Starting phenix.real_space_refine on Sun Dec 29 19:36:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7oe7_12861/12_2024/7oe7_12861.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oe7_12861/12_2024/7oe7_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_12861/12_2024/7oe7_12861.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oe7_12861/12_2024/7oe7_12861.map" model { file = "/net/cci-nas-00/data/ceres_data/7oe7_12861/12_2024/7oe7_12861.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oe7_12861/12_2024/7oe7_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 6.69, per 1000 atoms: 0.60 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: 2.41 Conformation dependent library (CDL) restraints added in 1.3 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: 1.25 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: 3.52 Time building geometry restraints manager: 2.85 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: 1.750 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: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 27.590 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: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.890 ------------------------------------------------------------------------------- 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 11322 Z= 0.133 Angle : 0.528 7.276 15269 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 *********************** 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 : 1.317 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: 0.2996 time to fit residues: 105.2279 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 : 1.314 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6777 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 11322 Z= 0.240 Angle : 0.650 11.900 15269 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 *********************** 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 : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 17 residues processed: 144 average time/residue: 0.2480 time to fit residues: 51.8190 Evaluate side-chains 103 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 1.347 ------------------------------------------------------------------------------- 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 69 optimal weight: 6.9990 chunk 38 optimal weight: 0.7980 chunk 104 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 135 optimal weight: 8.9990 chunk 111 optimal weight: 7.9990 chunk 124 optimal weight: 0.7980 chunk 42 optimal weight: 9.9990 chunk 100 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 379 ASN L1449 GLN L1549 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6804 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 11322 Z= 0.184 Angle : 0.587 10.329 15269 Z= 0.292 Chirality : 0.039 0.260 1735 Planarity : 0.003 0.042 1928 Dihedral : 3.998 17.192 1490 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 1.82 % Allowed : 12.21 % Favored : 85.96 % 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: 0.98 (0.20), residues: 717 sheet: -1.76 (0.64), residues: 57 loop : -3.31 (0.21), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L1664 HIS 0.004 0.001 HIS L 287 PHE 0.014 0.001 PHE L1303 TYR 0.014 0.001 TYR L 274 ARG 0.004 0.000 ARG L1347 *********************** 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 114 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 1.927 Fit side-chains revert: symmetry clash REVERT: L 302 LEU cc_start: 0.7119 (tp) cc_final: 0.6823 (mt) outliers start: 23 outliers final: 20 residues processed: 110 average time/residue: 0.2127 time to fit residues: 36.5131 Evaluate side-chains 105 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 1.579 ------------------------------------------------------------------------------- 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 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 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 1509 LEU Chi-restraints excluded: chain L residue 1524 SER Chi-restraints excluded: chain L residue 1550 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 124 optimal weight: 0.5980 chunk 94 optimal weight: 0.8980 chunk 65 optimal weight: 10.0000 chunk 13 optimal weight: 8.9990 chunk 59 optimal weight: 8.9990 chunk 84 optimal weight: 0.9990 chunk 125 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 111 optimal weight: 10.