Starting phenix.real_space_refine on Fri Jul 3 01:01:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qls_53233/07_2026/9qls_53233.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qls_53233/07_2026/9qls_53233.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9qls_53233/07_2026/9qls_53233.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qls_53233/07_2026/9qls_53233.map" model { file = "/net/cci-nas-00/data/ceres_data/9qls_53233/07_2026/9qls_53233.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qls_53233/07_2026/9qls_53233.cif" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 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: 5 Type Number sf(0) Gaussians Ca 6 9.91 5 S 56 5.16 5 C 7114 2.51 5 N 1898 2.21 5 O 2026 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11100 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 11094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1370, 11094 Classifications: {'peptide': 1370} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 4, 'PTRANS': 86, 'TRANS': 1279} Chain breaks: 11 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 0 Ad-hoc single atom residues: {' CA': 6} Chain breaks: 6 Time building chain proxies: 2.45, per 1000 atoms: 0.22 Number of scatterers: 11100 At special positions: 0 Unit cell: (102.24, 149.04, 92.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 6 19.99 S 56 16.00 O 2026 8.00 N 1898 7.00 C 7114 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 420.7 milliseconds 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2576 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 19 sheets defined 18.0% alpha, 27.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 273 through 278 Processing helix chain 'A' and resid 305 through 310 Processing helix chain 'A' and resid 311 through 315 removed outlier: 3.633A pdb=" N ALA A 315 " --> pdb=" O PRO A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 332 removed outlier: 3.708A pdb=" N GLY A 332 " --> pdb=" O PHE A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 485 No H-bonds generated for 'chain 'A' and resid 483 through 485' Processing helix chain 'A' and resid 539 through 545 removed outlier: 3.567A pdb=" N GLY A 545 " --> pdb=" O LEU A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 582 removed outlier: 3.912A pdb=" N LEU A 581 " --> pdb=" O ALA A 577 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ARG A 582 " --> pdb=" O ASP A 578 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 577 through 582' Processing helix chain 'A' and resid 583 through 586 Processing helix chain 'A' and resid 668 through 698 removed outlier: 3.550A pdb=" N THR A 674 " --> pdb=" O HIS A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 721 removed outlier: 3.646A pdb=" N GLU A 715 " --> pdb=" O GLN A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 761 Processing helix chain 'A' and resid 764 through 783 removed outlier: 3.735A pdb=" N GLN A 771 " --> pdb=" O ALA A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 814 Processing helix chain 'A' and resid 863 through 865 No H-bonds generated for 'chain 'A' and resid 863 through 865' Processing helix chain 'A' and resid 866 through 871 removed outlier: 4.192A pdb=" N PHE A 870 " --> pdb=" O GLU A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 918 removed outlier: 3.604A pdb=" N SER A 917 " --> pdb=" O PRO A 914 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE A 918 " --> pdb=" O LYS A 915 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 914 through 918' Processing helix chain 'A' and resid 1104 through 1112 removed outlier: 3.833A pdb=" N ALA A1107 " --> pdb=" O THR A1104 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA A1108 " --> pdb=" O GLY A1105 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL A1109 " --> pdb=" O PRO A1106 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N PHE A1110 " --> pdb=" O ALA A1107 " (cutoff:3.500A) Processing helix chain 'A' and resid 1213 through 1220 Processing helix chain 'A' and resid 1476 through 1486 removed outlier: 3.753A pdb=" N LYS A1480 " --> pdb=" O ASP A1476 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE A1485 " --> pdb=" O PHE A1481 " (cutoff:3.500A) Processing helix chain 'A' and resid 1487 through 1492 Processing helix chain 'A' and resid 1493 through 1495 No H-bonds generated for 'chain 'A' and resid 1493 through 1495' Processing helix chain 'A' and resid 1508 through 1512 removed outlier: 3.671A pdb=" N ASN A1511 " --> pdb=" O GLN A1508 " (cutoff:3.500A) Processing helix chain 'A' and resid 1613 through 1618 removed outlier: 3.635A pdb=" N TYR A1618 " --> pdb=" O GLN A1615 " (cutoff:3.500A) Processing helix chain 'A' and resid 1666 through 1672 removed outlier: 3.808A pdb=" N LEU A1670 " --> pdb=" O LEU A1666 " (cutoff:3.500A) Processing helix chain 'A' and resid 1697 through 1709 Processing helix chain 'A' and resid 1731 through 1733 No H-bonds generated for 'chain 'A' and resid 1731 through 1733' Processing helix chain 'A' and resid 1745 through 1758 Processing sheet with id=AA1, first strand: chain 'A' and resid 264 through 271 removed outlier: 6.730A pdb=" N LYS A 338 " --> pdb=" O ILE A 227 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N GLY A 229 " --> pdb=" O TYR A 336 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N TYR A 336 " --> pdb=" O GLY A 229 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 239 through 245 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 248 through 249 current: chain 'A' and resid 295 through 299 Processing sheet with id=AA3, first strand: chain 'A' and resid 518 through 527 removed outlier: 6.258A pdb=" N LEU A 558 " --> pdb=" O PRO A 520 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N TYR A 522 " --> pdb=" O LEU A 556 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU A 556 " --> pdb=" O TYR A 522 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ASN A 524 " --> pdb=" O GLY A 554 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N GLY A 554 " --> pdb=" O ASN A 524 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N TYR A 526 " --> pdb=" O TYR A 552 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N TYR A 552 " --> pdb=" O TYR A 526 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ARG A 555 " --> pdb=" O ALA A 388 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ALA A 388 " --> pdb=" O ARG A 555 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N LEU A 557 " --> pdb=" O PHE A 386 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ARG A 387 " --> pdb=" O TRP A 442 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N TRP A 442 " --> pdb=" O ARG A 387 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS A 571 " --> pdb=" O THR A 447 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 427 through 430 removed outlier: 6.269A pdb=" N MET A 459 " --> pdb=" O TYR A 479 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N TYR A 479 " --> pdb=" O MET A 459 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE A 461 " --> pdb=" O THR A 477 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N THR A 477 " --> pdb=" O ILE A 461 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE A 463 " --> pdb=" O VAL A 475 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 832 through 835 removed outlier: 6.159A pdb=" N GLN A 851 " --> pdb=" O ALA A 601 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ALA A 601 " --> pdb=" O GLN A 851 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ARG A 853 " --> pdb=" O TYR A 599 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N SER A 600 " --> pdb=" O VAL A 655 " (cutoff:3.500A) removed outlier: 11.464A pdb=" N VAL A 655 " --> pdb=" O SER A 600 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ILE A1142 " --> pdb=" O VAL A 658 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 611 through 617 removed outlier: 5.873A pdb=" N ILE A 793 " --> pdb=" O ARG A 808 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ARG A 808 " --> pdb=" O ILE A 793 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE A 795 " --> pdb=" O TYR A 806 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N TYR A 806 " --> pdb=" O ILE A 795 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N MET A 797 " --> pdb=" O VAL A 804 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 641 through 642 Processing sheet with id=AA8, first strand: chain 'A' and resid 879 through 886 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 904 through 905 current: chain 'A' and resid 1079 through 1080 Processing sheet with id=AA9, first strand: chain 'A' and resid 924 through 926 Processing sheet with id=AB1, first strand: chain 'A' and resid 948 through 951 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 948 through 951 current: chain 'A' and resid 1037 through 1048 No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 1148 through 1162 removed outlier: 6.660A pdb=" N ASN A1150 " --> pdb=" O GLU A1209 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLU A1209 " --> pdb=" O ASN A1150 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N TYR A1152 " --> pdb=" O GLU A1207 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU A1207 " --> pdb=" O TYR A1152 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1201 through 1210 current: chain 'A' and resid 1266 through 1278 Processing sheet with id=AB3, first strand: chain 'A' and resid 1184 through 1187 removed outlier: 3.807A pdb=" N GLY A1241 " --> pdb=" O LEU A1228 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ASP A1230 " --> pdb=" O PHE A1239 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N PHE A1239 " --> pdb=" O ASP A1230 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1313 through 1315 removed outlier: 3.634A pdb=" N GLU A1315 " --> pdb=" O ILE A1318 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1384 through 1391 removed outlier: 5.281A pdb=" N ILE A1334 " --> pdb=" O TYR A1552 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N TYR A1552 " --> pdb=" O ILE A1334 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILE A1336 " --> pdb=" O LYS A1550 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N LYS A1550 " --> pdb=" O ILE A1336 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N ALA A1338 " --> pdb=" O LEU A1548 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N LEU A1548 " --> pdb=" O ALA A1338 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY A1340 " --> pdb=" O LYS A1546 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY A1543 " --> pdb=" O LEU A1527 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1364 through 1370 removed outlier: 4.266A pdb=" N CYS A1361 " --> pdb=" O GLN A1364 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N LEU A1357 " --> pdb=" O SER A1368 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N VAL A1370 " --> pdb=" O PRO A1355 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N THR A1402 " --> pdb=" O GLU A1360 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ASP A1407 " --> pdb=" O VAL A1416 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N VAL A1416 " --> pdb=" O ASP A1407 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1503 through 1505 Processing sheet with id=AB8, first strand: chain 'A' and resid 1629 through 1636 removed outlier: 3.717A pdb=" N ILE A1584 " --> pdb=" O LYS A1629 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL A1585 " --> pdb=" O GLN A1784 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N GLN A1784 " --> pdb=" O VAL A1585 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N ALA A1587 " --> pdb=" O LYS A1782 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N LYS A1782 " --> pdb=" O ALA A1587 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N GLY A1781 " --> pdb=" O LEU A1770 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1610 through 1611 removed outlier: 3.931A pdb=" N SER A1606 " --> pdb=" O LYS A1644 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N LYS A1644 " --> pdb=" O SER A1606 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LEU A1643 " --> pdb=" O VAL A1663 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N VAL A1663 " --> pdb=" O LEU A1643 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ILE A1645 " --> pdb=" O GLU A1661 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N GLU A1661 " --> pdb=" O ILE A1645 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N LEU A1647 " --> pdb=" O ILE A1659 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1720 through 1723 303 hydrogen bonds defined for protein. 