Starting phenix.real_space_refine on Sat Sep 12 01:07:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5zal_6905/09_2026/5zal_6905.cif Found real_map, /net/cci-nas-00/data/ceres_data/5zal_6905/09_2026/5zal_6905.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/5zal_6905/09_2026/5zal_6905.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5zal_6905/09_2026/5zal_6905.cif" model { file = "/net/cci-nas-00/data/ceres_data/5zal_6905/09_2026/5zal_6905.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5zal_6905/09_2026/5zal_6905.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5zal_6905/09_2026/5zal_6905.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5zal_6905/09_2026/5zal_6905.map" } resolution = 4.7 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= 0.001 sd= 0.006 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 P 57 5.49 5 S 66 5.16 5 C 7640 2.51 5 N 2122 2.21 5 O 2461 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12346 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 10552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1314, 10552 Classifications: {'peptide': 1314} Link IDs: {'CIS': 18, 'PCIS': 4, 'PTRANS': 64, 'TRANS': 1227} Chain breaks: 8 Chain: "B" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 560 Classifications: {'peptide': 75} Link IDs: {'PCIS': 2, 'TRANS': 72} Chain: "C" Number of atoms: 1234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 1234 Classifications: {'RNAv2': 58} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 31, 'rna3p_pyr': 25} Link IDs: {'rna2p': 1, 'rna3p': 56} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.39, per 1000 atoms: 0.19 Number of scatterers: 12346 At special positions: 0 Unit cell: (112.34, 101.38, 160.29, 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) S 66 16.00 P 57 15.00 O 2461 8.00 N 2122 7.00 C 7640 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 443 " - pdb=" SG CYS A 531 " distance=2.04 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: 0.96 Conformation dependent library (CDL) restraints added in 460.9 milliseconds 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2666 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 7 sheets defined 46.5% alpha, 5.7% beta 18 base pairs and 38 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 55 through 57 No H-bonds generated for 'chain 'A' and resid 55 through 57' Processing helix chain 'A' and resid 69 through 84 removed outlier: 3.757A pdb=" N ILE A 73 " --> pdb=" O GLY A 69 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLN A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 114 removed outlier: 3.563A pdb=" N VAL A 110 " --> pdb=" O VAL A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 145 Processing helix chain 'A' and resid 151 through 160 Processing helix chain 'A' and resid 176 through 180 Processing helix chain 'A' and resid 185 through 192 Processing helix chain 'A' and resid 218 through 231 removed outlier: 3.577A pdb=" N LYS A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 267 removed outlier: 3.755A pdb=" N LEU A 266 " --> pdb=" O ARG A 263 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N TYR A 267 " --> pdb=" O SER A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 285 removed outlier: 3.716A pdb=" N MET A 272 " --> pdb=" O GLU A 268 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ASN A 285 " --> pdb=" O ILE A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 313 Processing helix chain 'A' and resid 316 through 336 removed outlier: 4.220A pdb=" N ALA A 322 " --> pdb=" O ALA A 318 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLY A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL A 326 " --> pdb=" O ALA A 322 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N LYS A 331 " --> pdb=" O ARG A 327 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N TYR A 332 " --> pdb=" O GLU A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 358 removed outlier: 4.088A pdb=" N LEU A 346 " --> pdb=" O ARG A 342 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE A 347 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N THR A 348 " --> pdb=" O PHE A 344 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N HIS A 356 " --> pdb=" O LEU A 352 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ALA A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LEU A 358 " --> pdb=" O LYS A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 383 Processing helix chain 'A' and resid 453 through 461 removed outlier: 4.007A pdb=" N LEU A 457 " --> pdb=" O THR A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 510 removed outlier: 3.605A pdb=" N ALA A 510 " --> pdb=" O ARG A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 516 removed outlier: 4.136A pdb=" N LEU A 515 " --> pdb=" O HIS A 511 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU A 516 " --> pdb=" O GLU A 512 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 511 through 516' Processing helix chain 'A' and resid 542 through 551 Processing helix chain 'A' and resid 569 through 573 Processing helix chain 'A' and resid 574 through 592 removed outlier: 4.271A pdb=" N GLU A 583 " --> pdb=" O TYR A 579 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N CYS A 590 " --> pdb=" O LEU A 586 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER A 591 " --> pdb=" O ARG A 587 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS A 592 " --> pdb=" O ASN A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 639 Processing helix chain 'A' and resid 690 through 698 Processing helix chain 'A' and resid 699 through 706 Processing helix chain 'A' and resid 714 through 724 Processing helix chain 'A' and resid 782 through 786 Processing helix chain 'A' and resid 794 through 798 Processing helix chain 'A' and resid 839 through 857 removed outlier: 4.410A pdb=" N SER A 855 " --> pdb=" O GLN A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 903 Processing helix