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 591 GLN L1055 ASN L1087 ASN ** L1299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L1798 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 11322 Z= 0.207 Angle : 0.594 13.763 15269 Z= 0.294 Chirality : 0.039 0.224 1735 Planarity : 0.004 0.039 1928 Dihedral : 4.048 18.292 1490 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 2.30 % Allowed : 14.12 % Favored : 83.58 % 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: -1.20 (0.23), residues: 1358 helix: 0.99 (0.21), residues: 717 sheet: -1.59 (0.66), residues: 57 loop : -3.19 (0.21), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP L 395 HIS 0.005 0.001 HIS L 707 PHE 0.013 0.001 PHE L1058 TYR 0.015 0.001 TYR L1688 ARG 0.015 0.001 ARG L 398 *********************** 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 120 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 91 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 302 LEU cc_start: 0.7181 (tp) cc_final: 0.6888 (mt) REVERT: L 1558 MET cc_start: 0.6615 (mmm) cc_final: 0.5466 (mmm) REVERT: L 1598 LYS cc_start: 0.8060 (OUTLIER) cc_final: 0.7464 (pptt) outliers start: 29 outliers final: 20 residues processed: 116 average time/residue: 0.1958 time to fit residues: 35.8474 Evaluate side-chains 105 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 1.309 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 75 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 113 optimal weight: 9.9990 chunk 92 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 68 optimal weight: 7.9990 chunk 119 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 415 GLN L1055 ASN L1234 HIS ** L1299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.4775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 11322 Z= 0.252 Angle : 0.625 10.609 15269 Z= 0.315 Chirality : 0.041 0.272 1735 Planarity : 0.004 0.040 1928 Dihedral : 4.308 16.976 1490 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 2.93 % Allowed : 16.10 % Favored : 80.97 % 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: -1.36 (0.23), residues: 1358 helix: 0.79 (0.20), residues: 725 sheet: -1.80 (0.62), residues: 63 loop : -3.21 (0.22), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP L1664 HIS 0.006 0.001 HIS L 707 PHE 0.014 0.002 PHE L 585 TYR 0.025 0.002 TYR L1688 ARG 0.003 0.001 ARG L1347 *********************** 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 135 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 98 time to evaluate : 1.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 350 ASP cc_start: 0.5973 (p0) cc_final: 0.5111 (t0) REVERT: L 1598 LYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7414 (pptt) outliers start: 37 outliers final: 28 residues processed: 127 average time/residue: 0.1921 time to fit residues: 38.2722 Evaluate side-chains 113 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 84 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 279 THR Chi-restraints excluded: chain L residue 379 ASN Chi-restraints excluded: chain L residue 449 ILE 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 830 ASN Chi-restraints excluded: chain L residue 857 VAL Chi-restraints excluded: chain L residue 871 TYR Chi-restraints excluded: chain L residue 1055 ASN 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 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 1513 PHE Chi-restraints excluded: chain L residue 1524 SER Chi-restraints excluded: chain L residue 1580 ILE Chi-restraints excluded: chain L residue 1598 LYS Chi-restraints excluded: chain L residue 1624 LEU Chi-restraints excluded: chain L residue 1628 CYS 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 120 optimal weight: 0.8980 chunk 26 optimal weight: 20.0000 chunk 78 optimal weight: 0.1980 chunk 32 optimal weight: 2.9990 chunk 133 optimal weight: 8.9990 chunk 110 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 11 optimal weight: 0.0570 chunk 44 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 128 optimal weight: 5.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 881 ASN L1087 ASN ** L1299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.4784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 11322 Z= 0.142 Angle : 0.573 11.735 15269 Z= 0.282 Chirality : 0.038 0.244 1735 Planarity : 0.003 0.039 1928 Dihedral : 3.963 16.702 1490 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 2.14 % Allowed : 18.00 % 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: -1.06 (0.23), residues: 1358 helix: 1.08 (0.20), residues: 720 sheet: -1.31 (0.60), residues: 67 loop : -3.16 (0.22), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 395 HIS 0.009 0.001 HIS L1234 PHE 0.016 0.001 PHE L1058 TYR 0.010 0.001 TYR L 471 ARG 0.004 0.000 ARG L1477 *********************** 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 120 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 93 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 302 LEU cc_start: 0.7227 (tp) cc_final: 0.6883 (mt) REVERT: L 350 ASP cc_start: 0.5953 (p0) cc_final: 0.5180 (t0) REVERT: L 395 TRP cc_start: 0.7353 (t-100) cc_final: 0.7136 (t60) REVERT: L 692 MET cc_start: 0.5314 (tpt) cc_final: 0.5061 (tpt) outliers start: 27 outliers final: 24 residues processed: 113 average time/residue: 0.2032 time to fit residues: 35.5824 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 : 1.255 ------------------------------------------------------------------------------- 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 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 882 LEU Chi-restraints excluded: chain L residue 1055 ASN Chi-restraints excluded: chain L residue 1122 SER 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 1624 LEU Chi-restraints excluded: chain L residue 1639 ILE Chi-restraints excluded: chain L residue 1661 VAL Chi-restraints excluded: chain L residue 1810 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 15 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 112 optimal weight: 10.0000 chunk 74 optimal weight: 1.9990 chunk 133 optimal weight: 0.0060 chunk 83 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 overall best weight: 0.