804 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.03 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3597 1.34 - 1.46: 2633 1.46 - 1.58: 5067 1.58 - 1.70: 0 1.70 - 1.82: 82 Bond restraints: 11379 Sorted by residual: bond pdb=" C ARG A1697 " pdb=" N PRO A1698 " ideal model delta sigma weight residual 1.335 1.370 -0.035 1.28e-02 6.10e+03 7.47e+00 bond pdb=" CA ARG A1413 " pdb=" C ARG A1413 " ideal model delta sigma weight residual 1.522 1.557 -0.034 1.43e-02 4.89e+03 5.78e+00 bond pdb=" CB ASP A1381 " pdb=" CG ASP A1381 " ideal model delta sigma weight residual 1.516 1.574 -0.058 2.50e-02 1.60e+03 5.47e+00 bond pdb=" CB ASP A 706 " pdb=" CG ASP A 706 " ideal model delta sigma weight residual 1.516 1.567 -0.051 2.50e-02 1.60e+03 4.11e+00 bond pdb=" N MET A 626 " pdb=" CA MET A 626 " ideal model delta sigma weight residual 1.457 1.482 -0.025 1.29e-02 6.01e+03 3.76e+00 ... (remaining 11374 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 15121 2.85 - 5.70: 247 5.70 - 8.55: 44 8.55 - 11.40: 12 11.40 - 14.25: 6 Bond angle restraints: 15430 Sorted by residual: angle pdb=" C SER A1767 " pdb=" N ARG A1768 " pdb=" CA ARG A1768 " ideal model delta sigma weight residual 120.83 128.96 -8.13 1.43e+00 4.89e-01 3.23e+01 angle pdb=" N PHE A 262 " pdb=" CA PHE A 262 " pdb=" C PHE A 262 " ideal model delta sigma weight residual 111.11 117.02 -5.91 1.20e+00 6.94e-01 2.42e+01 angle pdb=" C LEU A 261 " pdb=" N PHE A 262 " pdb=" CA PHE A 262 " ideal model delta sigma weight residual 120.54 126.60 -6.06 1.35e+00 5.49e-01 2.02e+01 angle pdb=" CA ASP A1381 " pdb=" CB ASP A1381 " pdb=" CG ASP A1381 " ideal model delta sigma weight residual 112.60 116.89 -4.29 1.00e+00 1.00e+00 1.84e+01 angle pdb=" CA MET A 451 " pdb=" CB MET A 451 " pdb=" CG MET A 451 " ideal model delta sigma weight residual 114.10 122.63 -8.53 2.00e+00 2.50e-01 1.82e+01 ... (remaining 15425 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 6037 17.82 - 35.65: 621 35.65 - 53.47: 144 53.47 - 71.30: 22 71.30 - 89.12: 17 Dihedral angle restraints: 6841 sinusoidal: 2850 harmonic: 3991 Sorted by residual: dihedral pdb=" CA GLU A1013 " pdb=" C GLU A1013 " pdb=" N TYR A1014 " pdb=" CA TYR A1014 " ideal model delta harmonic sigma weight residual 180.00 -152.55 -27.45 0 5.00e+00 4.00e-02 3.01e+01 dihedral pdb=" CA ARG A1342 " pdb=" C ARG A1342 " pdb=" N ASN A1343 " pdb=" CA ASN A1343 " ideal model delta harmonic sigma weight residual 180.00 156.84 23.16 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA GLU A 978 " pdb=" C GLU A 978 " pdb=" N LYS A 979 " pdb=" CA LYS A 979 " ideal model delta harmonic sigma weight residual -180.00 -158.58 -21.42 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 6838 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1297 0.055 - 0.110: 262 0.110 - 0.166: 85 0.166 - 0.221: 9 0.221 - 0.276: 3 Chirality restraints: 1656 Sorted by residual: chirality pdb=" CB ILE A1208 " pdb=" CA ILE A1208 " pdb=" CG1 ILE A1208 " pdb=" CG2 ILE A1208 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CB ILE A1401 " pdb=" CA ILE A1401 " pdb=" CG1 ILE A1401 " pdb=" CG2 ILE A1401 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CG LEU A 341 " pdb=" CB LEU A 341 " pdb=" CD1 LEU A 341 " pdb=" CD2 LEU A 341 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 1653 not shown) Planarity restraints: 1995 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A1094 " 0.030 2.00e-02 2.50e+03 2.47e-02 1.52e+01 pdb=" CG TRP A1094 " -0.067 2.00e-02 2.50e+03 pdb=" CD1 TRP A1094 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP A1094 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A1094 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A1094 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A1094 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1094 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1094 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A1094 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 775 " 0.024 2.00e-02 2.50e+03 2.43e-02 1.48e+01 pdb=" CG TRP A 775 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 TRP A 775 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP A 775 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 775 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 775 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 775 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 775 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 775 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 775 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 608 " 0.015 2.00e-02 2.50e+03 3.00e-02 8.97e+00 pdb=" CG ASP A 608 " -0.052 2.00e-02 2.50e+03 pdb=" OD1 ASP A 608 " 0.019 2.00e-02 2.50e+03 pdb=" OD2 ASP A 608 " 0.018 2.00e-02 2.50e+03 ... (remaining 1992 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 3875 2.91 - 3.40: 10281 3.40 - 3.90: 18655 3.90 - 4.40: 20434 4.40 - 4.90: 34576 Nonbonded interactions: 87821 Sorted by model distance: nonbonded pdb=" OD2 ASP A1168 " pdb="CA CA A2101 " model vdw 2.406 3.250 nonbonded pdb=" OD1 ASP A1232 " pdb="CA CA A2101 " model vdw 2.409 3.250 nonbonded pdb=" OD2 ASP A1174 " pdb="CA CA A2101 " model vdw 2.424 3.250 nonbonded pdb=" OD1 ASP A1232 " pdb="CA CA A2104 " model vdw 2.427 3.250 nonbonded pdb=" OD2 ASP A1232 " pdb="CA CA A2104 " model vdw 2.436 3.250 ... (remaining 87816 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: 7.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.330 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 11379 Z= 0.205 Angle : 0.982 14.252 15430 Z= 0.528 Chirality : 0.052 0.276 1656 Planarity : 0.008 0.085 1995 Dihedral : 15.524 89.122 4265 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.75 % Favored : 95.17 % Rotamer: Outliers : 1.57 % Allowed : 14.13 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.53 (0.21), residues: 1346 helix: -3.81 (0.18), residues: 186 sheet: -1.20 (0.25), residues: 428 loop : -1.31 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1693 TYR 0.018 0.002 TYR A 552 PHE 0.033 0.002 PHE A 954 TRP 0.067 0.003 TRP A1094 HIS 0.004 0.001 HIS A 812 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.20 (11379) covalent geometry : angle 0.98245 / 0.53 (15430) hydrogen bonds : bond 0.24973 / 17.07 ( 303) hydrogen bonds : angle 10.48950 / 7.26 ( 804) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 173 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 MET cc_start: 0.7099 (pmm) cc_final: 0.5548 (ttt) REVERT: A 309 TYR cc_start: 0.7797 (OUTLIER) cc_final: 0.7194 (t80) REVERT: A 827 ASN cc_start: 0.8325 (m-40) cc_final: 0.7662 (m110) REVERT: A 844 PRO cc_start: 0.7407 (Cg_exo) cc_final: 0.6995 (Cg_endo) REVERT: A 848 MET cc_start: 0.6843 (tpp) cc_final: 0.6236 (tpp) REVERT: A 1159 TYR cc_start: 0.7373 (t80) cc_final: 0.7136 (t80) REVERT: A 1390 MET cc_start: 0.8893 (mmp) cc_final: 0.8618 (mpp) REVERT: A 1391 LEU cc_start: 0.8091 (mt) cc_final: 0.7795 (mt) REVERT: A 1419 GLN cc_start: 0.8192 (mp10) cc_final: 0.7883 (pp30) REVERT: A 1630 MET cc_start: 0.6796 (OUTLIER) cc_final: 0.6070 (mmt) REVERT: A 1725 ASP cc_start: 0.7001 (m-30) cc_final: 0.6264 (p0) outliers start: 19 outliers final: 10 residues processed: 185 average time/residue: 0.1175 time to fit residues: 29.6321 Evaluate side-chains 117 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 919 ARG Chi-restraints excluded: chain A residue 946 HIS Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1357 LEU Chi-restraints excluded: chain A residue 1403 VAL Chi-restraints excluded: chain A residue 1630 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 ASN ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN A 771 GLN A 812 HIS A1753 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.146619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.102037 restraints weight = 35048.