Starting phenix.real_space_refine on Sat Aug 23 15:33:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5xjy_6724/08_2025/5xjy_6724.cif Found real_map, /net/cci-nas-00/data/ceres_data/5xjy_6724/08_2025/5xjy_6724.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5xjy_6724/08_2025/5xjy_6724.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5xjy_6724/08_2025/5xjy_6724.map" model { file = "/net/cci-nas-00/data/ceres_data/5xjy_6724/08_2025/5xjy_6724.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5xjy_6724/08_2025/5xjy_6724.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 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: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 8095 2.51 5 N 2245 2.21 5 O 2388 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12785 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 12626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1901, 12626 Classifications: {'peptide': 1901} Incomplete info: {'truncation_to_alanine': 733} Link IDs: {'PTRANS': 89, 'TRANS': 1811} Chain breaks: 15 Unresolved chain link angles: 25 Unresolved non-hydrogen bonds: 2560 Unresolved non-hydrogen angles: 3266 Unresolved non-hydrogen dihedrals: 2133 Unresolved non-hydrogen chiralities: 254 Planarities with less than four sites: {'ASN:plan1': 34, 'GLN:plan1': 28, 'ASP:plan': 39, 'PHE:plan': 41, 'GLU:plan': 50, 'TYR:plan': 21, 'HIS:plan': 23, 'ARG:plan': 40, 'TRP:plan': 9} Unresolved non-hydrogen planarities: 1320 Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 2.90, per 1000 atoms: 0.23 Number of scatterers: 12785 At special positions: 0 Unit cell: (101.91, 104.523, 220.805, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 57 16.00 O 2388 8.00 N 2245 7.00 C 8095 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 81 " distance=2.03 Simple disulfide: pdb=" SG CYS A 75 " - pdb=" SG CYS A 309 " distance=2.02 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 504 " distance=2.03 Simple disulfide: pdb=" SG CYS A1465 " - pdb=" SG CYS A1477 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-3 " BMA B 3 " - " BMA B 4 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " BETA1-6 " BMA B 3 " - " BMA B 5 " NAG-ASN " NAG A2301 " - " ASN A 98 " " NAG A2302 " - " ASN A 400 " " NAG A2303 " - " ASN A 489 " " NAG A2304 " - " ASN A 521 " " NAG A2305 " - " ASN A1453 " " NAG B 1 " - " ASN A1504 " " NAG C 1 " - " ASN A1637 " Time building additional restraints: 0.96 Conformation dependent library (CDL) restraints added in 595.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3570 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 8 sheets defined 54.7% alpha, 2.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 3 through 20 removed outlier: 4.017A pdb=" N LEU A 7 " --> pdb=" O CYS A 3 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG A 18 " --> pdb=" O ASN A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 45 Proline residue: A 32 - end of helix Processing helix chain 'A' and resid 65 through 75 Processing helix chain 'A' and resid 86 through 90 removed outlier: 3.538A pdb=" N ALA A 90 " --> pdb=" O PRO A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 117 removed outlier: 3.561A pdb=" N PHE A 106 " --> pdb=" O VAL A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 134 Processing helix chain 'A' and resid 200 through 210 removed outlier: 3.856A pdb=" N LEU A 206 " --> pdb=" O GLU A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 227 removed outlier: 3.631A pdb=" N GLU A 220 " --> pdb=" O GLY A 216 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 242 removed outlier: 3.713A pdb=" N MET A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP A 234 " --> pdb=" O ARG A 230 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) Proline residue: A 238 - end of helix Processing helix chain 'A' and resid 251 through 275 removed outlier: 3.768A pdb=" N ALA A 255 " --> pdb=" O SER A 251 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 286 Processing helix chain 'A' and resid 298 through 309 Processing helix chain 'A' and resid 353 through 365 Processing helix chain 'A' and resid 369 through 380 Proline residue: A 377 - end of helix removed outlier: 3.623A pdb=" N VAL A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 405 Processing helix chain 'A' and resid 410 through 427 removed outlier: 4.311A pdb=" N GLY A 414 " --> pdb=" O HIS A 410 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N TRP A 416 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU A 418 " --> pdb=" O GLY A 414 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N SER A 420 " --> pdb=" O TRP A 416 " (cutoff:3.500A) Proline residue: A 421 - end of helix Processing helix chain 'A' and resid 430 through 440 Processing helix chain 'A' and resid 443 through 448 Processing helix chain 'A' and resid 448 through 