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 824 ASN L1234 HIS L1299 ASN L1586 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 moved from start: 0.4949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 11322 Z= 0.148 Angle : 0.568 11.767 15269 Z= 0.277 Chirality : 0.038 0.235 1735 Planarity : 0.003 0.038 1928 Dihedral : 3.892 16.251 1490 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 2.54 % Allowed : 17.68 % Favored : 79.78 % 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: -0.96 (0.23), residues: 1358 helix: 1.19 (0.20), residues: 713 sheet: -1.32 (0.57), residues: 76 loop : -3.11 (0.22), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 395 HIS 0.006 0.001 HIS L 441 PHE 0.012 0.001 PHE L 329 TYR 0.012 0.001 TYR L1688 ARG 0.006 0.000 ARG L 695 *********************** 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 120 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 88 time to evaluate : 1.495 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 302 LEU cc_start: 0.7154 (tp) cc_final: 0.6831 (mt) REVERT: L 350 ASP cc_start: 0.6015 (p0) cc_final: 0.5195 (t0) REVERT: L 395 TRP cc_start: 0.7338 (t-100) cc_final: 0.7118 (t60) REVERT: L 700 LEU cc_start: 0.8568 (tt) cc_final: 0.8356 (mm) REVERT: L 1479 MET cc_start: 0.5520 (tpp) cc_final: 0.5138 (mmt) outliers start: 32 outliers final: 28 residues processed: 111 average time/residue: 0.2009 time to fit residues: 36.1719 Evaluate side-chains 112 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 84 time to evaluate : 1.445 ------------------------------------------------------------------------------- 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 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 53 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 25 optimal weight: 0.4980 chunk 84 optimal weight: 0.7980 chunk 90 optimal weight: 4.9990 chunk 65 optimal weight: 0.0770 chunk 12 optimal weight: 7.9990 chunk 104 optimal weight: 0.3980 chunk 120 optimal weight: 10.0000 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L1234 HIS L1449 GLN L1549 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.4997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11322 Z= 0.136 Angle : 0.570 14.124 15269 Z= 0.276 Chirality : 0.038 0.303 1735 Planarity : 0.003 0.038 1928 Dihedral : 3.810 16.088 1490 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 2.38 % Allowed : 18.16 % Favored : 79.46 % 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: -0.85 (0.23), residues: 1358 helix: 1.27 (0.21), residues: 707 sheet: -1.22 (0.57), residues: 76 loop : -3.01 (0.22), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 395 HIS 0.005 0.001 HIS L1234 PHE 0.016 0.001 PHE L1058 TYR 0.008 0.001 TYR L1688 ARG 0.003 0.000 ARG L 695 *********************** 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 119 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 89 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 302 LEU cc_start: 0.7096 (tp) cc_final: 0.6808 (mt) REVERT: L 313 GLU cc_start: 0.6784 (OUTLIER) cc_final: 0.6240 (mp0) REVERT: L 350 ASP cc_start: 0.6046 (p0) cc_final: 0.5256 (t0) REVERT: L 395 TRP cc_start: 0.7305 (t-100) cc_final: 0.7096 (t60) REVERT: L 1479 MET cc_start: 0.5665 (tpp) cc_final: 0.5304 (mmt) REVERT: L 1558 MET cc_start: 0.6260 (mmm) cc_final: 0.5854 (tpp) outliers start: 30 outliers final: 26 residues processed: 111 average time/residue: 0.1936 time to fit residues: 34.4058 Evaluate side-chains 111 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 84 time to evaluate : 1.289 ------------------------------------------------------------------------------- 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 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 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 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 1624 LEU Chi-restraints excluded: chain L residue 1639 ILE Chi-restraints excluded: chain L residue 1661 VAL Chi-restraints excluded: chain L residue 1810 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 127 optimal weight: 4.9990 chunk 116 optimal weight: 0.0570 chunk 123 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 97 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 112 optimal weight: 6.9990 chunk 117 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 overall best weight: 1.3902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L1087 ASN L1234 HIS ** L1549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 moved from start: 0.5191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11322 Z= 0.176 Angle : 0.591 14.754 15269 Z= 0.288 Chirality : 0.039 0.287 1735 Planarity : 0.003 0.037 1928 Dihedral : 3.862 16.311 1490 