71 (0.59), residues: 65 loop : -0.38 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1366 TYR 0.024 0.002 TYR A 648 PHE 0.019 0.002 PHE A 610 TRP 0.015 0.002 TRP A1516 HIS 0.007 0.001 HIS A 514 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (11411) covalent geometry : angle 0.59683 / 0.30 (15463) hydrogen bonds : bond 0.05263 / 3.48 ( 666) hydrogen bonds : angle 4.20237 / 3.06 ( 1959) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 102 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 MET cc_start: 0.8372 (mtp) cc_final: 0.7971 (mtt) REVERT: A 279 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.6978 (mmm160) REVERT: A 516 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.7758 (mmp80) REVERT: A 1253 ARG cc_start: 0.7930 (ttp-110) cc_final: 0.7712 (ttp80) REVERT: A 1268 ASP cc_start: 0.6921 (OUTLIER) cc_final: 0.6627 (t70) REVERT: A 1382 ARG cc_start: 0.7456 (OUTLIER) cc_final: 0.6848 (ptm160) REVERT: A 1411 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.7947 (tpt-90) outliers start: 40 outliers final: 16 residues processed: 129 average time/residue: 0.7263 time to fit residues: 99.9422 Evaluate side-chains 115 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 279 ARG Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 516 ARG Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 821 GLU Chi-restraints excluded: chain A residue 931 MET Chi-restraints excluded: chain A residue 1258 LEU Chi-restraints excluded: chain A residue 1268 ASP Chi-restraints excluded: chain A residue 1367 GLU Chi-restraints excluded: chain A residue 1382 ARG Chi-restraints excluded: chain A residue 1401 VAL Chi-restraints excluded: chain A residue 1411 ARG Chi-restraints excluded: chain A residue 1511 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: [46, 9, 64, 93, 41, 42, 69, 44, 74, 7, 97] chunk 46 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 97 optimal weight: 40.0000 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 332 GLN A 514 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.233050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.189994 restraints weight = 11838.565| |-----------------------------------------------------------------------------| r_work (start): 0.4053 rms_B_bonded: 1.77 r_work: 0.3641 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3572 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11411 Z= 0.158 Angle : 0.594 11.528 15463 Z= 0.301 Chirality : 0.041 0.157 1735 Planarity : 0.004 0.041 1999 Dihedral : 5.748 106.026 1536 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.01 % Allowed : 11.86 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.22), residues: 1385 helix: 1.44 (0.17), residues: 943 sheet: 0.78 (0.59), residues: 71 loop : -0.41 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1366 TYR 0.023 0.002 TYR A 648 PHE 0.018 0.002 PHE A 610 TRP 0.017 0.002 TRP A1516 HIS 0.006 0.001 HIS A 611 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (11411) covalent geometry : angle 0.59368 / 0.30 (15463) hydrogen bonds : bond 0.05040 / 3.33 ( 666) hydrogen bonds : angle 4.13725 / 3.00 ( 1959) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 102 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 MET cc_start: 0.8381 (mtp) cc_final: 0.7972 (mtt) REVERT: A 279 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7045 (mmm160) REVERT: A 516 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.7997 (mmp80) REVERT: A 1253 ARG cc_start: 0.8067 (ttp-110) cc_final: 0.7865 (ttp80) REVERT: A 1382 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.6901 (ptm160) REVERT: A 1411 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.7971 (tpt-90) outliers start: 36 outliers final: 18 residues processed: 127 average time/residue: 0.6910 time to fit residues: 93.7795 Evaluate side-chains 117 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 279 ARG Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 516 ARG Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 821 GLU Chi-restraints excluded: chain A residue 931 MET Chi-restraints excluded: chain A residue 1258 LEU Chi-restraints excluded: chain A residue 1367 GLU Chi-restraints excluded: chain A residue 1382 ARG Chi-restraints excluded: chain