Starting phenix.real_space_refine on Tue Jul 29 10:29:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7oe7_12861/07_2025/7oe7_12861.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oe7_12861/07_2025/7oe7_12861.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7oe7_12861/07_2025/7oe7_12861.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oe7_12861/07_2025/7oe7_12861.map" model { file = "/net/cci-nas-00/data/ceres_data/7oe7_12861/07_2025/7oe7_12861.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oe7_12861/07_2025/7oe7_12861.cif" } resolution = 3.73 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.018 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 Zn 1 6.06 5 Mg 1 5.21 5 S 63 5.16 5 C 7088 2.51 5 N 1881 2.21 5 O 2082 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11116 Number of models: 1 Model: "" Number of chains: 2 Chain: "L" Number of atoms: 11114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1382, 11114 Classifications: {'peptide': 1382} Link IDs: {'PTRANS': 42, 'TRANS': 1339} Chain breaks: 11 Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 998 SG CYS L 321 41.658 105.490 68.143 1.00100.99 S ATOM 1360 SG CYS L 366 39.678 105.920 71.466 1.00108.15 S Time building chain proxies: 6.94, per 1000 atoms: 0.62 Number of scatterers: 11116 At special positions: 0 Unit cell: (97.44, 133.11, 121.8, 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) Zn 1 29.99 S 63 16.00 Mg 1 11.99 O 2082 8.00 N 1881 7.00 C 7088 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS L1690 " - pdb=" SG CYS L1790 " distance=2.03 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: 2.89 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN L2301 " pdb="ZN ZN L2301 " - pdb=" NE2 HIS L 364 " pdb="ZN ZN L2301 " - pdb=" NE2 HIS L 316 " pdb="ZN ZN L2301 " - pdb=" SG CYS L 321 " pdb="ZN ZN L2301 " - pdb=" SG CYS L 366 " Number of angles added : 2 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2646 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 9 sheets defined 54.8% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'L' and resid 202 through 206 removed outlier: 3.713A pdb=" N VAL L 205 " --> pdb=" O SER L 202 " (cutoff:3.500A) Processing helix chain 'L' and resid 212 through 222 removed outlier: 4.263A pdb=" N GLU L 216 " --> pdb=" O SER L 212 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE L 217 " --> pdb=" O HIS L 213 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE L 218 " --> pdb=" O TYR L 214 " (cutoff:3.500A) Processing helix chain 'L' and resid 233 through 252 removed outlier: 3.505A pdb=" N GLN L 237 " --> pdb=" O GLU L 233 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS L 251 " --> pdb=" O ASN L 247 " (cutoff:3.500A) Processing helix chain 'L' and resid 262 through 272 Processing helix chain 'L' and resid 284 through 293 removed outlier: 3.577A pdb=" N LYS L 293 " --> pdb=" O ILE L 289 " (cutoff:3.500A) Processing helix chain 'L' and resid 296 through 302 Processing helix chain 'L' and resid 312 through 317 removed outlier: 3.811A pdb=" N THR L 317 " --> pdb=" O GLU L 313 " (cutoff:3.500A) Processing helix chain 'L' and resid 323 through 336 removed outlier: 3.542A pdb=" N LEU L 336 " --> pdb=" O LYS L 332 " (cutoff:3.500A) Processing helix chain 'L' and resid 343 through 361 removed outlier: 3.850A pdb=" N LEU L 352 " --> pdb=" O ILE L 348 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE L 353 " --> pdb=" O PHE L 349 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU L 354 " --> pdb=" O ASP L 350 " (cutoff:3.500A) Processing helix chain 'L' and resid 385 through 404 Processing helix chain 'L' and resid 414 through 436 removed outlier: 4.099A pdb=" N ILE L 418 " --> pdb=" O ASN L 414 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL L 435 " --> pdb=" O ALA L 431 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY L 436 " --> pdb=" O LEU L 432 " (cutoff:3.500A) Processing helix chain 'L' and resid 439 through 443 removed outlier: 3.526A pdb=" N TYR L 442 " --> pdb=" O VAL L 439 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS L 443 " --> pdb=" O GLU L 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 439 through 443' Processing helix chain 'L' and resid 445 through 449 removed outlier: 3.576A pdb=" N VAL L 448 " --> pdb=" O ASN L 445 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE L 449 " --> pdb=" O MET L 446 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 445 through 449' Processing helix chain 'L' and resid 453 through 458 removed outlier: 3.627A pdb=" N LEU L 458 " --> pdb=" O TYR L 454 " (cutoff:3.500A) Processing helix chain 'L' and resid 491 through 507 removed outlier: 3.864A pdb=" N GLU L 495 " --> pdb=" O SER L 491 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG L 496 " --> pdb=" O THR L 492 " (cutoff:3.500A) Processing helix chain 'L' and resid 588 through 599 Processing helix chain 'L' and resid 604 through 608 removed outlier: 3.950A pdb=" N GLU L 608 " --> pdb=" O SER L 605 " (cutoff:3.500A) Processing helix chain 'L' and resid 611 through 628 removed outlier: 3.596A pdb=" N ASN L 615 " --> pdb=" O LEU L 611 " (cutoff:3.500A) Processing helix chain 'L' and resid 633 through 639 removed outlier: 3.628A pdb=" N LEU L 637 " --> pdb=" O SER L 633 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN L 639 " --> pdb=" O LYS L 635 " (cutoff:3.500A) Processing helix chain 'L' and resid 639 through 648 removed outlier: 3.513A pdb=" N PHE L 643 " --> pdb=" O ASN L 639 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL L 648 " --> pdb=" O ILE L 644 " (cutoff:3.500A) Processing helix chain 'L' and resid 656 through 660 Processing helix chain 'L' and resid 668 through 684 Processing helix chain 'L' and resid 693 through 703 Processing helix chain 'L' and resid 704 through 709 removed outlier: 3.542A pdb=" N HIS L 707 " --> pdb=" O TYR L 704 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE L 709 " --> pdb=" O CYS L 706 " (cutoff:3.500A) Processing helix chain 'L' and resid 717 through 729 removed outlier: 4.087A pdb=" N LYS L 722 " --> pdb=" O THR L 718 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N CYS L 723 " --> pdb=" O ASP L 719 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE L 724 " --> pdb=" O GLN L 720 " (cutoff:3.500A) Processing helix chain 'L' and resid 729 through 734 removed outlier: 3.939A pdb=" N GLU L 733 " --> pdb=" O