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.100836 restraints weight = 20238.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.101529 restraints weight = 17074.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.102181 restraints weight = 13610.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.101981 restraints weight = 12760.358| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.078 11379 Z= 0.414 Angle : 0.889 12.886 15430 Z= 0.458 Chirality : 0.051 0.234 1656 Planarity : 0.007 0.069 1995 Dihedral : 6.804 48.924 1521 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.83 % Favored : 95.10 % Rotamer: Outliers : 4.46 % Allowed : 15.87 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.22), residues: 1346 helix: -0.73 (0.37), residues: 171 sheet: -1.35 (0.24), residues: 437 loop : -0.95 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1251 TYR 0.023 0.003 TYR A1157 PHE 0.030 0.003 PHE A1239 TRP 0.047 0.002 TRP A 775 HIS 0.012 0.002 HIS A 746 Details of bonding type rmsd/Z covalent geometry : bond 0.00932 / 0.41 (11379) covalent geometry : angle 0.88905 / 0.46 (15430) hydrogen bonds : bond 0.04944 / 3.52 ( 303) hydrogen bonds : angle 7.54061 / 5.18 ( 804) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 97 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 552 TYR cc_start: 0.8721 (t80) cc_final: 0.8420 (t80) REVERT: A 827 ASN cc_start: 0.8654 (m-40) cc_final: 0.8372 (m-40) REVERT: A 832 GLN cc_start: 0.8371 (tt0) cc_final: 0.8171 (tt0) REVERT: A 848 MET cc_start: 0.7950 (tpp) cc_final: 0.7659 (tpp) REVERT: A 953 VAL cc_start: 0.6021 (OUTLIER) cc_final: 0.5257 (t) REVERT: A 1039 ARG cc_start: 0.5202 (OUTLIER) cc_final: 0.4999 (mtt90) REVERT: A 1387 MET cc_start: 0.1075 (ptt) cc_final: 0.0796 (ptt) REVERT: A 1390 MET cc_start: 0.8694 (mmp) cc_final: 0.8484 (mmm) REVERT: A 1404 LYS cc_start: 0.7941 (OUTLIER) cc_final: 0.7442 (mmtt) REVERT: A 1419 GLN cc_start: 0.8806 (mp10) cc_final: 0.7908 (tm-30) REVERT: A 1725 ASP cc_start: 0.7016 (m-30) cc_final: 0.6691 (t0) REVERT: A 1766 GLU cc_start: 0.8467 (mp0) cc_final: 0.8206 (pm20) outliers start: 54 outliers final: 33 residues processed: 137 average time/residue: 0.1075 time to fit residues: 20.9880 Evaluate side-chains 116 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 80 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 622 ASN Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 919 ARG Chi-restraints excluded: chain A residue 946 HIS Chi-restraints excluded: chain A residue 949 PHE Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1109 VAL Chi-restraints excluded: chain A residue 1204 ILE Chi-restraints excluded: chain A residue 1287 ILE Chi-restraints excluded: chain A residue 1359 VAL Chi-restraints excluded: chain A residue 1403 VAL Chi-restraints excluded: chain A residue 1404 LYS Chi-restraints excluded: chain A residue 1406 ILE Chi-restraints excluded: chain A residue 1580 VAL Chi-restraints excluded: chain A residue 1600 ASP Chi-restraints excluded: chain A residue 1753 HIS Chi-restraints excluded: chain A residue 1785 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 3 optimal weight: 9.9990 chunk 100 optimal weight: 10.0000 chunk 28 optimal weight: 0.8980 chunk 67 optimal weight: 20.0000 chunk 54 optimal weight: 1.9990 chunk 98 optimal weight: 7.9990 chunk 48 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 103 optimal weight: 6.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 636 GLN A1802 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.149041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.102320 restraints weight = 35095.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.104801 restraints weight = 18059.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.105493 restraints weight = 11517.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.105770 restraints weight = 9761.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.105747 restraints weight = 9659.967| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11379 Z= 0.173 Angle : 0.669 12.099 15430 Z= 0.334 Chirality : 0.045 0.186 1656 Planarity : 0.005 0.049 1995 Dihedral : 5.924 42.997 1514 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 4.63 % Allowed : 17.27 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.23), residues: 1346 helix: 0.28 (0.40), residues: 173 sheet: -1.32 (0.24), residues: 437 loop : -0.87 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1251 TYR 0.014 0.001 TYR A 739 PHE 0.009 0.001 PHE A1801 TRP 0.029 0.001 TRP A 999 HIS 0.008 0.001 HIS A 746 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (11379) covalent geometry : angle 0.66857 / 0.33 (15430) hydrogen bonds : bond 0.03763 / 2.66 ( 303) hydrogen bonds : angle 6.73775 / 4.60 ( 804) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 98 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 MET cc_start: 0.8576 (pmm) cc_final: 0.8331 (pmm) REVERT: A 309 TYR cc_start: 0.8270 (OUTLIER) cc_final: 0.7969 (t80) REVERT: A 827 ASN cc_start: 0.8464 (m-40) cc_final: 0.7932 (m-40) REVERT: A 832 GLN cc_start: 0.8258 (tt0) cc_final: 0.7912 (tt0) REVERT: A 848 MET cc_start: 0.7909 (tpp) cc_final: 0.7532 (tpt) REVERT: A 968 MET cc_start: 0.3551 (mtp) cc_final: 0.3326 (mtm) REVERT: A 1159 TYR cc_start: 0.8083 (t80) cc_final: 0.7879 (t80) REVERT: A 1360 GLU cc_start: 0.8864 (mm-30) cc_final: 0.8469 (mp0) REVERT: A 1366 VAL cc_start: 0.3068 (OUTLIER) cc_final: 0.2726 (t) REVERT: A 1387 MET cc_start: 0.1101 (ptt) cc_final: 0.0603 (ptt) REVERT: A 1419 GLN cc_start: 0.8706 (mp10) cc_final: 0.7808 (tm-30) REVERT: A 1725 ASP cc_start: 0.7544 (m-30) cc_final: 0.7305 (t0) REVERT: A 1766 GLU cc_start: 0.8579 (mp0) cc_final: 0.8225 (pm20) outliers start: 56 outliers final: 32 residues processed: 141 average time/residue: 0.1113 time to fit residues: 22.1578 Evaluate side-chains 122 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 88 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 919 ARG Chi-restraints excluded: chain A residue 946 HIS Chi-restraints excluded: chain A residue 949 PHE Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1104 THR Chi-restraints excluded: chain A residue 1210 ILE Chi-restraints excluded: chain A residue 1287 ILE Chi-restraints excluded: chain A residue 1359 VAL Chi-restraints excluded: chain A residue 1366 VAL Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain A residue 1402 THR Chi-restraints excluded: chain A residue 1403 VAL Chi-restraints excluded: chain A residue 1406 ILE Chi-restraints excluded: chain A residue 1663 VAL Chi-restraints excluded: chain A residue 1753 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 133 optimal weight: 9.9990 chunk 120 optimal weight: 20.0000 chunk 49 optimal weight: 0.7980 chunk 109 optimal weight: 0.0770 chunk 74 optimal weight: 10.0000 chunk 58 optimal weight: 0.0170 chunk 6 optimal weight: 0.7980 chunk 70 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 60 optimal weight: 20.0000 chunk 8 optimal weight: 5.9990 overall best weight: 0.9378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 691 GLN A1753 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.152660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.108159 restraints weight = 37900.