A residue 1401 VAL Chi-restraints excluded: chain A residue 1406 ILE Chi-restraints excluded: chain A residue 1411 ARG Chi-restraints excluded: chain A residue 1511 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: [118, 38, 69, 34, 39, 89, 9, 25, 52, 72, 2] chunk 118 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 39 optimal weight: 0.3980 chunk 89 optimal weight: 20.0000 chunk 9 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 332 GLN A 514 HIS A1293 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.234083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.183111 restraints weight = 11974.391| |-----------------------------------------------------------------------------| r_work (start): 0.3987 rms_B_bonded: 1.88 r_work: 0.3695 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.3641 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11411 Z= 0.120 Angle : 0.538 11.315 15463 Z= 0.273 Chirality : 0.039 0.143 1735 Planarity : 0.004 0.040 1999 Dihedral : 5.578 109.929 1536 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.59 % Allowed : 12.36 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.22), residues: 1385 helix: 1.64 (0.17), residues: 943 sheet: 0.76 (0.58), residues: 71 loop : -0.42 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1366 TYR 0.019 0.001 TYR A 648 PHE 0.014 0.001 PHE A 610 TRP 0.019 0.001 TRP A1516 HIS 0.005 0.001 HIS A 611 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (11411) covalent geometry : angle 0.53765 / 0.27 (15463) hydrogen bonds : bond 0.04276 / 2.83 ( 666) hydrogen bonds : angle 3.96453 / 2.88 ( 1959) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 102 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.7118 (tpm170) REVERT: A 192 MET cc_start: 0.8323 (mtp) cc_final: 0.7892 (mtt) REVERT: A 516 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.7984 (mmp80) REVERT: A 525 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.7943 (ptp90) REVERT: A 1268 ASP cc_start: 0.6886 (OUTLIER) cc_final: 0.6581 (t70) REVERT: A 1286 ARG cc_start: 0.7179 (mmt-90) cc_final: 0.6956 (mpp-170) REVERT: A 1360 GLU cc_start: 0.6671 (tm-30) cc_final: 0.6133 (tm-30) REVERT: A 1382 ARG cc_start: 0.7466 (OUTLIER) cc_final: 0.6986 (ptm160) REVERT: A 1393 ARG cc_start: 0.7639 (mpt180) cc_final: 0.7330 (mtt-85) REVERT: A 1411 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.7921 (tpt-90) outliers start: 31 outliers final: 16 residues processed: 117 average time/residue: 0.6778 time to fit residues: 84.9547 Evaluate side-chains 116 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 167 ARG Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 516 ARG Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 525 ARG Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 821 GLU Chi-restraints excluded: chain A residue 931 MET Chi-restraints excluded: chain A residue 1268 ASP Chi-restraints excluded: chain A residue 1367 GLU Chi-restraints excluded: chain A residue 1382 ARG Chi-restraints excluded: chain A residue 1401 VAL Chi-restraints excluded: chain A residue 1411 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: [128, 114, 11, 91, 88, 19, 13, 18, 73, 9, 106] chunk 128 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 chunk 88 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 73 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 chunk 106 optimal weight: 10.0000 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 565 ASN A1259 GLN A1378 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.229476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.182712 restraints weight = 11691.399| |-----------------------------------------------------------------------------| r_work (start): 0.3972 rms_B_bonded: 1.92 r_work: 0.3519 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work: 0.3433 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.072 11411 Z= 0.347 Angle : 0.810 13.133 15463 Z= 0.409 Chirality : 0.053 0.338 1735 Planarity : 0.007 0.094 1999 Dihedral : 6.075 88.643 1536 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.09 % Allowed : 12.20 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.22), residues: 1385 helix: 0.97 (0.16), residues: 948 sheet: 0.23 (0.55), residues: 71 loop : -0.60 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1366 TYR 0.031 0.003 TYR A 648 PHE 0.035 0.003 PHE A1370 TRP 0.018 0.003 TRP A 630 HIS 0.010 0.002 HIS A 611 Details of bonding type rmsd/Z covalent geometry : bond 0.00844 / 0.35 (11411) covalent geometry : angle 0.80970 / 0.41 (15463) hydrogen bonds : bond 0.07174 / 4.74 ( 666) hydrogen bonds : angle 4.39796 / 3.20 ( 1959) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 95 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.7330 (tpm170) REVERT: A 192 MET cc_start: 0.8469 (mtp) cc_final: 0.8072 (mtt) REVERT: A 279 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7051 (mmm160) REVERT: A 332 GLN cc_start: 0.7590 (tm-30) cc_final: 0.7203 (tp-100) REVERT: A 516 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.8121 (mmp80) REVERT: A 525 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.8252 (ptp90) REVERT: A 635 GLU cc_start: 0.7984 (tt0) cc_final: 0.7747 (tt0) REVERT: A 1315 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8259 (mt) REVERT: A 1332 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.6523 (tp30) REVERT: A 1338 ASN cc_start: 0.8162 (m110) cc_final: 0.7836 (m-40) REVERT: A 1382 ARG cc_start: 0.7583 (OUTLIER) cc_final: 0.6858 (ptm160) REVERT: A 1393 ARG cc_start: 0.7677 (OUTLIER) cc_final: 0.7362 (mtt180) outliers start: 37 outliers final: 21 residues processed: 118 average time/residue: 0.6959 time to fit residues: 87.7102 Evaluate side-chains 123 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 94 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 167 ARG Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 279 ARG Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 516 ARG Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 525 ARG Chi-restraints excluded: chain A residue 642 GLU Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 821 GLU Chi-restraints excluded: chain A residue 931 MET Chi-restraints excluded: chain A residue 1315 LEU Chi-restraints excluded: chain A residue 1332 GLU Chi-restraints excluded: chain A residue 1367 GLU Chi-restraints excluded: chain A residue 1382 ARG Chi-restraints excluded: chain A residue 1393 ARG Chi-restraints excluded: chain A residue 1401 VAL Chi-restraints excluded: chain A residue 1406 ILE Chi-restraints excluded: chain A residue 1511 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: [126, 37, 90, 138, 103, 29, 81, 118, 131, 64, 6] chunk 126 optimal weight: 0.9980 chunk 37 optimal weight: 0.0870 chunk 90 optimal weight: 30.0000 chunk 138 optimal weight: 0.5980 chunk 103 optimal weight: 0.4980 chunk 29 optimal weight: 0.6980 chunk 81 optimal weight: 5.9990 chunk 118 optimal weight: 0.6980 chunk 131 optimal weight: 0.0970 chunk 64 optimal weight: 0.7980 chunk 6 optimal weight: 0.0670 overall best weight: 0.2694 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 565 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.235132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.190281 restraints weight = 11895.771| |-----------------------------------------------------------------------------| r_work (start): 0.4058 rms_B_bonded: 1.74 r_work: 0.3655 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3540 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.4149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11411 Z= 0.103 Angle : 0.526 11.953 15463 Z= 0.263 Chirality : 0.038 0.140 1735 Planarity : 0.004 0.047 1999 Dihedral : 5.473 109.666 1536 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.59 % Allowed : 14.12 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.22), residues: 1385 helix: 1.58 (0.17), residues: 946 sheet: 0.55 (0.58), residues: 71 loop : -0.54 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1366 TYR 0.015 0.001 TYR A 648 PHE 0.011 0.001 PHE A1083 TRP 0.022 0.001 TRP A1516 HIS 0.004 0.001 HIS A 611 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.10 (11411) covalent geometry : angle 0.52560 / 0.26 (15463) hydrogen bonds : bond 0.03706 / 2.44 ( 666) hydrogen bonds : angle 3.89512 / 2.84 ( 1959) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.7238 (tpm170) REVERT: A 192 MET cc_start: 0.8323 (mtp) cc_final: 0.7890 (mtt) REVERT: A 525 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.8104 (ptp90) REVERT: A 556 ARG cc_start: 0.7599 (OUTLIER) cc_final: 0.7346 (ttt180) REVERT: A 1286 ARG cc_start: 0.7247 (mmt-90) cc_final: 0.6945 (mpp-170) REVERT: A 1332 GLU cc_start: 0.7098 (OUTLIER) cc_final: 0.6185 (tp30) REVERT: A 1360 GLU cc_start: 0.6702 (tm-30) cc_final: 0.6118 (tm-30) REVERT: A 1382 ARG cc_start: 0.7473 (OUTLIER) cc_final: 0.6841 (ptm-80) REVERT: A 1393 ARG cc_start: 0.7704 (mpt180) cc_final: 0.7405 (mtt-85) outliers start: 19 outliers final: 6 residues processed: 104 average time/residue: 0.6986 time to fit residues: 77.7292 Evaluate side-chains 103 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ARG Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 525 ARG Chi-restraints excluded: chain A residue 556 ARG Chi-restraints excluded: chain A residue 821 GLU Chi-restraints excluded: chain A residue 931 MET Chi-restraints excluded: chain A residue 1332 GLU Chi-restraints excluded: chain A residue 1382 ARG Chi-restraints excluded: chain A residue 1401 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: [113, 54, 13, 16, 76, 58, 70, 61, 137, 136, 103] chunk 113 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 76 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 137 optimal weight: 0.0870 chunk 136 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.233776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.177269 restraints weight = 11699.905| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 2.02 r_work: 0.3635 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.3581 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.4187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11411 Z= 0.122 Angle : 0.558 11.981 15463 Z= 0.278 Chirality : 0.039 0.168 1735 Planarity : 0.004 0.048 1999 Dihedral : 5.539 109.955 1536 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.92 % Allowed : 14.04 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.22), residues: 1385 helix: 1.65 (0.17), residues: 947 sheet: 0.55 (0.58), residues: 71 loop : -0.48 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1366 TYR 0.019 0.001 TYR A 648 PHE 0.015 0.001 PHE A 610 TRP 0.020 0.001 TRP A1516 HIS 0.006 0.001 HIS A 611 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (11411) covalent geometry : angle 0.55756 / 0.28 (15463) hydrogen bonds : bond 0.04270 / 2.83 ( 666) hydrogen bonds : angle 3.90254 / 2.84 ( 1959) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 ARG cc_start: 0.7827 (OUTLIER) cc_final: 0.7211 (tpm170) REVERT: A 192 MET cc_start: 0.8280 (mtp) cc_final: 0.7893 (mtm) REVERT: A 516 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.8027 (mmp80) REVERT: A 525 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.7970 (ptp90) REVERT: A 556 ARG cc_start: 0.7679 (OUTLIER) cc_final: 0.7415 (ttt180) REVERT: A 1332 GLU cc_start: 0.7023 (OUTLIER) cc_final: 0.6103 (tp30) REVERT: A 1360 GLU cc_start: 0.6782 (tm-30) cc_final: 0.6186 (tm-30) REVERT: A 1382 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.6739 (ptm-80) REVERT: A 1393 ARG cc_start: 0.7583 (mpt180) cc_final: 0.7352 (mtt-85) outliers start: 23 outliers final: 10 residues processed: 107 average time/residue: 0.6619 time to fit residues: 75.9791 Evaluate side-chains 109 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 167 ARG Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 516 ARG Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 525 ARG Chi-restraints excluded: chain A residue 556 ARG Chi-restraints excluded: chain A residue 821 GLU Chi-restraints excluded: chain A residue 931 MET Chi-restraints excluded: chain A residue 1315 LEU Chi-restraints excluded: chain A residue 1332 GLU Chi-restraints excluded: chain A residue 1382 ARG Chi-restraints excluded: chain A residue 1401 VAL Chi-restraints excluded: chain A residue 1511 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: [118, 9, 94, 80, 1, 19, 106, 17, 136, 78, 67] chunk 118 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 94 optimal weight: 7.9990 chunk 80 optimal weight: 7.9990 chunk 1 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 106 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 332 GLN ** A 514 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 = 0.4452 r_free = 