GLU L 729 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N PHE L 734 " --> pdb=" O PRO L 730 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 729 through 734' Processing helix chain 'L' and resid 746 through 760 Processing helix chain 'L' and resid 780 through 793 Processing helix chain 'L' and resid 800 through 804 removed outlier: 3.656A pdb=" N LYS L 803 " --> pdb=" O SER L 800 " (cutoff:3.500A) Processing helix chain 'L' and resid 818 through 823 Processing helix chain 'L' and resid 843 through 862 removed outlier: 4.485A pdb=" N ARG L 860 " --> pdb=" O GLU L 856 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS L 861 " --> pdb=" O VAL L 857 " (cutoff:3.500A) Processing helix chain 'L' and resid 870 through 881 removed outlier: 3.663A pdb=" N ALA L 878 " --> pdb=" O LYS L 874 " (cutoff:3.500A) Processing helix chain 'L' and resid 907 through 925 removed outlier: 3.965A pdb=" N LYS L 915 " --> pdb=" O PHE L 911 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLU L 916 " --> pdb=" O ASP L 912 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N THR L 917 " --> pdb=" O GLN L 913 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL L 918 " --> pdb=" O LEU L 914 " (cutoff:3.500A) Processing helix chain 'L' and resid 1059 through 1068 Processing helix chain 'L' and resid 1075 through 1084 Processing helix chain 'L' and resid 1093 through 1098 removed outlier: 3.714A pdb=" N CYS L1097 " --> pdb=" O LEU L1093 " (cutoff:3.500A) Processing helix chain 'L' and resid 1137 through 1158 removed outlier: 3.664A pdb=" N ARG L1145 " --> pdb=" O LYS L1141 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU L1146 " --> pdb=" O MET L1142 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ILE L1147 " --> pdb=" O PHE L1143 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LEU L1158 " --> pdb=" O LEU L1154 " (cutoff:3.500A) Processing helix chain 'L' and resid 1166 through 1182 removed outlier: 3.646A pdb=" N GLU L1170 " --> pdb=" O GLU L1166 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU L1182 " --> pdb=" O LEU L1178 " (cutoff:3.500A) Processing helix chain 'L' and resid 1199 through 1208 removed outlier: 3.784A pdb=" N PHE L1203 " --> pdb=" O CYS L1199 " (cutoff:3.500A) Processing helix chain 'L' and resid 1216 through 1236 removed outlier: 3.779A pdb=" N ASP L1220 " --> pdb=" O ASP L1216 " (cutoff:3.500A) Processing helix chain 'L' and resid 1242 through 1259 removed outlier: 3.667A pdb=" N GLN L1257 " --> pdb=" O PHE L1253 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU L1258 " --> pdb=" O ILE L1254 " (cutoff:3.500A) Processing helix chain 'L' and resid 1270 through 1278 removed outlier: 3.641A pdb=" N ASN L1276 " --> pdb=" O PHE L1272 " (cutoff:3.500A) Processing helix chain 'L' and resid 1297 through 1320 removed outlier: 3.522A pdb=" N SER L1301 " --> pdb=" O LEU L1297 " (cutoff:3.500A) Processing helix chain 'L' and resid 1338 through 1348 removed outlier: 3.719A pdb=" N GLN L1346 " --> pdb=" O THR L1342 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG L1347 " --> pdb=" O GLU L1343 " (cutoff:3.500A) Processing helix chain 'L' and resid 1348 through 1365 removed outlier: 3.851A pdb=" N THR L1354 " --> pdb=" O GLU L1350 " (cutoff:3.500A) Processing helix chain 'L' and resid 1396 through 1406 removed outlier: 3.860A pdb=" N HIS L1406 " --> pdb=" O ALA L1402 " (cutoff:3.500A) Processing helix chain 'L' and resid 1414 through 1429 removed outlier: 4.074A pdb=" N GLU L1418 " --> pdb=" O HIS L1414 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA L1429 " --> pdb=" O ASP L1425 " (cutoff:3.500A) Processing helix chain 'L' and resid 1433 through 1451 removed outlier: 4.030A pdb=" N CYS L1437 " --> pdb=" O PRO L1433 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA L1451 " --> pdb=" O LEU L1447 " (cutoff:3.500A) Processing helix chain 'L' and resid 1466 through 1471 Processing helix chain 'L' and resid 1473 through 1486 removed outlier: 3.576A pdb=" N ARG L1477 " --> pdb=" O ASN L1473 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE L1478 " --> pdb=" O ARG L1474 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG L1484 " --> pdb=" O ARG L1480 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU L1485 " --> pdb=" O GLN L1481 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE L1486 " --> pdb=" O ILE L1482 " (cutoff:3.500A) Processing helix chain 'L' and resid 1492 through 1506 removed outlier: 4.371A pdb=" N ARG L1498 " --> pdb=" O ARG L1494 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR L1506 " --> pdb=" O ASN L1502 " (cutoff:3.500A) Processing helix chain 'L' and resid 1521 through 1533 removed outlier: 3.730A pdb=" N LEU L1533 " --> pdb=" O LEU L1529 " (cutoff:3.500A) Processing helix chain 'L' and resid 1539 through 1543 removed outlier: 3.878A pdb=" N LEU L1543 " --> pdb=" O GLU L1540 " (cutoff:3.500A) Processing helix chain 'L' and resid 1579 through 1589 Processing helix chain 'L' and resid 1592 through 1605 Processing helix chain 'L' and resid 1613 through 1624 Processing helix chain 'L' and resid 1639 through 1649 Processing helix chain 'L' and resid 1668 through 1672 removed outlier: 4.427A pdb=" N ASP L1672 " --> pdb=" O ASN L1669 " (cutoff:3.500A) Processing helix chain 'L' and resid 1677 through 1679 No H-bonds generated for 'chain 'L' and resid 1677 through 1679' Processing helix chain 'L' and resid 1684 through 1699 Processing helix chain 'L' and resid 1701 through 1705 removed outlier: 3.669A pdb=" N LEU L1704 " --> pdb=" O ALA L1701 " (cutoff:3.500A) Processing helix chain 'L' and resid 1778 through 1790 removed outlier: 4.136A pdb=" N VAL L1788 " --> pdb=" O VAL L1784 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ASN L1789 " --> pdb=" O ALA L1785 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N CYS L1790 " --> pdb=" O LEU L1786 " (cutoff:3.500A) Processing helix chain 'L' and resid 1794 through 1800 removed outlier: 3.585A pdb=" N HIS L1798 " --> pdb=" O SER L1794 " (cutoff:3.500A) Processing helix chain 'L' and resid 1812 through 1817 removed outlier: 3.690A pdb=" N ARG L1816 " --> pdb=" O SER L1812 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N LEU L1817 " --> pdb=" O SER L1813 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 1812 through 1817' Processing sheet with id=AA1, first strand: chain 'L' and resid 207 through 208 removed outlier: 6.631A pdb=" N LEU L 207 " --> pdb=" O TYR L1107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'L' and resid 259 through 260 Processing sheet with id=AA3, first strand: chain 'L' and resid 535 through 541 removed outlier: 3.950A pdb=" N CYS L 571 " --> pdb=" O ILE L 562 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 826 through 828 removed outlier: 3.534A pdb=" N VAL L 827 " --> pdb=" O GLU L1073 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 1132 through 1136 removed outlier: 4.450A pdb=" N LEU L1121 " --> pdb=" O GLU L1240 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 1333 through 1336 removed outlier: 3.949A pdb=" N GLN L1333 " --> pdb=" O MET L1189 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 1381 through 1382 Processing sheet with id=AA8, first strand: chain 'L' and resid 1653 through 1655 Processing sheet with id=AA9, first strand: chain 'L' and resid 1723 through 1726 removed outlier: 3.727A pdb=" N VAL L1810 " --> pdb=" O PHE L1724 " (cutoff:3.500A) 479 hydrogen bonds defined for protein. 1371 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: 3.80 Time building geometry restraints manager: 3.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3590 1.34 - 1.46: 2442 1.46 - 1.58: 5196 1.58 - 1.69: 0 1.69 - 1.81: 94 Bond restraints: 11322 Sorted by residual: bond pdb=" C PHE L 581 " pdb=" N PRO L 582 " ideal model delta sigma weight residual 1.335 1.359 -0.024 1.19e-02 7.06e+03 4.17e+00 bond pdb=" CA MET L 446 " pdb=" C MET L 446 " ideal model delta sigma weight residual 1.522 1.540 -0.018 1.38e-02 5.25e+03 1.62e+00 bond pdb=" CA ASP L1216 " pdb=" C ASP L1216 " ideal model delta sigma weight residual 1.523 1.533 -0.010 1.10e-02 8.26e+03 8.15e-01 bond pdb=" CA LYS L 635 " pdb=" C LYS L 635 " ideal model delta sigma weight residual 1.522 1.510 0.012 1.38e-02 5.25e+03 7.85e-01 bond pdb=" CA PRO L 410 " pdb=" C PRO L 410 " ideal model delta sigma weight residual 1.525 1.543 -0.018 2.10e-02 2.27e+03 7.43e-01 ... (remaining 11317 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 14907 1.46 - 2.91: 294 2.91 - 4.37: 56 4.37 - 5.82: 11 5.82 - 7.28: 1 Bond angle restraints: 15269 Sorted by residual: angle pdb=" N ILE L1613 " pdb=" CA ILE L1613 " pdb=" C ILE L1613 " ideal model delta sigma weight residual 111.90 108.46 3.44 8.10e-01 1.52e+00 1.80e+01 angle pdb=" N ILE L 318 " pdb=" CA ILE L 318 " pdb=" C ILE L 318 " ideal model delta sigma weight residual 112.98 108.33 4.65 1.25e+00 6.40e-01 1.39e+01 angle pdb=" N ILE L1639 " pdb=" CA ILE L1639 " pdb=" C ILE L1639 " ideal model delta sigma weight residual 111.81 108.66 3.15 8.60e-01 1.35e+00 1.34e+01 angle pdb=" N SER L 211 " pdb=" CA SER L 211 " pdb=" C SER L 211 " ideal model delta sigma weight residual 110.97 114.81 -3.84 1.09e+00 8.42e-01 1.24e+01 angle pdb=" C ILE L1486 " pdb=" CA ILE L1486 " pdb=" CB ILE L1486 " ideal model delta sigma weight residual 111.08 114.21 -3.13 9.50e-01 1.11e+00 1.09e+01 ... (remaining 15264 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.94: 6055 16.94 - 33.87: 684 33.87 - 50.81: 126 50.81 - 67.74: 20 67.74 - 84.68: 10 Dihedral angle restraints: 6895 sinusoidal: 2827 harmonic: 4068 Sorted by residual: dihedral pdb=" CB CYS L1690 " pdb=" SG CYS L1690 " pdb=" SG CYS L1790 " pdb=" CB CYS L1790 " ideal model delta sinusoidal sigma weight residual -86.00 -131.89 45.89 1 1.00e+01 1.00e-02 2.92e+01 dihedral pdb=" CA THR L 710 " pdb=" C THR L 710 " pdb=" N LYS L 711 " pdb=" CA LYS L 711 " ideal model delta harmonic sigma weight residual 180.00 161.88 18.12 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA VAL L 275 " pdb=" C VAL L 275 " pdb=" N ASP L 276 " pdb=" CA ASP L 276 " ideal model delta harmonic sigma weight residual 180.00 162.93 17.07 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 6892 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1440 0.049 - 0.097: 253 0.097 - 0.146: 40 0.146 - 0.195: 1 0.195 - 0.244: 1 Chirality restraints: 1735 Sorted by residual: chirality pdb=" CB THR L 710 " pdb=" CA THR L 710 " pdb=" OG1 THR L 710 " pdb=" CG2 THR L 710 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CB VAL L 601 " pdb=" CA VAL L 601 " pdb=" CG1 VAL L 601 " pdb=" CG2 VAL L 601 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.71e-01 chirality pdb=" CA ILE L1241 " pdb=" N ILE L1241 " pdb=" C ILE L1241 " pdb=" CB ILE L1241 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.62e-01 ... (remaining 1732 not shown) Planarity restraints: 1928 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE L1486 " -0.029 5.00e-02 4.00e+02 4.43e-02 3.14e+00 pdb=" N PRO L1487 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO L1487 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO L1487 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU L1412 " 0.027 5.00e-02 4.00e+02 4.04e-02 2.61e+00 pdb=" N PRO L1413 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO L1413 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO L1413 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE L 709 " -0.008 2.00e-02 2.50e+03 1.60e-02 2.57e+00 pdb=" C ILE L 709 " 0.028 2.00e-02 2.50e+03 pdb=" O ILE L 709 " -0.010 2.00e-02 2.50e+03 pdb=" N THR L 710 " -0.009 2.00e-02 2.50e+03 ... (remaining 1925 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 100 2.65 - 3.21: 9785 3.21 - 3.77: 14997 3.77 - 4.34: 20108 4.34 - 4.90: 33890 Nonbonded interactions: 78880 Sorted by model distance: nonbonded pdb=" OD1 ASP L1332 " pdb="MG MG L2302 " model vdw 2.084 2.170 nonbonded pdb=" OD1 ASP L1657 " pdb=" N SER L1658 " model vdw 2.125 3.120 nonbonded pdb=" OG SER L 498 " pdb=" O ILE L 584 " model vdw 2.156 3.040 nonbonded pdb=" OG SER L 685 " pdb=" OD1 ASP L 687 " model vdw 2.158 3.040 nonbonded pdb=" OG SER L1161 " pdb=" OD2 ASP L1302 " model vdw 2.167 3.040 ... (remaining 78875 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 group one per residue 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: 1.730 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: 0.510 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 30.410 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6419 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 11327 Z= 0.112 Angle : 0.528 7.276 15273 Z= 0.306 Chirality : 0.038 0.244 1735 Planarity : 0.003 0.044 1928 Dihedral : 14.332 84.676 4246 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.23), residues: 1358 helix: 0.92 (0.21), residues: 697 sheet: -1.94 (0.67), residues: 57 loop : -3.38 (0.20), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP L 395 HIS 0.002 0.001 HIS L 364 PHE 0.015 0.001 PHE L1303 TYR 0.018 0.001 TYR L 574 ARG 0.002 0.000 ARG L1665 Details of bonding type rmsd hydrogen bonds : bond 0.16300 ( 479) hydrogen bonds : angle 4.66308 ( 1371) metal coordination : bond 0.00258 ( 4) metal coordination : angle 0.80032 ( 2) SS BOND : bond 0.00078 ( 1) SS BOND : angle 0.38634 ( 2) covalent geometry : bond 0.00205 (11322) covalent geometry : angle 0.52792 (15269) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 259 average time/residue: 0.3034 time to fit residues: 108.3488 Evaluate side-chains 106 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 0.0060 chunk 104 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 70 optimal weight: 8.9990 chunk 55 optimal weight: 3.9990 chunk 108 optimal weight: 30.0000 chunk 41 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 80 optimal weight: 5.9990 chunk 125 optimal weight: 7.9990 overall best weight: 1.9602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 359 HIS L 379 ASN L 441 HIS L 830 ASN L1126 GLN L1208 GLN L1807 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.102532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.082454 restraints weight = 39304.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.083407 restraints weight = 22599.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.083929 restraints weight = 16840.876| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11327 Z= 0.161 Angle : 0.651 11.900 15273 Z= 0.326 Chirality : 0.041 0.221 1735 Planarity : 0.004 0.049 1928 Dihedral : 4.110 18.735 1490 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 2.22 % Allowed : 9.99 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.23), residues: 1358 helix: 0.80 (0.20), residues: 721 sheet: -1.93 (0.64), residues: 57 loop : -3.37 (0.21), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L1664 HIS 0.005 0.001 HIS L1798 PHE 0.016 0.001 PHE L1303 TYR 0.017 0.002 TYR L 471 ARG 0.008 0.001 ARG L 920 Details of bonding type rmsd hydrogen bonds : bond 0.04256 ( 479) hydrogen bonds : angle 4.00482 ( 1371) metal coordination : bond 0.01275 ( 4) metal coordination : angle 2.14819 ( 2) SS BOND : bond 0.00138 ( 1) SS BOND : angle 0.22897 ( 2) covalent geometry : bond 0.00366 (11322) covalent geometry : angle 0.65026 (15269) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 119 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 1292 MET cc_start: 0.8039 (tmm) cc_final: 0.7761 (tmm) REVERT: L 1492 ARG cc_start: 0.7080 (mtt90) cc_final: 0.6583 (mtm180) outliers start: 28 outliers final: 17 residues processed: 144 average time/residue: 0.2276 time to fit residues: 47.8868 Evaluate side-chains 104 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 379 ASN Chi-restraints excluded: chain L residue 390 ARG Chi-restraints excluded: chain L residue 611 LEU Chi-restraints excluded: chain L residue 671 LEU Chi-restraints excluded: chain L residue 704 TYR Chi-restraints excluded: chain L residue 846 LEU Chi-restraints excluded: chain L residue 871 TYR Chi-restraints excluded: chain L residue 1319 ILE Chi-restraints excluded: chain L residue 1328 THR Chi-restraints excluded: chain L residue 1408 ILE Chi-restraints excluded: chain L residue 1434 VAL Chi-restraints excluded: chain L residue 1464 THR Chi-restraints excluded: chain L residue 1468 ASP Chi-restraints excluded: chain L residue 1524 SER Chi-restraints excluded: chain L residue 1550 LEU Chi-restraints excluded: chain L residue 1639 ILE Chi-restraints excluded: chain L residue 1659 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 127 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 119 optimal weight: 9.9990 chunk 80 optimal weight: 9.9990 chunk 20 optimal weight: 8.9990 chunk 114 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 88 optimal weight: 0.0970 chunk 92 optimal weight: 3.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 591 GLN L1055 ASN ** L1299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L1449 GLN ** L1549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L1798 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.099448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.080358 restraints weight = 41218.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.080320 restraints weight = 24349.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.081042 restraints weight = 20602.414| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 11327 Z= 0.181 Angle : 0.652 10.143 15273 Z= 0.330 Chirality : 0.042 0.267 1735 Planarity : 0.004 0.058 1928 Dihedral : 4.353 17.677 1490 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 2.46 % Allowed : 12.93 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.23), residues: 1358 helix: 0.78 (0.20), residues: 716 sheet: -2.10 (0.60), residues: 67 loop : -3.34 (0.21), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L1664 HIS 0.006 0.001 HIS L 707 PHE 0.015 0.002 PHE L 585 TYR 0.017 0.002 TYR L1688 ARG 0.005 0.001 ARG L1477 Details of bonding type rmsd hydrogen bonds : bond 0.04531 ( 479) hydrogen bonds : angle 4.05016 ( 1371) metal coordination : bond 0.01128 ( 4) metal coordination : angle 2.19164 ( 2) SS BOND : bond 0.00125 ( 1) SS BOND : angle 0.64615 ( 2) covalent geometry : bond 0.00418 (11322) covalent geometry : angle 0.65198 (15269) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 93 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 302 LEU cc_start: 0.8168 (tp) cc_final: 0.7136 (mt) REVERT: L 395 TRP cc_start: 0.8712 (t60) cc_final: 0.8085 (t60) REVERT: L 1292 MET cc_start: 0.8142 (tmm) cc_final: 0.7920 (tmm) REVERT: L 1492 ARG cc_start: 0.7041 (mtt90) cc_final: 0.6611 (mtm180) REVERT: L 1598 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.7787 (pptt) outliers start: 31 outliers final: 20 residues processed: 120 average time/residue: 0.2161 time to fit residues: 39.3587 Evaluate side-chains 108 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 611 LEU Chi-restraints excluded: chain L residue 671 LEU Chi-restraints excluded: chain L residue 710 THR Chi-restraints excluded: chain L residue 830 ASN Chi-restraints excluded: chain L residue 857 VAL Chi-restraints excluded: chain L residue 871 TYR Chi-restraints excluded: chain L residue 1122 SER Chi-restraints excluded: chain L