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.109369 restraints weight = 21112.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.110917 restraints weight = 14402.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.111030 restraints weight = 11364.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.110846 restraints weight = 10798.299| |-----------------------------------------------------------------------------| r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11379 Z= 0.132 Angle : 0.628 12.613 15430 Z= 0.312 Chirality : 0.045 0.156 1656 Planarity : 0.005 0.050 1995 Dihedral : 5.452 42.106 1510 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 4.13 % Allowed : 17.44 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.23), residues: 1346 helix: 0.64 (0.40), residues: 173 sheet: -1.21 (0.24), residues: 440 loop : -0.76 (0.23), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A1251 TYR 0.032 0.001 TYR A 552 PHE 0.015 0.001 PHE A 878 TRP 0.016 0.001 TRP A 775 HIS 0.007 0.001 HIS A 746 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (11379) covalent geometry : angle 0.62816 / 0.31 (15430) hydrogen bonds : bond 0.03270 / 2.30 ( 303) hydrogen bonds : angle 6.25039 / 4.27 ( 804) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 90 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 309 TYR cc_start: 0.8309 (OUTLIER) cc_final: 0.8010 (t80) REVERT: A 827 ASN cc_start: 0.8520 (m-40) cc_final: 0.8256 (m-40) REVERT: A 832 GLN cc_start: 0.8259 (tt0) cc_final: 0.7990 (tt0) REVERT: A 848 MET cc_start: 0.7897 (tpp) cc_final: 0.7562 (tpt) REVERT: A 1159 TYR cc_start: 0.7881 (t80) cc_final: 0.7546 (t80) REVERT: A 1366 VAL cc_start: 0.3053 (OUTLIER) cc_final: 0.2805 (t) REVERT: A 1387 MET cc_start: 0.1510 (ptt) cc_final: 0.1288 (ppp) REVERT: A 1419 GLN cc_start: 0.8643 (mp10) cc_final: 0.7770 (tm-30) REVERT: A 1785 MET cc_start: 0.5294 (tmm) cc_final: 0.4735 (tmm) outliers start: 50 outliers final: 27 residues processed: 129 average time/residue: 0.1065 time to fit residues: 19.6161 Evaluate side-chains 113 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 84 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 919 ARG Chi-restraints excluded: chain A residue 946 HIS Chi-restraints excluded: chain A residue 949 PHE Chi-restraints excluded: chain A residue 1210 ILE Chi-restraints excluded: chain A residue 1227 GLU Chi-restraints excluded: chain A residue 1287 ILE Chi-restraints excluded: chain A residue 1359 VAL Chi-restraints excluded: chain A residue 1366 VAL Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain A residue 1402 THR Chi-restraints excluded: chain A residue 1663 VAL Chi-restraints excluded: chain A residue 1711 VAL Chi-restraints excluded: chain A residue 1753 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 130 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 113 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 73 optimal weight: 0.0050 chunk 35 optimal weight: 0.9990 chunk 1 optimal weight: 8.9990 overall best weight: 0.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 636 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.149860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.107565 restraints weight = 35000.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.105636 restraints weight = 22962.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.105702 restraints weight = 20372.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.106659 restraints weight = 14810.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.106793 restraints weight = 12834.635| |-----------------------------------------------------------------------------| r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11379 Z= 0.135 Angle : 0.634 13.249 15430 Z= 0.313 Chirality : 0.045 0.148 1656 Planarity : 0.005 0.052 1995 Dihedral : 5.342 42.377 1509 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.47 % Allowed : 17.60 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.23), residues: 1346 helix: 0.82 (0.41), residues: 173 sheet: -1.15 (0.24), residues: 446 loop : -0.75 (0.23), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1251 TYR 0.012 0.001 TYR A1528 PHE 0.010 0.001 PHE A 419 TRP 0.042 0.001 TRP A 999 HIS 0.007 0.001 HIS A 746 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (11379) covalent geometry : angle 0.63396 / 0.31 (15430) hydrogen bonds : bond 0.03176 / 2.24 ( 303) hydrogen bonds : angle 6.05686 / 4.13 ( 804) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 88 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 TYR cc_start: 0.8136 (OUTLIER) cc_final: 0.7771 (t80) REVERT: A 827 ASN cc_start: 0.8381 (m-40) cc_final: 0.8105 (m-40) REVERT: A 832 GLN cc_start: 0.8217 (tt0) cc_final: 0.7950 (tt0) REVERT: A 848 MET cc_start: 0.7960 (tpp) cc_final: 0.7692 (tpt) REVERT: A 968 MET cc_start: 0.3867 (mtm) cc_final: 0.3448 (mpp) REVERT: A 1159 TYR cc_start: 0.7687 (t80) cc_final: 0.7401 (t80) REVERT: A 1366 VAL cc_start: 0.2510 (OUTLIER) cc_final: 0.2130 (t) REVERT: A 1419 GLN cc_start: 0.8706 (mp10) cc_final: 0.7765 (tm-30) REVERT: A 1665 ASP cc_start: 0.8513 (p0) cc_final: 0.8228 (p0) REVERT: A 1785 MET cc_start: 0.5212 (tmm) cc_final: 0.4962 (tmm) outliers start: 42 outliers final: 34 residues processed: 120 average time/residue: 0.0973 time to fit residues: 17.3051 Evaluate side-chains 119 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 83 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 614 GLU Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 701 SER Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 919 ARG Chi-restraints excluded: chain A residue 946 HIS Chi-restraints excluded: chain A residue 949 PHE Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1104 THR Chi-restraints excluded: chain A residue 1210 ILE Chi-restraints excluded: chain A residue 1227 GLU Chi-restraints excluded: chain A residue 1264 SER Chi-restraints excluded: chain A residue 1287 ILE Chi-restraints excluded: chain A residue 1359 VAL Chi-restraints excluded: chain A residue 1366 VAL Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain A residue 1402 THR Chi-restraints excluded: chain A residue 1663 VAL Chi-restraints excluded: chain A residue 1711 VAL Chi-restraints excluded: chain A residue 1801 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 132 optimal weight: 1.9990 chunk 109 optimal weight: 9.9990 chunk 67 optimal weight: 6.9990 chunk 136 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 129 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 87 optimal weight: 2.9990 chunk 71 optimal weight: 20.0000 chunk 95 optimal weight: 0.0040 overall best weight: 1.