0.4452 target = 0.231693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.188258 restraints weight = 11795.315| |-----------------------------------------------------------------------------| r_work (start): 0.4032 rms_B_bonded: 1.82 r_work: 0.3619 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.3551 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.4219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11411 Z= 0.185 Angle : 0.637 12.149 15463 Z= 0.318 Chirality : 0.043 0.170 1735 Planarity : 0.005 0.057 1999 Dihedral : 5.747 103.177 1536 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.59 % Allowed : 14.29 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.22), residues: 1385 helix: 1.47 (0.17), residues: 949 sheet: 0.54 (0.59), residues: 71 loop : -0.56 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1366 TYR 0.025 0.002 TYR A 648 PHE 0.022 0.002 PHE A1370 TRP 0.016 0.002 TRP A1516 HIS 0.007 0.001 HIS A 611 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.19 (11411) covalent geometry : angle 0.63659 / 0.32 (15463) hydrogen bonds : bond 0.05374 / 3.56 ( 666) hydrogen bonds : angle 4.03831 / 2.93 ( 1959) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.7259 (tpm170) REVERT: A 192 MET cc_start: 0.8411 (mtp) cc_final: 0.8007 (mtt) REVERT: A 516 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.8083 (mmp80) REVERT: A 525 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.8050 (ptp90) REVERT: A 635 GLU cc_start: 0.7923 (tt0) cc_final: 0.7700 (tt0) REVERT: A 1332 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6252 (tp30) REVERT: A 1360 GLU cc_start: 0.6813 (tm-30) cc_final: 0.6401 (tm-30) REVERT: A 1382 ARG cc_start: 0.7470 (OUTLIER) cc_final: 0.7014 (ptm160) outliers start: 19 outliers final: 10 residues processed: 107 average time/residue: 0.6667 time to fit residues: 76.4542 Evaluate side-chains 108 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 167 ARG Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 516 ARG Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 525 ARG Chi-restraints excluded: chain A residue 821 GLU Chi-restraints excluded: chain A residue 931 MET Chi-restraints excluded: chain A residue 1332 GLU Chi-restraints excluded: chain A residue 1382 ARG Chi-restraints excluded: chain A residue 1401 VAL Chi-restraints excluded: chain A residue 1511 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: [82, 45, 70, 78, 106, 19, 47, 100, 88, 125, 111] chunk 82 optimal weight: 9.9990 chunk 45 optimal weight: 0.5980 chunk 70 optimal weight: 0.6980 chunk 78 optimal weight: 0.6980 chunk 106 optimal weight: 10.0000 chunk 19 optimal weight: 0.0980 chunk 47 optimal weight: 0.9990 chunk 100 optimal weight: 30.0000 chunk 88 optimal weight: 4.9990 chunk 125 optimal weight: 0.8980 chunk 111 optimal weight: 0.0770 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 332 GLN ** A 514 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 = 0.4477 r_free = 0.4477 target = 0.234512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.180795 restraints weight = 11975.085| |-----------------------------------------------------------------------------| r_work (start): 0.3954 rms_B_bonded: 1.84 r_work: 0.3679 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3625 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.4344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 11411 Z= 0.104 Angle : 0.536 11.980 15463 Z= 0.266 Chirality : 0.038 0.163 1735 Planarity : 0.004 0.049 1999 Dihedral : 5.456 110.942 1536 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.25 % Allowed : 14.62 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.23), residues: 1385 helix: 1.71 (0.17), residues: 949 sheet: 0.58 (0.59), residues: 71 loop : -0.49 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1366 TYR 0.017 0.001 TYR A 648 PHE 0.012 0.001 PHE A1083 TRP 0.021 0.001 TRP A1516 HIS 0.004 0.001 HIS A 611 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (11411) covalent geometry : angle 0.53606 / 0.27 (15463) hydrogen bonds : bond 0.03782 / 2.50 ( 666) hydrogen bonds : angle 3.84466 / 2.80 ( 1959) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4057.78 seconds wall clock time: 69 minutes 58.58 seconds (4198.58 seconds total)