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 2.22 % Allowed : 18.56 % Favored : 79.22 % 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: -0.90 (0.23), residues: 1358 helix: 1.22 (0.20), residues: 713 sheet: -1.38 (0.55), residues: 82 loop : -3.05 (0.22), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 395 HIS 0.006 0.001 HIS L1234 PHE 0.010 0.001 PHE L1303 TYR 0.015 0.001 TYR L1688 ARG 0.003 0.000 ARG L1498 *********************** 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 117 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 89 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 302 LEU cc_start: 0.7152 (tp) cc_final: 0.6823 (mt) REVERT: L 325 TYR cc_start: 0.5713 (m-80) cc_final: 0.5440 (m-80) REVERT: L 350 ASP cc_start: 0.6176 (p0) cc_final: 0.5330 (t0) REVERT: L 1479 MET cc_start: 0.5493 (tpp) cc_final: 0.5144 (mmt) outliers start: 28 outliers final: 27 residues processed: 109 average time/residue: 0.1887 time to fit residues: 33.9281 Evaluate side-chains 111 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 84 time to evaluate : 1.396 ------------------------------------------------------------------------------- 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 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 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 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 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 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 79 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 137 optimal weight: 9.9990 chunk 126 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 11 optimal weight: 8.9990 chunk 84 optimal weight: 0.0270 chunk 67 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 overall best weight: 1.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 322 GLN L1234 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.5384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 11322 Z= 0.210 Angle : 0.636 16.553 15269 Z= 0.306 Chirality : 0.040 0.272 1735 Planarity : 0.003 0.036 1928 Dihedral : 3.975 16.406 1490 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 2.22 % Allowed : 19.03 % Favored : 78.75 % 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: -0.96 (0.23), residues: 1358 helix: 1.16 (0.20), residues: 715 sheet: -1.42 (0.55), residues: 82 loop : -3.07 (0.22), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP L 395 HIS 0.009 0.001 HIS L1234 PHE 0.016 0.001 PHE L1058 TYR 0.019 0.001 TYR L1688 ARG 0.004 0.000 ARG L1498 ********************** 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 116 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 88 time to evaluate : 1.388 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 325 TYR cc_start: 0.5830 (m-80) cc_final: 0.5493 (m-80) REVERT: L 350 ASP cc_start: 0.6161 (p0) cc_final: 0.5294 (t0) REVERT: L 1479 MET cc_start: 0.5603 (tpp) cc_final: 0.5254 (mmt) outliers start: 28 outliers final: 27 residues processed: 107 average time/residue: 0.1825 time to fit residues: 32.0565 Evaluate side-chains 111 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 84 time to evaluate : 1.345 ------------------------------------------------------------------------------- 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 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 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 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 1559 VAL Chi-restraints excluded: chain L residue 1624 LEU Chi-restraints excluded: chain L residue 1639 ILE 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 33 optimal weight: 8.9990 chunk 100 optimal weight: 0.0270 chunk 16 optimal weight: 0.0970 chunk 30 optimal weight: 7.9990 chunk 109 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 112 optimal weight: 6.9990 chunk 13 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 overall best weight: 1.0038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L1234 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.099541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.079973 restraints weight = 42243.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.080697 restraints weight = 25583.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.081380 restraints weight = 18879.658| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.5445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 11322 Z= 0.153 Angle : 0.610 14.200 15269 Z= 0.291 Chirality : 0.039 0.262 1735 Planarity : 0.003 0.038 1928 Dihedral : 3.869 16.250 1490 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 2.14 % Allowed : 19.19 % Favored : 78.67 % 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: -0.84 (0.23), residues: 1358 helix: 1.25 (0.20), residues: 716 sheet: -1.29 (0.55), residues: 82 loop : -3.02 (0.22), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP L 395 HIS 0.011 0.001 HIS L1234 PHE 0.011 0.001 PHE L 421 TYR 0.012 0.001 TYR L 574 ARG 0.006 0.000 ARG L1498 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2094.27 seconds wall clock time: 39 minutes 45.46 seconds (2385.46 seconds total)