chain 'A' and resid 967 through 975 Processing helix chain 'A' and resid 1002 through 1011 Processing helix chain 'A' and resid 1015 through 1019 removed outlier: 3.742A pdb=" N LYS A1019 " --> pdb=" O SER A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1022 through 1031 removed outlier: 3.834A pdb=" N LEU A1027 " --> pdb=" O LYS A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1044 through 1052 Processing helix chain 'A' and resid 1053 through 1072 removed outlier: 3.690A pdb=" N ILE A1057 " --> pdb=" O CYS A1053 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N HIS A1062 " --> pdb=" O LEU A1058 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N CYS A1063 " --> pdb=" O TYR A1059 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLU A1069 " --> pdb=" O LEU A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1294 through 1301 Processing helix chain 'A' and resid 1312 through 1334 removed outlier: 4.253A pdb=" N MET A1317 " --> pdb=" O GLU A1313 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LEU A1318 " --> pdb=" O ARG A1314 " (cutoff:3.500A) Processing helix chain 'A' and resid 1339 through 1351 removed outlier: 4.176A pdb=" N TYR A1345 " --> pdb=" O GLY A1341 " (cutoff:3.500A) Processing helix chain 'A' and resid 1352 through 1362 removed outlier: 3.861A pdb=" N LEU A1356 " --> pdb=" O SER A1352 " (cutoff:3.500A) Processing helix chain 'A' and resid 1364 through 1369 Processing helix chain 'A' and resid 1558 through 1573 removed outlier: 3.768A pdb=" N CYS A1569 " --> pdb=" O ALA A1565 " (cutoff:3.500A) Processing helix chain 'A' and resid 1575 through 1584 Processing helix chain 'A' and resid 1592 through 1597 removed outlier: 3.598A pdb=" N ARG A1596 " --> pdb=" O VAL A1593 " (cutoff:3.500A) Processing helix chain 'A' and resid 1617 through 1621 removed outlier: 4.348A pdb=" N SER A1620 " --> pdb=" O LEU A1617 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N CYS A1621 " --> pdb=" O SER A1618 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1617 through 1621' Processing helix chain 'A' and resid 1655 through 1663 Processing helix chain 'A' and resid 1666 through 1673 Processing helix chain 'A' and resid 1679 through 1687 removed outlier: 4.165A pdb=" N LEU A1683 " --> pdb=" O ASN A1679 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE A1687 " --> pdb=" O LEU A1683 " (cutoff:3.500A) Processing helix chain 'A' and resid 1693 through 1697 removed outlier: 3.662A pdb=" N ILE A1697 " --> pdb=" O TYR A1694 " (cutoff:3.500A) Processing helix chain 'A' and resid 1701 through 1722 removed outlier: 4.426A pdb=" N ALA A1710 " --> pdb=" O PHE A1706 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE A1711 " --> pdb=" O LEU A1707 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASP A1713 " --> pdb=" O ASP A1709 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR A1717 " --> pdb=" O ASP A1713 " (cutoff:3.500A) Processing helix chain 'A' and resid 1730 through 1739 Processing helix chain 'A' and resid 1741 through 1752 removed outlier: 3.605A pdb=" N SER A1747 " --> pdb=" O THR A1743 " (cutoff:3.500A) Processing helix chain 'A' and resid 1762 through 1776 removed outlier: 4.047A pdb=" N PHE A1766 " --> pdb=" O SER A1762 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N VAL A1768 " --> pdb=" O GLU A1764 " (cutoff:3.500A) Processing helix chain 'A' and resid 1807 through 1823 removed outlier: 3.827A pdb=" N ILE A1811 " --> pdb=" O ALA A1807 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N PHE A1812 " --> pdb=" O MET A1808 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N TYR A1820 " --> pdb=" O ALA A1816 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N MET A1821 " --> pdb=" O GLY A1817 " (cutoff:3.500A) Processing helix chain 'A' and resid 1828 through 1848 removed outlier: 3.937A pdb=" N TYR A1835 " --> pdb=" O TRP A1831 " (cutoff:3.500A) Proline residue: A1836 - end of helix Proline residue: A1840 - end of helix Processing helix chain 'A' and resid 1852 through 1861 Processing helix chain 'A' and resid 1896 through 1911 removed outlier: 3.708A pdb=" N ALA A1903 " --> pdb=" O ILE A1899 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA A1904 " --> pdb=" O ALA A1900 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 302 removed outlier: 4.003A pdb=" N SER B 299 " --> pdb=" O CYS B 295 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLU B 300 " --> pdb=" O ARG B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 353 Processing helix chain 'B' and resid 354 through 356 No H-bonds generated for 'chain 'B' and resid 354 through 356' Processing sheet with id=AA1, first strand: chain 'A' and resid 121 through 123 removed outlier: 3.728A pdb=" N ILE A 149 " --> pdb=" O GLY A 122 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N PHE A 98 " --> pdb=" O MET A 150 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU A 172 " --> pdb=" O ARG A 201 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU A 203 " --> pdb=" O LEU A 172 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 253 through 254 removed outlier: 6.214A pdb=" N ILE A 253 " --> pdb=" O MET A 562 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 816 through 819 removed outlier: 4.870A pdb=" N PHE A 802 " --> pdb=" O ILE A 773 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N MET A 775 " --> pdb=" O ARG A 800 " (cutoff:3.500A) removed outlier: 8.930A pdb=" N ARG A 800 " --> pdb=" O MET A 775 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1032 through 1033 removed outlier: 6.260A pdb=" N ASP A 991 " --> pdb=" O VAL A 947 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N VAL A 947 " --> pdb=" O ASP A 991 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N VAL A 931 " --> pdb=" O HIS A1041 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1865 through 1866 removed outlier: 3.651A pdb=" N VAL A1882 " --> pdb=" O PHE A1890 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 309 through 310 Processing sheet with id=AA7, first strand: chain 'B' and resid 313 through 317 removed outlier: 6.841A pdb=" N GLU B 316 " --> pdb=" O GLN B 324 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLN B 324 " --> pdb=" O GLU B 316 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 398 hydrogen bonds defined for protein. 