residue 1234 HIS Chi-restraints excluded: chain L residue 1319 ILE Chi-restraints excluded: chain L residue 1328 THR Chi-restraints excluded: chain L residue 1408 ILE Chi-restraints excluded: chain L residue 1434 VAL Chi-restraints excluded: chain L residue 1464 THR Chi-restraints excluded: chain L residue 1465 ASP Chi-restraints excluded: chain L residue 1509 LEU Chi-restraints excluded: chain L residue 1524 SER Chi-restraints excluded: chain L residue 1598 LYS Chi-restraints excluded: chain L residue 1624 LEU Chi-restraints excluded: chain L residue 1639 ILE Chi-restraints excluded: chain L residue 1659 HIS Chi-restraints excluded: chain L residue 1694 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 23 optimal weight: 7.9990 chunk 60 optimal weight: 0.0980 chunk 8 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 63 optimal weight: 0.0570 chunk 106 optimal weight: 0.0770 chunk 111 optimal weight: 9.9990 chunk 113 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 overall best weight: 1.4460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 881 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L1087 ASN L1234 HIS ** L1299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.101019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.081992 restraints weight = 42545.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.082818 restraints weight = 26187.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.083117 restraints weight = 23323.902| |-----------------------------------------------------------------------------| r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.4244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 11327 Z= 0.123 Angle : 0.572 8.173 15273 Z= 0.288 Chirality : 0.039 0.191 1735 Planarity : 0.003 0.043 1928 Dihedral : 4.132 17.449 1490 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 1.82 % Allowed : 15.38 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.23), residues: 1358 helix: 0.96 (0.20), residues: 715 sheet: -1.61 (0.66), residues: 57 loop : -3.20 (0.22), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP L1664 HIS 0.004 0.001 HIS L 287 PHE 0.013 0.001 PHE L1303 TYR 0.012 0.001 TYR L1688 ARG 0.006 0.000 ARG L 398 Details of bonding type rmsd hydrogen bonds : bond 0.03807 ( 479) hydrogen bonds : angle 3.88323 ( 1371) metal coordination : bond 0.00975 ( 4) metal coordination : angle 1.32180 ( 2) SS BOND : bond 0.00031 ( 1) SS BOND : angle 0.51781 ( 2) covalent geometry : bond 0.00278 (11322) covalent geometry : angle 0.57190 (15269) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 302 LEU cc_start: 0.8023 (tp) cc_final: 0.7039 (mt) REVERT: L 350 ASP cc_start: 0.6762 (p0) cc_final: 0.6001 (t0) outliers start: 23 outliers final: 20 residues processed: 112 average time/residue: 0.1833 time to fit residues: 33.1109 Evaluate side-chains 106 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 313 GLU Chi-restraints excluded: chain L residue 611 LEU Chi-restraints excluded: chain L residue 671 LEU Chi-restraints excluded: chain L residue 704 TYR Chi-restraints excluded: chain L residue 710 THR Chi-restraints excluded: chain L residue 817 THR Chi-restraints excluded: chain L residue 830 ASN Chi-restraints excluded: chain L residue 857 VAL Chi-restraints excluded: chain L residue 871 TYR Chi-restraints excluded: chain L residue 1234 HIS Chi-restraints excluded: chain L residue 1319 ILE Chi-restraints excluded: chain L residue 1328 THR Chi-restraints excluded: chain L residue 1408 ILE Chi-restraints excluded: chain L residue 1434 VAL Chi-restraints excluded: chain L residue 1464 THR Chi-restraints excluded: chain L residue 1465 ASP Chi-restraints excluded: chain L residue 1509 LEU Chi-restraints excluded: chain L residue 1624 LEU Chi-restraints excluded: chain L residue 1639 ILE Chi-restraints excluded: chain L residue 1659 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 71 optimal weight: 10.0000 chunk 63 optimal weight: 0.0060 chunk 97 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 80 optimal weight: 7.9990 overall best weight: 2.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 415 GLN L 824 ASN ** L1299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.098667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.078920 restraints weight = 40447.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.080053 restraints weight = 23378.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.080729 restraints weight = 17485.549| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.4664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 11327 Z= 0.161 Angle : 0.601 10.255 15273 Z= 0.305 Chirality : 0.040 0.216 1735 Planarity : 0.004 0.042 1928 Dihedral : 4.230 17.880 1490 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 2.38 % Allowed : 16.97 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.23), residues: 1358 helix: 0.88 (0.20), residues: 723 sheet: -1.71 (0.63), residues: 63 loop : -3.23 (0.22), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 395 HIS 0.021 0.001 HIS L1234 PHE 0.014 0.002 PHE L1058 TYR 0.021 0.001 TYR L1688 ARG 0.004 0.000 ARG L1477 Details of bonding type rmsd hydrogen bonds : bond 0.04205 ( 479) hydrogen bonds : angle 4.01678 ( 1371) metal coordination : bond 0.00731 ( 4) metal coordination : angle 1.00667 ( 2) SS BOND : bond 0.00169 ( 1) SS BOND : angle 0.65748 ( 2) covalent geometry : bond 0.00371 (11322) covalent geometry : angle 0.60088 (15269) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 94 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 302 LEU cc_start: 0.8126 (tp) cc_final: 0.7101 (mt) REVERT: L 350 ASP cc_start: 0.7076 (p0) cc_final: 0.6201 (t0) REVERT: L 692 MET cc_start: 0.6628 (tpt) cc_final: 0.6403 (tpt) outliers start: 30 outliers final: 23 residues processed: 113 average time/residue: 0.1805 time to fit residues: 33.0890 Evaluate side-chains 107 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 279 THR Chi-restraints excluded: chain L residue 313 GLU Chi-restraints excluded: chain L residue 611 LEU Chi-restraints excluded: chain L residue 625 ILE Chi-restraints excluded: chain L residue 671 LEU Chi-restraints excluded: chain L residue 710 THR Chi-restraints excluded: chain L residue 817 THR Chi-restraints excluded: chain L residue 830 ASN Chi-restraints excluded: chain L residue 857 VAL Chi-restraints excluded: chain L residue 871 TYR Chi-restraints excluded: chain L residue 882 LEU Chi-restraints excluded: chain L residue 1189 MET Chi-restraints excluded: chain L residue 1319 ILE Chi-restraints excluded: chain L residue 1328 THR Chi-restraints excluded: chain L residue 1408 ILE Chi-restraints excluded: chain L residue 1434 VAL Chi-restraints excluded: chain L residue 1464 THR Chi-restraints excluded: chain L residue 1465 ASP Chi-restraints excluded: chain L residue 1580 ILE Chi-restraints excluded: chain L residue 1624 LEU Chi-restraints excluded: chain L residue 1639 ILE Chi-restraints excluded: chain L residue 1659 HIS Chi-restraints excluded: chain L residue 1661 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 56 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 26 optimal weight: 20.0000 chunk 66 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 chunk 133 optimal weight: 7.