455 Processing helix chain 'A' and resid 461 through 468 Processing helix chain 'A' and resid 483 through 502 removed outlier: 4.168A pdb=" N ASN A 489 " --> pdb=" O ARG A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 529 Processing helix chain 'A' and resid 592 through 609 removed outlier: 3.727A pdb=" N LEU A 596 " --> pdb=" O GLY A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 639 Processing helix chain 'A' and resid 640 through 665 removed outlier: 4.343A pdb=" N ALA A 647 " --> pdb=" O PHE A 643 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N TRP A 648 " --> pdb=" O MET A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 674 Processing helix chain 'A' and resid 677 through 706 removed outlier: 3.796A pdb=" N LEU A 681 " --> pdb=" O ASP A 677 " (cutoff:3.500A) Proline residue: A 692 - end of helix removed outlier: 3.528A pdb=" N LEU A 706 " --> pdb=" O VAL A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 736 removed outlier: 3.933A pdb=" N VAL A 718 " --> pdb=" O ASP A 714 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N PHE A 719 " --> pdb=" O PRO A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 759 removed outlier: 5.794A pdb=" N GLY A 751 " --> pdb=" O ALA A 747 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILE A 752 " --> pdb=" O ALA A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 765 Processing helix chain 'A' and resid 773 through 781 removed outlier: 3.966A pdb=" N LEU A 781 " --> pdb=" O ILE A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 797 removed outlier: 3.603A pdb=" N GLY A 790 " --> pdb=" O ALA A 786 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 844 removed outlier: 3.588A pdb=" N SER A 824 " --> pdb=" O ASN A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 948 Processing helix chain 'A' and resid 964 through 968 removed outlier: 3.700A pdb=" N MET A 968 " --> pdb=" O ARG A 965 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1002 Processing helix chain 'A' and resid 1006 through 1020 removed outlier: 3.698A pdb=" N ALA A1010 " --> pdb=" O LYS A1006 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLU A1013 " --> pdb=" O LYS A1009 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN A1014 " --> pdb=" O ALA A1010 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP A1018 " --> pdb=" O GLN A1014 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL A1019 " --> pdb=" O MET A1015 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLY A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1021 through 1028 Processing helix chain 'A' and resid 1037 through 1047 Processing helix chain 'A' and resid 1063 through 1065 No H-bonds generated for 'chain 'A' and resid 1063 through 1065' Processing helix chain 'A' and resid 1066 through 1078 Processing helix chain 'A' and resid 1079 through 1081 No H-bonds generated for 'chain 'A' and resid 1079 through 1081' Processing helix chain 'A' and resid 1091 through 1097 Processing helix chain 'A' and resid 1114 through 1122 Processing helix chain 'A' and resid 1129 through 1137 removed outlier: 4.504A pdb=" N VAL A1135 " --> pdb=" O VAL A1131 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU A1136 " --> pdb=" O LYS A1132 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER A1137 " --> pdb=" O LYS A1133 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1176 Processing helix chain 'A' and resid 1206 through 1212 removed outlier: 3.955A pdb=" N TYR A1210 " --> pdb=" O TYR A1206 " (cutoff:3.500A) Processing helix chain 'A' and resid 1323 through 1342 Processing helix chain 'A' and resid 1348 through 1366 Proline residue: A1354 - end of helix Processing helix chain 'A' and resid 1400 through 1409 removed outlier: 3.542A pdb=" N ALA A1407 " --> pdb=" O GLU A1403 " (cutoff:3.500A) Processing helix chain 'A' and resid 1444 through 1453 Processing helix chain 'A' and resid 1504 through 1523 removed outlier: 3.636A pdb=" N LYS A1522 " --> pdb=" O ALA A1518 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASN A1523 " --> pdb=" O LYS A1519 " (cutoff:3.500A) Processing helix chain 'A' and resid 1547 through 1561 Processing helix chain 'A' and resid 1569 through 1582 Processing helix chain 'A' and resid 1600 through 1618 removed outlier: 3.865A pdb=" N SER A1604 " --> pdb=" O HIS A1600 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU A1606 " --> pdb=" O ILE A1602 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU A1618 " --> pdb=" O LEU A1614 " (cutoff:3.500A) Processing helix chain 'A' and resid 1639 through 1665 removed outlier: 4.130A pdb=" N VAL A1657 " --> pdb=" O VAL A1653 " (cutoff:3.500A) Processing helix chain 'A' and resid 1668 through 1681 removed outlier: 4.186A pdb=" N PHE A1672 " --> pdb=" O VAL A1668 " (cutoff:3.500A) Processing helix chain 'A' and resid 1683 through 1691 removed outlier: 