1137 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 41 hydrogen bonds 70 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 38 stacking parallelities Total time for adding SS restraints: 2.31 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2887 1.33 - 1.46: 3401 1.46 - 1.58: 6220 1.58 - 1.71: 113 1.71 - 1.84: 90 Bond restraints: 12711 Sorted by residual: bond pdb=" C PRO A 961 " pdb=" N SER A 962 " ideal model delta sigma weight residual 1.331 1.253 0.078 2.83e-02 1.25e+03 7.56e+00 bond pdb=" CA PHE A 372 " pdb=" C PHE A 372 " ideal model delta sigma weight residual 1.526 1.558 -0.032 1.28e-02 6.10e+03 6.10e+00 bond pdb=" CB TYR A1692 " pdb=" CG TYR A1692 " ideal model delta sigma weight residual 1.512 1.458 0.054 2.20e-02 2.07e+03 6.07e+00 bond pdb=" CA THR A 134 " pdb=" C THR A 134 " ideal model delta sigma weight residual 1.519 1.547 -0.028 1.19e-02 7.06e+03 5.66e+00 bond pdb=" CA GLU A 128 " pdb=" C GLU A 128 " ideal model delta sigma weight residual 1.522 1.550 -0.027 1.20e-02 6.94e+03 5.10e+00 ... (remaining 12706 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.22: 16753 3.22 - 6.44: 594 6.44 - 9.65: 93 9.65 - 12.87: 21 12.87 - 16.09: 7 Bond angle restraints: 17468 Sorted by residual: angle pdb=" C LEU A 649 " pdb=" N ALA A 650 " pdb=" CA ALA A 650 " ideal model delta sigma weight residual 121.70 136.28 -14.58 1.80e+00 3.09e-01 6.56e+01 angle pdb=" C THR A 134 " pdb=" N LYS A 135 " pdb=" CA LYS A 135 " ideal model delta sigma weight residual 121.70 135.75 -14.05 1.80e+00 3.09e-01 6.10e+01 angle pdb=" N GLY A 93 " pdb=" CA GLY A 93 " pdb=" C GLY A 93 " ideal model delta sigma weight residual 110.21 116.65 -6.44 9.10e-01 1.21e+00 5.00e+01 angle pdb=" N PRO A1376 " pdb=" CA PRO A1376 " pdb=" C PRO A1376 " ideal model delta sigma weight residual 110.70 118.76 -8.06 1.22e+00 6.72e-01 4.36e+01 angle pdb=" C SER A 167 " pdb=" N ASP A 168 " pdb=" CA ASP A 168 " ideal model delta sigma weight residual 121.70 132.85 -11.15 1.80e+00 3.09e-01 3.84e+01 ... (remaining 17463 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 7013 17.84 - 35.69: 490 35.69 - 53.53: 128 53.53 - 71.37: 28 71.37 - 89.21: 6 Dihedral angle restraints: 7665 sinusoidal: 3562 harmonic: 4103 Sorted by residual: dihedral pdb=" C4' C C 73 " pdb=" C3' C C 73 " pdb=" C2' C C 73 " pdb=" C1' C C 73 " ideal model delta sinusoidal sigma weight residual 36.34 -32.78 69.12 1 3.10e+00 1.04e-01 6.43e+02 dihedral pdb=" C4' C C 72 " pdb=" C3' C C 72 " pdb=" C2' C C 72 " pdb=" C1' C C 72 " ideal model delta sinusoidal sigma weight residual 36.34 -25.74 62.08 1 3.10e+00 1.04e-01 5.31e+02 dihedral pdb=" O4' C C 73 " pdb=" C4' C C 73 " pdb=" C3' C C 73 " pdb=" C2' C C 73 " ideal model delta sinusoidal sigma weight residual -35.15 17.51 -52.66 1 4.00e+00 6.25e-02 2.36e+02 ... (remaining 7662 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1687 0.096 - 0.192: 271 0.192 - 0.287: 75 0.287 - 0.383: 2 0.383 - 0.479: 1 Chirality restraints: 2036 Sorted by residual: chirality pdb=" CG LEU A 81 " pdb=" CB LEU A 81 " pdb=" CD1 LEU A 81 " pdb=" CD2 LEU A 81 " both_signs ideal model delta sigma weight residual False -2.59 -2.11 -0.48 2.00e-01 2.50e+01 5.74e+00 chirality pdb=" C2' C C 72 " pdb=" C3' C C 72 " pdb=" O2' C C 72 " pdb=" C1' C C 72 " both_signs ideal model delta sigma weight residual False -2.79 -2.47 -0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" P C C 72 " pdb=" OP1 C C 72 " pdb=" OP2 C C 72 " pdb=" O5' C C 72 " both_signs ideal model delta sigma weight residual True 2.17 -2.46 -0.29 2.00e-01 2.50e+01 2.12e+00 ... (remaining 2033 not shown) Planarity restraints: 2012 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A1293 " -0.060 5.00e-02 4.00e+02 9.06e-02 1.31e+01 pdb=" N PRO A1294 " 0.157 5.00e-02 4.00e+02 pdb=" CA PRO A1294 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO A1294 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A1335 " -0.056 5.00e-02 4.00e+02 8.43e-02 1.14e+01 pdb=" N PRO A1336 " 0.146 5.00e-02 4.00e+02 pdb=" CA PRO A1336 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO A1336 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A1376 " -0.048 5.00e-02 4.00e+02 7.10e-02 8.06e+00 pdb=" N PRO A1377 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO A1377 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A1377 " -0.041 5.00e-02 4.00e+02 ... (remaining 2009 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1853 2.75 - 3.29: 12927 3.29 - 3.83: 23544 3.83 - 4.36: 27802 4.36 - 4.90: 41011 Nonbonded interactions: 107137 Sorted by model distance: nonbonded pdb=" NE2 HIS A 703 " pdb=" OD2 ASP A 709 " model vdw 2.215 3.120 nonbonded pdb=" OG1 THR B 331 " pdb=" O PRO B 333 " model vdw 2.240 3.040 nonbonded pdb=" O GLY A1568 " pdb=" OG1 THR A1572 " model vdw 2.240 3.040 nonbonded pdb=" O VAL A 75 " pdb=" OG1 THR A 78 " model vdw 2.244 3.040 nonbonded pdb=" OH TYR A 47 " pdb=" OG1 THR A 238 " model vdw 2.248 3.040 ... (remaining 107132 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 0.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.160 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: 14.