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1753 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.149202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.103044 restraints weight = 35029.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.105632 restraints weight = 19245.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.105148 restraints weight = 11393.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.105699 restraints weight = 12608.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.105672 restraints weight = 11186.444| |-----------------------------------------------------------------------------| r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11379 Z= 0.155 Angle : 0.639 13.369 15430 Z= 0.314 Chirality : 0.045 0.163 1656 Planarity : 0.005 0.049 1995 Dihedral : 5.305 44.509 1509 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.97 % Allowed : 17.27 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.23), residues: 1346 helix: 1.04 (0.41), residues: 172 sheet: -1.14 (0.24), residues: 439 loop : -0.75 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1251 TYR 0.010 0.001 TYR A 647 PHE 0.010 0.001 PHE A 419 TRP 0.022 0.001 TRP A 999 HIS 0.008 0.001 HIS A 746 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 (11379) covalent geometry : angle 0.63886 / 0.31 (15430) hydrogen bonds : bond 0.03118 / 2.18 ( 303) hydrogen bonds : angle 5.94726 / 4.05 ( 804) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 90 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 TYR cc_start: 0.8219 (OUTLIER) cc_final: 0.7865 (t80) REVERT: A 827 ASN cc_start: 0.8440 (m-40) cc_final: 0.8194 (m-40) REVERT: A 832 GLN cc_start: 0.8207 (tt0) cc_final: 0.7973 (tt0) REVERT: A 848 MET cc_start: 0.7883 (tpp) cc_final: 0.7577 (tpt) REVERT: A 1033 MET cc_start: 0.5203 (pmm) cc_final: 0.3288 (tpp) REVERT: A 1159 TYR cc_start: 0.7775 (t80) cc_final: 0.7509 (t80) REVERT: A 1366 VAL cc_start: 0.2732 (OUTLIER) cc_final: 0.2247 (t) REVERT: A 1419 GLN cc_start: 0.8708 (mp10) cc_final: 0.7792 (tm-30) REVERT: A 1665 ASP cc_start: 0.8526 (p0) cc_final: 0.8180 (p0) REVERT: A 1785 MET cc_start: 0.5106 (tmm) cc_final: 0.4874 (tmm) outliers start: 48 outliers final: 36 residues processed: 126 average time/residue: 0.0973 time to fit residues: 18.1518 Evaluate side-chains 125 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 87 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 614 GLU Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 701 SER Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 919 ARG Chi-restraints excluded: chain A residue 946 HIS Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1104 THR Chi-restraints excluded: chain A residue 1210 ILE Chi-restraints excluded: chain A residue 1227 GLU Chi-restraints excluded: chain A residue 1264 SER Chi-restraints excluded: chain A residue 1287 ILE Chi-restraints excluded: chain A residue 1359 VAL Chi-restraints excluded: chain A residue 1366 VAL Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain A residue 1402 THR Chi-restraints excluded: chain A residue 1501 THR Chi-restraints excluded: chain A residue 1663 VAL Chi-restraints excluded: chain A residue 1711 VAL Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1801 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 11 optimal weight: 20.0000 chunk 40 optimal weight: 0.7980 chunk 121 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 132 optimal weight: 8.9990 chunk 43 optimal weight: 6.9990 chunk 65 optimal weight: 0.0670 chunk 119 optimal weight: 8.9990 chunk 2 optimal weight: 20.0000 chunk 13 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 overall best weight: 1.9122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 722 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.147550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.104552 restraints weight = 35249.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.104139 restraints weight = 21025.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.103802 restraints weight = 15877.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.104398 restraints weight = 15602.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.104458 restraints weight = 12923.789| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.4288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11379 Z= 0.195 Angle : 0.663 12.702 15430 Z= 0.328 Chirality : 0.045 0.173 1656 Planarity : 0.005 0.045 1995 Dihedral : 5.421 48.577 1509 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 3.64 % Allowed : 18.26 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.23), residues: 1346 helix: 0.62 (0.39), residues: 185 sheet: -1.18 (0.24), residues: 422 loop : -0.84 (0.23), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1677 TYR 0.016 0.001 TYR A1159 PHE 0.017 0.001 PHE A 452 TRP 0.066 0.002 TRP A 999 HIS 0.009 0.001 HIS A 746 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.19 (11379) covalent geometry : angle 0.66291 / 0.33 (15430) hydrogen bonds : bond 0.03367 / 2.36 ( 303) hydrogen bonds : angle 6.04821 / 4.13 ( 804) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 94 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 TYR cc_start: 0.8167 (OUTLIER) cc_final: 0.7785 (t80) REVERT: A 643 ASP cc_start: 0.7553 (OUTLIER) cc_final: 0.6952 (p0) REVERT: A 740 LEU cc_start: 0.8377 (mm) cc_final: 0.8061 (mm) REVERT: A 827 ASN cc_start: 0.8520 (m-40) cc_final: 0.7962 (m-40) REVERT: A 832 GLN cc_start: 0.8275 (tt0) cc_final: 0.7938 (tt0) REVERT: A 968 MET cc_start: 0.4020 (mtm) cc_final: 0.3666 (mpp) REVERT: A 1033 MET cc_start: 0.5152 (pmm) cc_final: 0.3230 (tpp) REVERT: A 1366 VAL cc_start: 0.2670 (OUTLIER) cc_final: 0.2240 (t) REVERT: A 1419 GLN cc_start: 0.8732 (mp10) cc_final: 0.7797 (tm-30) REVERT: A 1665 ASP cc_start: 0.8408 (p0) cc_final: 0.8059 (p0) outliers start: 