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 824 ASN L 881 ASN L1087 ASN L1234 HIS ** L1299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.099881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.079962 restraints weight = 41139.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.081319 restraints weight = 23432.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.081532 restraints weight = 17888.129| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.4811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 11327 Z= 0.106 Angle : 0.561 11.476 15273 Z= 0.278 Chirality : 0.039 0.299 1735 Planarity : 0.003 0.044 1928 Dihedral : 4.013 16.889 1490 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 1.98 % Allowed : 18.16 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.23), residues: 1358 helix: 1.11 (0.20), residues: 718 sheet: -1.39 (0.60), residues: 67 loop : -3.16 (0.22), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP L 395 HIS 0.004 0.001 HIS L 287 PHE 0.022 0.001 PHE L 421 TYR 0.011 0.001 TYR L1688 ARG 0.003 0.000 ARG L1477 Details of bonding type rmsd hydrogen bonds : bond 0.03462 ( 479) hydrogen bonds : angle 3.83597 ( 1371) metal coordination : bond 0.01085 ( 4) metal coordination : angle 0.30309 ( 2) SS BOND : bond 0.00159 ( 1) SS BOND : angle 0.76415 ( 2) covalent geometry : bond 0.00241 (11322) covalent geometry : angle 0.56050 (15269) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 302 LEU cc_start: 0.8047 (tp) cc_final: 0.7071 (mt) REVERT: L 350 ASP cc_start: 0.7164 (p0) cc_final: 0.6266 (t0) outliers start: 25 outliers final: 22 residues processed: 111 average time/residue: 0.1868 time to fit residues: 32.8119 Evaluate side-chains 104 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 82 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 279 THR Chi-restraints excluded: chain L residue 449 ILE Chi-restraints excluded: chain L residue 508 MET Chi-restraints excluded: chain L residue 611 LEU Chi-restraints excluded: chain L residue 625 ILE Chi-restraints excluded: chain L residue 671 LEU Chi-restraints excluded: chain L residue 704 TYR Chi-restraints excluded: chain L residue 710 THR Chi-restraints excluded: chain L residue 830 ASN Chi-restraints excluded: chain L residue 857 VAL Chi-restraints excluded: chain L residue 871 TYR Chi-restraints excluded: chain L residue 882 LEU Chi-restraints excluded: chain L residue 1234 HIS Chi-restraints excluded: chain L residue 1328 THR Chi-restraints excluded: chain L residue 1362 MET Chi-restraints excluded: chain L residue 1375 VAL Chi-restraints excluded: chain L residue 1408 ILE Chi-restraints excluded: chain L residue 1464 THR Chi-restraints excluded: chain L residue 1465 ASP Chi-restraints excluded: chain L residue 1624 LEU Chi-restraints excluded: chain L residue 1639 ILE Chi-restraints excluded: chain L residue 1661 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 105 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 128 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 134 optimal weight: 9.9990 chunk 104 optimal weight: 0.8980 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 506 ASN L1234 HIS ** L1299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.097569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.078006 restraints weight = 41906.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.079206 restraints weight = 24905.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.079499 restraints weight = 18120.626| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.5305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 11327 Z= 0.193 Angle : 0.662 11.457 15273 Z= 0.332 Chirality : 0.042 0.289 1735 Planarity : 0.004 0.040 1928 Dihedral : 4.413 18.734 1490 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.87 % Favored : 90.13 % Rotamer: Outliers : 2.78 % Allowed : 18.40 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.23), residues: 1358 helix: 0.91 (0.20), residues: 709 sheet: -1.81 (0.56), residues: 82 loop : -3.19 (0.23), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP L 395 HIS 0.006 0.001 HIS L 707 PHE 0.024 0.002 PHE L 421 TYR 0.028 0.002 TYR L1688 ARG 0.006 0.000 ARG L 695 Details of bonding type rmsd hydrogen bonds : bond 0.04728 ( 479) hydrogen bonds : angle 4.22795 ( 1371) metal coordination : bond 0.00916 ( 4) metal coordination : angle 0.76862 ( 2) SS BOND : bond 0.00341 ( 1) SS BOND : angle 0.84477 ( 2) covalent geometry : bond 0.00446 (11322) covalent geometry : angle 0.66188 (15269) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 89 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 350 ASP cc_start: 0.6970 (p0) cc_final: 0.5927 (t0) REVERT: L 1479 MET cc_start: 0.4265 (tpp) cc_final: 0.3871 (mmt) outliers start: 35 outliers final: 30 residues processed: 113 average time/residue: 0.2617 time to fit residues: 46.2470 Evaluate side-chains 110 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 80 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 279 THR Chi-restraints excluded: chain L residue 313 GLU Chi-restraints excluded: chain L residue 379 ASN Chi-restraints excluded: chain L residue 508 MET Chi-restraints excluded: chain L residue 625 ILE Chi-restraints excluded: chain L residue 671 LEU Chi-restraints excluded: chain L residue 710 THR Chi-restraints excluded: chain L residue 817 THR Chi-restraints excluded: chain L residue 830 ASN Chi-restraints excluded: chain L residue 857 VAL Chi-restraints excluded: chain L residue 871 TYR Chi-restraints