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 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 : 0.008 0.103 12712 Z= 0.408 Angle : 1.461 16.091 17470 Z= 0.781 Chirality : 0.079 0.479 2036 Planarity : 0.010 0.091 2012 Dihedral : 13.677 89.214 4996 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 18.94 Ramachandran Plot: Outliers : 0.66 % Allowed : 16.14 % Favored : 83.20 % Rotamer: Outliers : 0.97 % Allowed : 3.46 % Favored : 95.57 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 1.22 % Twisted Proline : 5.71 % Twisted General : 1.22 % 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: -5.19 (0.18), residues: 1369 helix: -3.37 (0.15), residues: 544 sheet: -3.71 (0.44), residues: 78 loop : -3.57 (0.20), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG A 636 TYR 0.037 0.005 TYR A 876 PHE 0.038 0.005 PHE A1812 TRP 0.030 0.006 TRP A1048 HIS 0.018 0.003 HIS A 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00836 / 0.41 (12711) covalent geometry : angle 1.46113 / 0.78 (17468) SS BOND : bond 0.00809 / 0.43 ( 1) SS BOND : angle 1.30399 / 0.69 ( 2) hydrogen bonds : bond 0.19850 / 13.30 ( 439) hydrogen bonds : angle 9.33078 / 6.26 ( 1207) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 176 time to evaluate : 0.465 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 494 MET cc_start: 0.6770 (mtm) cc_final: 0.6273 (ttm) REVERT: A 509 ARG cc_start: 0.9273 (mtt180) cc_final: 0.8887 (ptp-110) REVERT: A 528 ILE cc_start: 0.6813 (OUTLIER) cc_final: 0.6413 (tp) REVERT: A 562 MET cc_start: 0.7700 (tpt) cc_final: 0.7240 (tpt) REVERT: A 573 GLU cc_start: 0.9293 (tt0) cc_final: 0.9027 (tt0) REVERT: A 579 TYR cc_start: 0.9081 (m-80) cc_final: 0.8346 (m-10) REVERT: A 589 LYS cc_start: 0.9428 (mptt) cc_final: 0.9226 (mmtm) REVERT: A 858 LEU cc_start: 0.9197 (mt) cc_final: 0.8750 (tt) REVERT: A 977 ASN cc_start: 0.9637 (m-40) cc_final: 0.9420 (t0) REVERT: A 1313 GLU cc_start: 0.9111 (mt-10) cc_final: 0.8885 (mp0) REVERT: A 1687 PHE cc_start: 0.9401 (m-80) cc_final: 0.8980 (m-80) REVERT: A 1767 HIS cc_start: 0.8375 (t-170) cc_final: 0.8122 (t70) REVERT: A 1825 MET cc_start: 0.8600 (mpt) cc_final: 0.7970 (mpt) REVERT: A 1895 ARG cc_start: 0.8222 (ptt180) cc_final: 0.7946 (mpp-170) REVERT: B 296 ARG cc_start: 0.7766 (tmm160) cc_final: 0.7336 (mmt180) outliers start: 12 outliers final: 2 residues processed: 187 average time/residue: 0.1308 time to fit residues: 32.6736 Evaluate side-chains 107 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 104 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.2980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 6.9990 chunk 55 optimal weight: 10.0000 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 ASN A 140 GLN A 157 ASN A 279 ASN A 356 HIS A 514 ASN ** A 648 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1028 GLN A1339 HIS A1355 ASN A1660 ASN A1693 HIS ** A1695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.066522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.048345 restraints weight = 117192.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.049820 restraints weight = 85439.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.050970 restraints weight = 66543.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.051855 restraints weight = 54678.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.052540 restraints weight = 46484.802| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6052 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 12712 Z= 0.188 Angle : 0.977 14.098 17470 Z= 0.491 Chirality : 0.056 0.555 2036 Planarity : 0.007 0.075 2012 Dihedral : 12.740 82.855 2208 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 25.09 Ramachandran Plot: Outliers : 0.44 % Allowed : 15.63 % Favored : 83.93 % Rotamer: Outliers : 0.24 % Allowed : 4.43 % Favored : 95.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 1.38 % Twisted Proline : 1.43 % Twisted General : 0.53 % 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: -4.26 (0.20), residues: 1369 helix: -2.21 (0.18), residues: 554 sheet: -3.75 (0.43), residues: 92 loop : -3.28 (0.22), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 187 TYR 0.028 0.002 TYR A 971 PHE 0.038 0.002 PHE A 351 TRP 0.034 0.003 TRP A 316 HIS 0.010 0.001 HIS A 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.19 (12711) covalent geometry : angle 0.97632 / 0.49 (17468) SS BOND : bond 0.00137 / 0.07 ( 1) SS BOND : angle 2.03437 / 1.10 ( 2) hydrogen bonds : bond 0.06880 / 4.79 ( 439) hydrogen bonds : angle 7.14178 / 4.90 ( 1207) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 142 time to evaluate : 0.349 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ILE cc_start: 0.7930 (mp) cc_final: 0.7652 (mp) REVERT: A 543 TYR cc_start: 0.8764 (p90) cc_final: 0.8343 (p90) REVERT: A 579 TYR cc_start: 0.7720 (m-80) cc_final: 0.7420 (m-10) REVERT: A 837 MET cc_start: 0.4592 (mmm) cc_final: 0.4379 (mmm) REVERT: A 1687 PHE cc_start: 0.8663 (m-80) cc_final: 0.8438 (m-80) REVERT: A 1812 PHE cc_start: 0.9068 (t80) cc_final: 0.8808 (t80) REVERT: A 1848 ASN cc_start: 0.9391 (t0) cc_final: 0.9160 (p0) REVERT: B 296 ARG cc_start: 0.7662 (tmm160) cc_final: 0.7402 (mmt180) outliers start: 3 outliers final: 1 residues processed: 144 average time/residue: 0.1377 time to fit residues: 26.5785 Evaluate side-chains 100 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 99 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 81 optimal weight: 8.9990 chunk 78 optimal weight: 0.0770 chunk 127 optimal weight: 10.0000 chunk 106 optimal weight: 8.9990 chunk 105 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 120 optimal weight: 0.6980 chunk 101 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 overall best weight: 1.3342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 48 GLN A 109 GLN A 195 ASN A 282 ASN ** A 648 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1028 GLN ** A1661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1668 ASN ** A1695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.069700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.051878 restraints weight = 110962.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.053452 restraints weight = 78268.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.054663 restraints weight = 59641.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.055573 restraints weight = 47922.