44 outliers final: 32 residues processed: 127 average time/residue: 0.0991 time to fit residues: 18.2886 Evaluate side-chains 122 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 87 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 701 SER Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 919 ARG Chi-restraints excluded: chain A residue 946 HIS Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1104 THR Chi-restraints excluded: chain A residue 1210 ILE Chi-restraints excluded: chain A residue 1227 GLU Chi-restraints excluded: chain A residue 1264 SER Chi-restraints excluded: chain A residue 1287 ILE Chi-restraints excluded: chain A residue 1359 VAL Chi-restraints excluded: chain A residue 1366 VAL Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain A residue 1402 THR Chi-restraints excluded: chain A residue 1501 THR Chi-restraints excluded: chain A residue 1663 VAL Chi-restraints excluded: chain A residue 1711 VAL Chi-restraints excluded: chain A residue 1801 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 5.9990 chunk 2 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 134 optimal weight: 9.9990 chunk 107 optimal weight: 10.0000 chunk 91 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 8 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 ASN A 636 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.147580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.103830 restraints weight = 34897.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.104263 restraints weight = 19812.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.104428 restraints weight = 13867.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.104999 restraints weight = 12968.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.104907 restraints weight = 11559.113| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.4417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11379 Z= 0.182 Angle : 0.683 13.279 15430 Z= 0.335 Chirality : 0.045 0.151 1656 Planarity : 0.005 0.047 1995 Dihedral : 5.442 51.273 1509 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.39 % Allowed : 19.09 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.23), residues: 1346 helix: 0.58 (0.39), residues: 185 sheet: -1.14 (0.24), residues: 430 loop : -0.88 (0.23), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1677 TYR 0.040 0.001 TYR A 552 PHE 0.011 0.001 PHE A 595 TRP 0.048 0.002 TRP A 999 HIS 0.009 0.001 HIS A 746 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 (11379) covalent geometry : angle 0.68310 / 0.34 (15430) hydrogen bonds : bond 0.03273 / 2.31 ( 303) hydrogen bonds : angle 6.01659 / 4.11 ( 804) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 91 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 TYR cc_start: 0.8273 (OUTLIER) cc_final: 0.7939 (t80) REVERT: A 827 ASN cc_start: 0.8483 (m-40) cc_final: 0.7929 (m-40) REVERT: A 832 GLN cc_start: 0.8236 (tt0) cc_final: 0.7922 (tt0) REVERT: A 968 MET cc_start: 0.4194 (mtm) cc_final: 0.3399 (mpp) REVERT: A 1033 MET cc_start: 0.5245 (pmm) cc_final: 0.3558 (tpp) REVERT: A 1366 VAL cc_start: 0.2901 (OUTLIER) cc_final: 0.2472 (t) REVERT: A 1387 MET cc_start: 0.1505 (ppp) cc_final: 0.1298 (ppp) REVERT: A 1419 GLN cc_start: 0.8687 (mp10) cc_final: 0.7771 (tm-30) REVERT: A 1665 ASP cc_start: 0.8484 (p0) cc_final: 0.8131 (p0) REVERT: A 1766 GLU cc_start: 0.8692 (mp0) cc_final: 0.7915 (pm20) outliers start: 41 outliers final: 37 residues processed: 121 average time/residue: 0.0931 time to fit residues: 16.6590 Evaluate side-chains 128 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 89 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 614 GLU Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 701 SER Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 919 ARG Chi-restraints excluded: chain A residue 946 HIS Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1104 THR Chi-restraints excluded: chain A residue 1204 ILE Chi-restraints excluded: chain A residue 1227 GLU Chi-restraints excluded: chain A residue 1264 SER Chi-restraints excluded: chain A residue 1287 ILE Chi-restraints excluded: chain A residue 1359 VAL Chi-restraints excluded: chain A residue 1366 VAL Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain A residue 1402 THR Chi-restraints excluded: chain A residue 1501 THR Chi-restraints excluded: chain A residue 1663 VAL Chi-restraints excluded: chain A residue 1753 HIS Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1801 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 44 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 125 optimal weight: 20.0000 chunk 36 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 108 optimal weight: 8.9990 chunk 102 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 255 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.148451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.103574 restraints weight = 34521.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.104251 restraints weight = 19332.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.104277 restraints weight = 14449.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.104926 restraints weight = 12483.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.104570 restraints weight = 11445.381| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.4534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11379 Z= 0.160 Angle : 0.673 13.439 15430 Z= 0.328 Chirality : 0.045 0.153 1656 Planarity : 0.005 0.046 1995 Dihedral : 5.393 53.635 1509 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.47 % Allowed : 18.84 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.23), residues: 1346 helix: 0.75 (0.39), residues: 184 sheet: -1.13 (0.24), residues: 431 loop : -0.87 (0.23), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1710 TYR 0.038 0.001 TYR A 552 PHE 0.015 0.001 PHE A 452 TRP 0.049 0.001 TRP A 999 HIS 0.008 0.001 HIS A 746 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (11379) covalent geometry : angle 0.67333 / 0.33 (15430) hydrogen bonds : bond 0.03127 / 2.19 ( 303) hydrogen bonds : angle 5.89005 / 4.02 ( 804) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 90 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 643 ASP cc_start: 0.7480 (OUTLIER) cc_final: 0.6898 (p0) REVERT: A 827 ASN cc_start: 0.8476 (m-40) cc_final: 0.7894 (m-40) REVERT: A 832 GLN cc_start: 0.8243 (tt0) cc_final: 0.7948 (tt0) REVERT: A 968 MET cc_start: 0.4251 (mtm) cc_final: 0.3461 (mpp) REVERT: A 1033 MET cc_start: 0.5217 (pmm) cc_final: 0.3586 (tpp) REVERT: A 1366 VAL cc_start: 0.3139 (OUTLIER) cc_final: 0.2724 (t) REVERT: A 1419 GLN cc_start: 0.8708 (mp10) cc_final: 0.7823 (tm-30) REVERT: A 1665 ASP cc_start: 0.8511 (p0) cc_final: 0.8167 (p0) outliers start: 42 outliers final: 37 residues processed: 122 average time/residue: 0.0912 time to fit residues: 16.6320 Evaluate side-chains 127 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 88 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 614 GLU Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 701 SER Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 919 ARG Chi-restraints excluded: chain A residue 946 HIS Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1104 THR Chi-restraints excluded: chain A residue 1204 ILE Chi-restraints excluded: chain A residue 1210 ILE Chi-restraints excluded: chain A residue 1227 GLU Chi-restraints excluded: chain A residue 1264 SER Chi-restraints excluded: chain A residue 1287 ILE Chi-restraints excluded: chain A residue 1359 VAL Chi-restraints excluded: chain A residue 1366 VAL Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain A residue 1402 THR Chi-restraints excluded: chain A residue 1403 VAL Chi-restraints excluded: chain A residue 1501 THR Chi-restraints excluded: chain A residue 1663 VAL Chi-restraints excluded: chain A residue 1753 HIS Chi-restraints excluded: chain A residue 1787 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 20 optimal weight: 2.9990 chunk 96 optimal weight: 0.1980 chunk 104 optimal weight: 1.9990 chunk 122 optimal weight: 40.0000 chunk 54 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 58 optimal weight: 0.1980 chunk 115 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.149264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.102088 restraints weight = 34811.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.104416 restraints weight = 16865.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.105740 restraints weight = 11411.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.106342 restraints weight = 9538.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.107206 restraints weight = 8773.068| |-----------------------------------------------------------------------------| r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.4563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 11379 Z= 0.130 Angle : 0.670 14.192 15430 Z= 0.326 Chirality : 0.045 0.152 1656 Planarity : 0.004 0.047 1995 Dihedral : 5.308 54.829 1509 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.98 % Allowed : 19.42 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.23), residues: 1346 helix: 0.82 (0.39), residues: 184 sheet: -1.02 (0.24), residues: 435 loop : -0.84 (0.23), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 302 TYR 0.036 0.001 TYR A 552 PHE 0.009 0.001 PHE A 419 TRP 0.049 0.001 TRP A 999 HIS 0.007 0.001 HIS A 746 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (11379) covalent geometry : angle 0.67045 / 0.33 (15430) hydrogen bonds : bond 0.03060 / 2.14 ( 303) hydrogen bonds : angle 5.70154 / 3.89 ( 804) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 90 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 643 ASP cc_start: 0.7318 (OUTLIER) cc_final: 0.6743 (p0) REVERT: A 827 ASN cc_start: 0.8491 (m-40) cc_final: 0.8201 (m-40) REVERT: A 832 GLN cc_start: 0.8225 (tt0) cc_final: 0.8015 (tt0) REVERT: A 968 MET cc_start: 0.3955 (mtm) cc_final: 0.3155 (mpp) REVERT: A 1033 MET cc_start: 0.5152 (pmm) cc_final: 0.3535 (tpp) REVERT: A 1103 LYS cc_start: 0.8349 (tptt) cc_final: 0.8067 (tptp) REVERT: A 1366 VAL cc_start: 0.2486 (OUTLIER) cc_final: 0.1962 (t) REVERT: A 1390 MET cc_start: 0.8520 (mmm) cc_final: 0.8273 (mpp) REVERT: A 1419 GLN cc_start: 0.8673 (mp10) cc_final: 0.7758 (tm-30) REVERT: A 1665 ASP cc_start: 0.8544 (p0) cc_final: 0.7679 (p0) REVERT: A 1785 MET cc_start: 0.5009 (tpt) cc_final: 0.4754 (tpt) outliers start: 36 outliers final: 32 residues processed: 117 average time/residue: 0.0944 time to fit residues: 16.7095 Evaluate side-chains 120 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 86 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 614 GLU Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 701 SER Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 919 ARG Chi-restraints excluded: chain A residue 946 HIS Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1104 THR Chi-restraints excluded: chain A residue 1210 ILE Chi-restraints excluded: chain A residue 1227 GLU Chi-restraints excluded: chain A residue 1264 SER Chi-restraints excluded: chain A residue 1359 VAL Chi-restraints excluded: chain A residue 1366 VAL Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain A residue 1402 THR Chi-restraints excluded: chain A residue 1403 VAL Chi-restraints excluded: chain A residue 1501 THR Chi-restraints excluded: chain A residue 1663 VAL Chi-restraints excluded: chain A residue 1753 HIS Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1801 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 88 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 131 optimal weight: 30.0000 chunk 37 optimal weight: 1.9990 chunk 34 optimal weight: 0.2980 chunk 72 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 chunk 67 optimal weight: 10.0000 chunk 35 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 83 optimal weight: 5.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.148796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.103962 restraints weight = 35235.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.104056 restraints weight = 21623.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.104608 restraints weight = 15038.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.105149 restraints weight = 12927.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.105155 restraints weight = 11767.170| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.4690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11379 Z= 0.147 Angle : 0.666 13.741 15430 Z= 0.324 Chirality : 0.045 0.150 1656 Planarity : 0.005 0.047 1995 Dihedral : 5.307 57.402 1509 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 3.06 % Allowed : 19.67 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.23), residues: 1346 helix: 0.87 (0.40), residues: 178 sheet: -0.97 (0.25), residues: 431 loop : -0.89 (0.23), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 302 TYR 0.036 0.001 TYR A 552 PHE 0.015 0.001 PHE A 452 TRP 0.046 0.001 TRP A 999 HIS 0.008 0.001 HIS A 746 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (11379) covalent geometry : angle 0.66616 / 0.32 (15430) hydrogen bonds : bond 0.03070 / 2.16 ( 303) hydrogen bonds : angle 5.70310 / 3.90 ( 804) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2281.23 seconds wall clock time: 40 minutes 2.25 seconds (2402.25 seconds total)