excluded: chain L residue 882 LEU Chi-restraints excluded: chain L residue 1122 SER Chi-restraints excluded: chain L residue 1189 MET Chi-restraints excluded: chain L residue 1234 HIS Chi-restraints excluded: chain L residue 1319 ILE Chi-restraints excluded: chain L residue 1328 THR Chi-restraints excluded: chain L residue 1362 MET Chi-restraints excluded: chain L residue 1375 VAL Chi-restraints excluded: chain L residue 1408 ILE Chi-restraints excluded: chain L residue 1464 THR Chi-restraints excluded: chain L residue 1465 ASP Chi-restraints excluded: chain L residue 1478 ILE Chi-restraints excluded: chain L residue 1513 PHE Chi-restraints excluded: chain L residue 1524 SER Chi-restraints excluded: chain L residue 1559 VAL Chi-restraints excluded: chain L residue 1580 ILE Chi-restraints excluded: chain L residue 1624 LEU Chi-restraints excluded: chain L residue 1639 ILE Chi-restraints excluded: chain L residue 1661 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 12 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 51 optimal weight: 0.0980 chunk 22 optimal weight: 0.8980 chunk 7 optimal weight: 7.9990 chunk 56 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 19 optimal weight: 0.0980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 506 ASN ** L1055 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L1087 ASN L1234 HIS ** L1299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L1585 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.099583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.079721 restraints weight = 42667.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.081059 restraints weight = 27017.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.081458 restraints weight = 18381.681| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.5256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 11327 Z= 0.100 Angle : 0.596 12.896 15273 Z= 0.291 Chirality : 0.039 0.245 1735 Planarity : 0.003 0.043 1928 Dihedral : 4.042 17.707 1490 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 1.82 % Allowed : 19.98 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.23), residues: 1358 helix: 1.19 (0.20), residues: 709 sheet: -1.50 (0.57), residues: 76 loop : -3.09 (0.22), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP L 395 HIS 0.004 0.001 HIS L1234 PHE 0.027 0.001 PHE L 421 TYR 0.026 0.001 TYR L 574 ARG 0.004 0.000 ARG L1167 Details of bonding type rmsd hydrogen bonds : bond 0.03374 ( 479) hydrogen bonds : angle 3.86654 ( 1371) metal coordination : bond 0.01224 ( 4) metal coordination : angle 0.44635 ( 2) SS BOND : bond 0.00184 ( 1) SS BOND : angle 0.90562 ( 2) covalent geometry : bond 0.00218 (11322) covalent geometry : angle 0.59598 (15269) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 88 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 313 GLU cc_start: 0.6947 (OUTLIER) cc_final: 0.6418 (mp0) REVERT: L 350 ASP cc_start: 0.7122 (p0) cc_final: 0.6182 (t0) REVERT: L 1479 MET cc_start: 0.3952 (tpp) cc_final: 0.3560 (mmt) outliers start: 23 outliers final: 19 residues processed: 104 average time/residue: 0.1770 time to fit residues: 30.0416 Evaluate side-chains 104 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 279 THR Chi-restraints excluded: chain L residue 313 GLU Chi-restraints excluded: chain L residue 508 MET Chi-restraints excluded: chain L residue 625 ILE Chi-restraints excluded: chain L residue 671 LEU Chi-restraints excluded: chain L residue 704 TYR Chi-restraints excluded: chain L residue 710 THR Chi-restraints excluded: chain L residue 830 ASN Chi-restraints excluded: chain L residue 857 VAL Chi-restraints excluded: chain L residue 871 TYR Chi-restraints excluded: chain L residue 882 LEU Chi-restraints excluded: chain L residue 1234 HIS Chi-restraints excluded: chain L residue 1328 THR Chi-restraints excluded: chain L residue 1408 ILE Chi-restraints excluded: chain L residue 1464 THR Chi-restraints excluded: chain L residue 1465 ASP Chi-restraints excluded: chain L residue 1478 ILE Chi-restraints excluded: chain L residue 1624 LEU Chi-restraints excluded: chain L residue 1639 ILE Chi-restraints excluded: chain L residue 1661 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 114 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 0.8980 chunk 17 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L1055 ASN L1234 HIS ** L1299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.099576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.080219 restraints weight = 41353.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.080669 restraints weight = 25313.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.081403 restraints weight = 18737.122| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.5329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 11327 Z= 0.103 Angle : 0.600 14.668 15273 Z= 0.290 Chirality : 0.039 0.301 1735 Planarity : 0.003 0.042 1928 Dihedral : 3.926 16.801 1490 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 1.98 % Allowed : 19.83 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.23), residues: 1358 helix: 1.22 (0.20), residues: 711 sheet: -1.41 (0.57), residues: 76 loop : -3.05 (0.22), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP L 395 HIS 0.010 0.001 HIS L1234 PHE 0.030 0.001 PHE L 421 TYR 0.020 0.001 TYR L 574 ARG 0.003 0.000 ARG L1484 Details of bonding type rmsd hydrogen bonds : bond 0.03396 ( 479) hydrogen bonds : angle 3.86334 ( 1371) metal coordination : bond 0.01053 ( 4) metal coordination : angle 0.29671 ( 2) SS BOND : bond 0.00188 ( 1) SS BOND : angle 0.74714 ( 2) covalent geometry : bond 0.00232 (11322) covalent geometry : angle 0.60038 (15269) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 83 time to evaluate : 1.536 Fit side-chains revert: symmetry clash REVERT: L 313 GLU cc_start: 0.6909 (OUTLIER) cc_final: 0.6427 (mp0) REVERT: L 336 LEU cc_start: 0.7397 (tp) cc_final: 0.7090 (mp) REVERT: L 350 ASP cc_start: 0.7081 (p0) cc_final: 0.6101 (t0) REVERT: L 700 LEU cc_start: 0.8471 (tt) cc_final: 0.8128 (mm) REVERT: L 1479 MET cc_start: 0.3944 (tpp) cc_final: 0.3581 (mmt) outliers start: 25 outliers final: 22 residues processed: 100 average time/residue: 0.1743 time to fit residues: 28.8943 Evaluate side-chains 102 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 79 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 279 THR