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.056318 restraints weight = 40183.841| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6333 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 12712 Z= 0.158 Angle : 0.890 12.095 17470 Z= 0.450 Chirality : 0.053 0.393 2036 Planarity : 0.006 0.064 2012 Dihedral : 12.039 79.574 2208 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 22.40 Ramachandran Plot: Outliers : 0.37 % Allowed : 14.10 % Favored : 85.54 % Rotamer: Outliers : 0.24 % Allowed : 4.43 % Favored : 95.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 1.30 % Twisted Proline : 1.43 % Twisted General : 0.46 % 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: -3.79 (0.21), residues: 1369 helix: -1.75 (0.20), residues: 572 sheet: -3.43 (0.46), residues: 92 loop : -3.11 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1879 TYR 0.020 0.002 TYR A 163 PHE 0.020 0.002 PHE A 351 TRP 0.019 0.002 TRP A 316 HIS 0.007 0.001 HIS A1004 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.16 (12711) covalent geometry : angle 0.89036 / 0.45 (17468) SS BOND : bond 0.00193 / 0.10 ( 1) SS BOND : angle 1.57448 / 0.86 ( 2) hydrogen bonds : bond 0.05411 / 3.78 ( 439) hydrogen bonds : angle 6.52328 / 4.53 ( 1207) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 138 time to evaluate : 0.381 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: symmetry clash 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: symmetry clash REVERT: A 543 TYR cc_start: 0.8887 (p90) cc_final: 0.8381 (p90) REVERT: A 562 MET cc_start: 0.5965 (tpt) cc_final: 0.3752 (tpp) REVERT: A 579 TYR cc_start: 0.8076 (m-80) cc_final: 0.7564 (m-10) REVERT: A 837 MET cc_start: 0.4714 (mmm) cc_final: 0.4336 (mmm) REVERT: A 1688 THR cc_start: 0.6768 (OUTLIER) cc_final: 0.6271 (p) REVERT: A 1848 ASN cc_start: 0.9405 (t0) cc_final: 0.9193 (p0) REVERT: B 296 ARG cc_start: 0.7625 (tmm160) cc_final: 0.7317 (mmt180) outliers start: 3 outliers final: 1 residues processed: 141 average time/residue: 0.1368 time to fit residues: 26.2551 Evaluate side-chains 93 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 91 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 140 optimal weight: 20.0000 chunk 7 optimal weight: 0.0670 chunk 109 optimal weight: 9.9990 chunk 71 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 118 optimal weight: 0.2980 chunk 113 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 86 optimal weight: 30.0000 chunk 84 optimal weight: 5.9990 chunk 32 optimal weight: 20.0000 overall best weight: 2.0724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 48 GLN A 157 ASN ** A 648 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 711 HIS ** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.068737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.050114 restraints weight = 114076.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.051540 restraints weight = 83809.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.052675 restraints weight = 66318.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.053558 restraints weight = 54523.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.054219 restraints weight = 46472.065| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6349 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 12712 Z= 0.162 Angle : 0.873 12.043 17470 Z= 0.442 Chirality : 0.052 0.345 2036 Planarity : 0.006 0.061 2012 Dihedral : 11.761 79.659 2208 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 23.97 Ramachandran Plot: Outliers : 0.29 % Allowed : 14.02 % Favored : 85.68 % Rotamer: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 1.30 % Twisted Proline : 1.43 % Twisted General : 0.46 % 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: -3.59 (0.21), residues: 1369 helix: -1.59 (0.20), residues: 573 sheet: -3.36 (0.46), residues: 92 loop : -2.99 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 187 TYR 0.027 0.002 TYR A 668 PHE 0.018 0.002 PHE A1812 TRP 0.011 0.002 TRP A 316 HIS 0.006 0.001 HIS A1004 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.16 (12711) covalent geometry : angle 0.87306 / 0.44 (17468) SS BOND : bond 0.00231 / 0.12 ( 1) SS BOND : angle 1.50661 / 0.82 ( 2) hydrogen bonds : bond 0.05222 / 3.61 ( 439) hydrogen bonds : angle 6.27800 / 4.35 ( 1207) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.389 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 543 TYR cc_start: 0.9048 (p90) cc_final: 0.8580 (p90) REVERT: A 562 MET cc_start: 0.5315 (tpt) cc_final: 0.3407 (tpp) REVERT: A 579 TYR cc_start: 0.8128 (m-80) cc_final: 0.7604 (m-10) REVERT: A 837 MET cc_start: 0.4776 (mmm) cc_final: 0.4413 (mmm) REVERT: A 1748 LEU cc_start: 0.8280 (mt) cc_final: 0.7854 (mt) REVERT: A 1848 ASN cc_start: 0.9416 (t0) cc_final: 0.9174 (p0) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.1374 time to fit residues: 23.5600 Evaluate side-chains 89 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 13 optimal weight: 0.8980 chunk 58 optimal weight: 6.9990 chunk 109 optimal weight: 0.0570 chunk 138 optimal weight: 10.0000 chunk 45 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 92 optimal weight: 0.8980 chunk 41 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 81 optimal weight: 8.9990 overall best weight: 2.9702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 48 GLN A 356 HIS ** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 648 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.068550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.051124 restraints weight = 110443.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.052664 restraints weight = 77550.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.053831 restraints weight = 58941.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.054750 restraints weight = 47354.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.055494 restraints weight = 39487.767| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6147 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12712 Z= 0.175 Angle : 0.870 11.967 17470 Z= 0.442 Chirality : 0.051 0.331 2036 Planarity : 0.006 0.063 2012 Dihedral : 11.711 79.619 2208 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 26.08 Ramachandran Plot: Outliers : 0.29 % Allowed : 15.12 % Favored : 84.59 % Rotamer: Outliers : 0.08 % Allowed : 4.35 % Favored : 95.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 1.30 % Twisted Proline : 1.43 % Twisted General : 0.38 % 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: -3.52 (0.21), residues: 1369 helix: -1.42 (0.20), residues: 577 sheet: -3.19 (0.47), residues: 95 loop : -3.09 (0.23), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 187 TYR 0.022 0.002 TYR A1757 PHE 0.024 0.002 PHE A 351 TRP 0.027 0.002 TRP A 133 HIS 0.007 0.001 HIS A1755 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.17 (12711) covalent geometry : angle 0.87019 / 0.44 (17468) SS BOND : bond 0.00257 / 0.14 ( 1) SS BOND : angle 1.48071 / 0.80 ( 2) hydrogen bonds : bond 0.05188 / 3.57 ( 439) hydrogen bonds : angle 6.13984 / 4.24 ( 1207) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 113 time to evaluate : 0.348 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 503 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7328 (mm-30) REVERT: A 543 TYR cc_start: 0.8958 (p90) cc_final: 0.8547 (p90) REVERT: A 562 MET cc_start: 0.4723 (tpt) cc_final: 0.2890 (tpp) REVERT: A 579 TYR cc_start: 0.7970 (m-80) cc_final: 0.7485 (m-10) REVERT: A 837 MET cc_start: 0.4701 (mmm) cc_final: 0.4390 (mmm) REVERT: A 1668 ASN cc_start: 0.8714 (t0) cc_final: 0.8392 (t0) REVERT: A 1687 PHE cc_start: 0.8979 (m-80) cc_final: 0.8772 (m-80) REVERT: B 296 ARG cc_start: 0.7557 (tmm160) cc_final: 0.7271 (mmt180) outliers start: 1 outliers final: 1 residues processed: 113 average time/residue: 0.1421 time to fit residues: 22.2627 Evaluate side-chains 82 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 81 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 127 optimal weight: 0.0770 chunk 13 optimal weight: 4.9990 chunk 125 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 136 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 101 optimal weight: 4.9990 chunk 113 optimal weight: 0.6980 chunk 30 optimal weight: 7.9990 chunk 17 optimal weight: 0.0030 overall best weight: 1.9552 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 48 GLN ** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN ** A 648 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.068895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.050312 restraints weight = 114377.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.051766 restraints weight = 84512.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.052895 restraints weight = 66587.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.053775 restraints weight = 55103.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.054480 restraints weight = 47023.495| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6362 moved from start: 0.4329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 12712 Z= 0.153 Angle : 0.859 12.060 17470 Z= 0.435 Chirality : 0.051 0.295 2036 Planarity : 0.006 0.063 2012 Dihedral : 11.638 77.513 2208 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 23.93 Ramachandran Plot: Outliers : 0.22 % Allowed : 13.73 % Favored : 86.05 % Rotamer: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 1.30 % Twisted Proline : 1.43 % Twisted General : 0.31 % 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: -3.40 (0.22), residues: 1369 helix: -1.36 (0.20), residues: 591 sheet: -3.40 (0.50), residues: 79 loop : -2.99 (0.23), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 187 TYR 0.026 0.002 TYR A1757 PHE 0.017 0.002 PHE A1812 TRP 0.008 0.002 TRP A 133 HIS 0.005 0.001 HIS A 850 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (12711) covalent geometry : angle 0.85936 / 0.43 (17468) SS BOND : bond 0.00244 / 0.13 ( 1) SS BOND : angle 1.51824 / 0.82 ( 2) hydrogen bonds : bond 0.04783 / 3.30 ( 439) hydrogen bonds : angle 6.10799 / 4.23 ( 1207) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.467 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: 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 543 TYR cc_start: 0.9055 (p90) cc_final: 0.8596 (p90) REVERT: A 562 MET cc_start: 0.5156 (tpt) cc_final: 0.3248 (tpp) REVERT: A 579 TYR cc_start: 0.8150 (m-80) cc_final: 0.7657 (m-10) REVERT: A 837 MET cc_start: 0.4843 (mmm) cc_final: 0.4461 (mmm) REVERT: A 1754 TYR cc_start: 0.9186 (m-80) cc_final: 0.8872 (m-10) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1263 time to fit residues: 20.5866 Evaluate side-chains 82 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 19 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 75 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 46 optimal weight: 0.5980 chunk 21 optimal weight: 0.0470 chunk 52 optimal weight: 8.9990 overall best weight: 0.9082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 116 HIS A 493 GLN ** A 648 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.071546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.053639 restraints weight = 107501.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.055291 restraints weight = 75705.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.056589 restraints weight = 57409.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.057535 restraints weight = 45956.