Chi-restraints excluded: chain L residue 313 GLU Chi-restraints excluded: chain L residue 508 MET Chi-restraints excluded: chain L residue 625 ILE Chi-restraints excluded: chain L residue 671 LEU Chi-restraints excluded: chain L residue 704 TYR Chi-restraints excluded: chain L residue 710 THR Chi-restraints excluded: chain L residue 817 THR Chi-restraints excluded: chain L residue 830 ASN Chi-restraints excluded: chain L residue 857 VAL Chi-restraints excluded: chain L residue 871 TYR Chi-restraints excluded: chain L residue 882 LEU Chi-restraints excluded: chain L residue 1234 HIS Chi-restraints excluded: chain L residue 1319 ILE Chi-restraints excluded: chain L residue 1328 THR Chi-restraints excluded: chain L residue 1362 MET Chi-restraints excluded: chain L residue 1408 ILE Chi-restraints excluded: chain L residue 1464 THR Chi-restraints excluded: chain L residue 1465 ASP Chi-restraints excluded: chain L residue 1478 ILE Chi-restraints excluded: chain L residue 1624 LEU Chi-restraints excluded: chain L residue 1639 ILE Chi-restraints excluded: chain L residue 1661 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 85 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 104 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 106 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L1234 HIS ** L1299 ASN ** 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 = 0.3991 r_free = 0.3991 target = 0.099728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.080893 restraints weight = 41182.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.081276 restraints weight = 24536.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.081953 restraints weight = 18970.633| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.5430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11327 Z= 0.117 Angle : 0.619 15.806 15273 Z= 0.301 Chirality : 0.039 0.282 1735 Planarity : 0.003 0.042 1928 Dihedral : 3.943 16.559 1490 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 1.98 % Allowed : 19.90 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.23), residues: 1358 helix: 1.20 (0.20), residues: 711 sheet: -1.45 (0.55), residues: 82 loop : -3.05 (0.22), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP L 395 HIS 0.012 0.001 HIS L1234 PHE 0.033 0.001 PHE L 421 TYR 0.018 0.001 TYR L 574 ARG 0.003 0.000 ARG L1484 Details of bonding type rmsd hydrogen bonds : bond 0.03543 ( 479) hydrogen bonds : angle 3.90686 ( 1371) metal coordination : bond 0.00961 ( 4) metal coordination : angle 0.21187 ( 2) SS BOND : bond 0.00219 ( 1) SS BOND : angle 0.74296 ( 2) covalent geometry : bond 0.00270 (11322) covalent geometry : angle 0.61898 (15269) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 86 time to evaluate : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 313 GLU cc_start: 0.6966 (OUTLIER) cc_final: 0.6469 (mp0) REVERT: L 350 ASP cc_start: 0.7030 (p0) cc_final: 0.5906 (t0) REVERT: L 579 ARG cc_start: 0.5738 (mtp85) cc_final: 0.5365 (mtp85) REVERT: L 1479 MET cc_start: 0.4100 (tpp) cc_final: 0.3737 (mmt) REVERT: L 1558 MET cc_start: 0.6304 (mtt) cc_final: 0.6074 (mtt) outliers start: 25 outliers final: 23 residues processed: 103 average time/residue: 0.1899 time to fit residues: 31.3817 Evaluate side-chains 108 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 84 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 279 THR Chi-restraints excluded: chain L residue 313 GLU Chi-restraints excluded: chain L residue 508 MET Chi-restraints excluded: chain L residue 625 ILE Chi-restraints excluded: chain L residue 671 LEU Chi-restraints excluded: chain L residue 704 TYR Chi-restraints excluded: chain L residue 710 THR Chi-restraints excluded: chain L residue 817 THR Chi-restraints excluded: chain L residue 830 ASN Chi-restraints excluded: chain L residue 857 VAL Chi-restraints excluded: chain L residue 871 TYR Chi-restraints excluded: chain L residue 882 LEU Chi-restraints excluded: chain L residue 1234 HIS Chi-restraints excluded: chain L residue 1328 THR Chi-restraints excluded: chain L residue 1362 MET Chi-restraints excluded: chain L residue 1408 ILE Chi-restraints excluded: chain L residue 1464 THR Chi-restraints excluded: chain L residue 1465 ASP Chi-restraints excluded: chain L residue 1478 ILE Chi-restraints excluded: chain L residue 1624 LEU Chi-restraints excluded: chain L residue 1639 ILE Chi-restraints excluded: chain L residue 1659 HIS Chi-restraints excluded: chain L residue 1661 VAL Chi-restraints excluded: chain L residue 1810 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 50 optimal weight: 0.6980 chunk 109 optimal weight: 9.9990 chunk 83 optimal weight: 4.9990 chunk 102 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 45 optimal weight: 0.0040 chunk 119 optimal weight: 8.9990 chunk 87 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 overall best weight: 0.8794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L1087 ASN L1234 HIS L1299 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.101237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.082785 restraints weight = 42275.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.082630 restraints weight = 25344.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.083430 restraints weight = 20182.056| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.5486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 11327 Z= 0.103 Angle : 0.608 14.611 15273 Z= 0.292 Chirality : 0.039 0.275 1735 Planarity : 0.003 0.042 1928 Dihedral : 3.866 16.210 1490 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 2.14 % Allowed : 19.83 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.23), residues: 1358 helix: 1.30 (0.20), residues: 709 sheet: -1.37 (0.54), residues: 82 loop : -2.98 (0.22), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP L 395 HIS 0.007 0.001 HIS L1234 PHE 0.033 0.001 PHE L 421 TYR 0.018 0.001 TYR L 574 ARG 0.003 0.000 ARG L1484 Details of bonding type rmsd hydrogen bonds : bond 0.03345 ( 479) hydrogen bonds : angle 3.83438 ( 1371) metal coordination : bond 0.00961 ( 4) metal coordination : angle 0.39481 ( 2) SS BOND : bond 0.00173 ( 1) SS BOND : angle 0.69818 ( 2) covalent geometry : bond 0.00233 (11322) covalent geometry : angle 0.60796 (15269) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3438.34 seconds wall clock time: 61 minutes 0.73 seconds (3660.73 seconds total)