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.058338 restraints weight = 38374.423| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6063 moved from start: 0.4801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 12712 Z= 0.140 Angle : 0.838 12.400 17470 Z= 0.423 Chirality : 0.050 0.250 2036 Planarity : 0.006 0.060 2012 Dihedral : 11.410 77.402 2208 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 20.63 Ramachandran Plot: Outliers : 0.22 % Allowed : 13.88 % Favored : 85.90 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 1.30 % Twisted Proline : 1.43 % Twisted General : 0.31 % 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: -3.23 (0.22), residues: 1369 helix: -1.22 (0.20), residues: 598 sheet: -2.99 (0.52), residues: 81 loop : -2.96 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 187 TYR 0.014 0.002 TYR A 452 PHE 0.021 0.002 PHE A 351 TRP 0.028 0.002 TRP A1048 HIS 0.006 0.001 HIS A1719 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (12711) covalent geometry : angle 0.83801 / 0.42 (17468) SS BOND : bond 0.00200 / 0.11 ( 1) SS BOND : angle 1.31899 / 0.72 ( 2) hydrogen bonds : bond 0.04508 / 3.09 ( 439) hydrogen bonds : angle 5.89595 / 4.08 ( 1207) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.527 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 HIS cc_start: 0.9433 (t-90) cc_final: 0.9199 (t-90) REVERT: A 447 PHE cc_start: 0.9090 (m-80) cc_final: 0.8704 (m-80) REVERT: A 562 MET cc_start: 0.4689 (tpt) cc_final: 0.2677 (tpp) REVERT: A 837 MET cc_start: 0.4752 (mmm) cc_final: 0.4441 (mmm) REVERT: A 928 GLN cc_start: 0.9626 (mm110) cc_final: 0.9352 (pp30) REVERT: A 1050 LYS cc_start: 0.9160 (ttpt) cc_final: 0.8863 (ptmt) REVERT: A 1687 PHE cc_start: 0.9014 (m-80) cc_final: 0.8783 (m-80) REVERT: A 1754 TYR cc_start: 0.9085 (m-80) cc_final: 0.8642 (m-10) REVERT: B 296 ARG cc_start: 0.7813 (tmm160) cc_final: 0.7559 (mmt180) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.1213 time to fit residues: 22.1034 Evaluate side-chains 84 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 127 optimal weight: 20.0000 chunk 10 optimal weight: 0.9990 chunk 71 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 142 optimal weight: 20.0000 chunk 112 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 60 optimal weight: 8.9990 chunk 58 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 648 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1695 ASN ** 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 = 0.3776 r_free = 0.3776 target = 0.068335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.051381 restraints weight = 113842.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.052932 restraints weight = 79633.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.054101 restraints weight = 60395.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.055006 restraints weight = 48532.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.055707 restraints weight = 40551.799| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6184 moved from start: 0.4777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 12712 Z= 0.210 Angle : 0.920 14.186 17470 Z= 0.465 Chirality : 0.053 0.300 2036 Planarity : 0.007 0.094 2012 Dihedral : 11.673 78.510 2208 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 29.54 Ramachandran Plot: Outliers : 0.29 % Allowed : 14.76 % Favored : 84.95 % Rotamer: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 1.30 % Twisted Proline : 1.43 % Twisted General : 0.38 % 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: -3.22 (0.22), residues: 1369 helix: -1.24 (0.20), residues: 582 sheet: -3.33 (0.48), residues: 89 loop : -2.83 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A 187 TYR 0.021 0.002 TYR A1721 PHE 0.025 0.002 PHE A1812 TRP 0.059 0.004 TRP A 316 HIS 0.010 0.002 HIS A1719 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.21 (12711) covalent geometry : angle 0.92012 / 0.47 (17468) SS BOND : bond 0.00243 / 0.13 ( 1) SS BOND : angle 1.65326 / 0.88 ( 2) hydrogen bonds : bond 0.05350 / 3.61 ( 439) hydrogen bonds : angle 6.04282 / 4.18 ( 1207) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.485 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 HIS cc_start: 0.9408 (t-90) cc_final: 0.9206 (t-90) REVERT: A 837 MET cc_start: 0.4810 (mmm) cc_final: 0.4482 (mmm) REVERT: A 1687 PHE cc_start: 0.8959 (m-80) cc_final: 0.8598 (m-80) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.1261 time to fit residues: 19.1101 Evaluate side-chains 79 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 51 optimal weight: 0.0870 chunk 91 optimal weight: 8.9990 chunk 71 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 11 optimal weight: 0.0980 chunk 29 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 13 optimal weight: 10.0000 chunk 102 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 116 HIS ** A 648 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.070475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.051532 restraints weight = 113856.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.053081 restraints weight = 82573.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.054206 restraints weight = 64321.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.055211 restraints weight = 52613.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.055958 restraints weight = 44562.241| |-----------------------------------------------------------------------------| r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5941 moved from start: 0.5198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 12712 Z= 0.146 Angle : 0.867 12.185 17470 Z= 0.439 Chirality : 0.051 0.259 2036 Planarity : 0.006 0.086 2012 Dihedral : 11.570 78.612 2208 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 21.66 Ramachandran Plot: Outliers : 0.15 % Allowed : 13.15 % Favored : 86.71 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 1.30 % Twisted Proline : 1.43 % Twisted General : 0.23 % 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: -3.09 (0.22), residues: 1369 helix: -1.17 (0.20), residues: 583 sheet: -3.10 (0.50), residues: 87 loop : -2.75 (0.23), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 187 TYR 0.019 0.002 TYR A1721 PHE 0.020 0.002 PHE A 351 TRP 0.054 0.004 TRP A 316 HIS 0.004 0.001 HIS A1661 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.15 (12711) covalent geometry : angle 0.86702 / 0.44 (17468) SS BOND : bond 0.00219 / 0.12 ( 1) SS BOND : angle 1.45149 / 0.79 ( 2) hydrogen bonds : bond 0.04627 / 3.14 ( 439) hydrogen bonds : angle 5.98802 / 4.14 ( 1207) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.471 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 PHE cc_start: 0.9433 (m-80) cc_final: 0.9222 (m-80) REVERT: A 447 PHE cc_start: 0.8936 (m-80) cc_final: 0.8565 (m-80) REVERT: A 503 GLU cc_start: 0.8648 (pp20) cc_final: 0.8053 (mp0) REVERT: A 837 MET cc_start: 0.4815 (mmm) cc_final: 0.4495 (mmm) REVERT: A 1323 LEU cc_start: 0.7974 (pp) cc_final: 0.7764 (pp) REVERT: A 1571 LEU cc_start: 0.7916 (tp) cc_final: 0.7620 (mt) REVERT: A 1687 PHE cc_start: 0.8975 (m-80) cc_final: 0.8745 (m-80) REVERT: A 1754 TYR cc_start: 0.9011 (m-80) cc_final: 0.8789 (m-10) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.1265 time to fit residues: 20.6034 Evaluate side-chains 82 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 69 optimal weight: 0.3980 chunk 132 optimal weight: 0.5980 chunk 115 optimal weight: 3.9990 chunk 16 optimal weight: 8.9990 chunk 123 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 118 optimal weight: 0.9980 chunk 40 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 116 HIS ** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 648 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.070334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.051569 restraints weight = 115144.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.053033 restraints weight = 85270.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.054177 restraints weight = 67181.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.055098 restraints weight = 55466.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.055822 restraints weight = 47266.503| |-----------------------------------------------------------------------------| r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5991 moved from start: 0.5419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 12712 Z= 0.149 Angle : 0.855 12.032 17470 Z= 0.433 Chirality : 0.050 0.247 2036 Planarity : 0.006 0.079 2012 Dihedral : 11.492 79.309 2208 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 23.39 Ramachandran Plot: Outliers : 0.07 % Allowed : 14.61 % Favored : 85.32 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 1.30 % Twisted Proline : 1.43 % Twisted General : 0.38 % 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: -3.05 (0.22), residues: 1369 helix: -1.12 (0.20), residues: 582 sheet: -3.14 (0.50), residues: 87 loop : -2.72 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 187 TYR 0.020 0.002 TYR A 579 PHE 0.014 0.002 PHE A 351 TRP 0.052 0.004 TRP A 316 HIS 0.004 0.001 HIS A1661 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 (12711) covalent geometry : angle 0.85510 / 0.43 (17468) SS BOND : bond 0.00182 / 0.10 ( 1) SS BOND : angle 1.09125 / 0.60 ( 2) hydrogen bonds : bond 0.04563 / 3.07 ( 439) hydrogen bonds : angle 5.94308 / 4.13 ( 1207) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.376 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 HIS cc_start: 0.9394 (t-90) cc_final: 0.9187 (t-90) REVERT: A 447 PHE cc_start: 0.8823 (m-80) cc_final: 0.8440 (m-80) REVERT: A 543 TYR cc_start: 0.8708 (p90) cc_final: 0.8435 (p90) REVERT: A 562 MET cc_start: 0.4476 (tpt) cc_final: 0.2806 (tpt) REVERT: A 837 MET cc_start: 0.5029 (mmm) cc_final: 0.4738 (mmm) REVERT: A 1050 LYS cc_start: 0.9300 (ttpp) cc_final: 0.8839 (mmtt) REVERT: A 1687 PHE cc_start: 0.9137 (m-80) cc_final: 0.8760 (m-80) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.1169 time to fit residues: 18.3880 Evaluate side-chains 77 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 118 optimal weight: 0.9980 chunk 44 optimal weight: 9.9990 chunk 17 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 chunk 141 optimal weight: 20.0000 chunk 119 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 chunk 106 optimal weight: 9.9990 chunk 84 optimal weight: 7.9990 chunk 49 optimal weight: 0.3980 chunk 6 optimal weight: 4.9990 overall best weight: 3.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 648 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1695 ASN ** 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 = 0.3784 r_free = 0.3784 target = 0.068891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.051476 restraints weight = 110483.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.053033 restraints weight = 77196.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.054208 restraints weight = 59189.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.055129 restraints weight = 47805.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.055847 restraints weight = 40045.853| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6272 moved from start: 0.5320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12712 Z= 0.195 Angle : 0.913 11.881 17470 Z= 0.462 Chirality : 0.052 0.292 2036 Planarity : 0.007 0.094 2012 Dihedral : 11.729 79.776 2208 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 29.25 Ramachandran Plot: Outliers : 0.07 % Allowed : 15.27 % Favored : 84.66 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 1.30 % Twisted Proline : 1.43 % Twisted General : 0.23 % 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: -3.16 (0.22), residues: 1369 helix: -1.29 (0.20), residues: 583 sheet: -3.33 (0.47), residues: 91 loop : -2.67 (0.24), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 187 TYR 0.024 0.002 TYR A1721 PHE 0.016 0.002 PHE A 347 TRP 0.050 0.004 TRP A 316 HIS 0.005 0.001 HIS A 648 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.19 (12711) covalent geometry : angle 0.91274 / 0.46 (17468) SS BOND : bond 0.00198 / 0.10 ( 1) SS BOND : angle 1.34087 / 0.71 ( 2) hydrogen bonds : bond 0.05049 / 3.35 ( 439) hydrogen bonds : angle 6.13131 / 4.25 ( 1207) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2090.23 seconds wall clock time: 37 minutes 15.44 seconds (2235.44 seconds total)