3.627A pdb=" N SER A1691 " --> pdb=" O LEU A1687 " (cutoff:3.500A) Processing helix chain 'A' and resid 1695 through 1724 removed outlier: 4.241A pdb=" N VAL A1712 " --> pdb=" O CYS A1708 " (cutoff:3.500A) Proline residue: A1713 - end of helix Processing helix chain 'A' and resid 1735 through 1753 removed outlier: 4.205A pdb=" N LEU A1741 " --> pdb=" O VAL A1737 " (cutoff:3.500A) Proline residue: A1751 - end of helix Processing helix chain 'A' and resid 1765 through 1785 Processing helix chain 'A' and resid 1797 through 1803 Processing helix chain 'A' and resid 1804 through 1809 Processing helix chain 'A' and resid 1815 through 1838 Processing helix chain 'A' and resid 1850 through 1859 removed outlier: 3.947A pdb=" N PHE A1854 " --> pdb=" O GLY A1850 " (cutoff:3.500A) Processing helix chain 'A' and resid 1861 through 1874 removed outlier: 3.701A pdb=" N PHE A1874 " --> pdb=" O ILE A1870 " (cutoff:3.500A) Processing helix chain 'A' and resid 1953 through 1961 Processing helix chain 'A' and resid 2002 through 2013 Processing helix chain 'A' and resid 2019 through 2023 Processing helix chain 'A' and resid 2025 through 2030 Processing helix chain 'A' and resid 2048 through 2060 removed outlier: 3.567A pdb=" N LYS A2052 " --> pdb=" O GLY A2048 " (cutoff:3.500A) Processing helix chain 'A' and resid 2078 through 2093 Processing helix chain 'A' and resid 2103 through 2111 removed outlier: 3.579A pdb=" N CYS A2107 " --> pdb=" O SER A2103 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU A2110 " --> pdb=" O GLU A2106 " (cutoff:3.500A) Processing helix chain 'A' and resid 2127 through 2135 Processing helix chain 'A' and resid 2142 through 2149 Processing helix chain 'A' and resid 2161 through 2170 removed outlier: 3.956A pdb=" N GLY A2165 " --> pdb=" O LEU A2161 " (cutoff:3.500A) Processing helix chain 'A' and resid 2192 through 2206 removed outlier: 3.901A pdb=" N GLN A2196 " --> pdb=" O SER A2192 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS A2198 " --> pdb=" O LEU A2194 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LYS A2199 " --> pdb=" O SER A2195 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 50 Processing sheet with id=AA2, first strand: chain 'A' and resid 158 through 161 removed outlier: 4.204A pdb=" N LEU A 158 " --> pdb=" O THR A 168 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS A 166 " --> pdb=" O HIS A 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 384 through 385 removed outlier: 7.033A pdb=" N LEU A 384 " --> pdb=" O ILE A 536 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 617 through 621 removed outlier: 3.583A pdb=" N SER A1392 " --> pdb=" O PHE A1535 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 904 through 906 Processing sheet with id=AA6, first strand: chain 'A' and resid 977 through 978 removed outlier: 4.069A pdb=" N CYS A 978 " --> pdb=" O ILE A1055 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP A1057 " --> pdb=" O CYS A 978 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N LEU A1056 " --> pdb=" O SER A1087 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 1101 through 1104 removed outlier: 6.419A pdb=" N ILE A1101 " --> pdb=" O VAL A1112 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N VAL A1112 " --> pdb=" O ILE A1101 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE A1103 " --> pdb=" O CYS A1110 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1183 through 1184 675 hydrogen bonds defined for protein. 1989 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.47 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4075 1.34 - 1.46: 3200 1.46 - 1.59: 5633 1.59 - 1.72: 0 1.72 - 1.84: 91 Bond restraints: 12999 Sorted by residual: bond pdb=" C LEU A1353 " pdb=" N PRO A1354 " ideal model delta sigma weight residual 1.336 1.385 -0.049 1.20e-02 6.94e+03 1.69e+01 bond pdb=" C1 NAG A2305 " pdb=" O5 NAG A2305 " ideal model delta sigma weight residual 1.406 1.468 -0.062 2.00e-02 2.50e+03 9.60e+00 bond pdb=" CB GLN A 621 " pdb=" CG GLN A 621 " ideal model delta sigma weight residual 1.520 1.429 0.091 3.00e-02 1.11e+03 9.24e+00 bond pdb=" CB PHE A1605 " pdb=" CG PHE A1605 " ideal model delta sigma weight residual 1.502 1.437 0.065 2.30e-02 1.89e+03 8.08e+00 bond pdb=" CB VAL A 399 " pdb=" CG1 VAL A 399 " ideal model delta sigma weight residual 1.521 1.434 0.087 3.30e-02 9.18e+02 6.95e+00 ... (remaining 12994 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.68: 17355 3.68 - 7.35: 376 7.35 - 11.03: 54 11.03 - 14.71: 7 14.71 - 18.39: 1 Bond angle restraints: 17793 Sorted by residual: angle pdb=" C GLY A 926 " pdb=" N GLN A 927 " pdb=" CA GLN A 927 " ideal model delta sigma weight residual 121.54 133.77 -12.23 1.91e+00 2.74e-01 4.10e+01 angle pdb=" N GLN A 768 " pdb=" CA GLN A 768 " pdb=" CB GLN A 768 " ideal model delta sigma weight residual 114.17 107.20 6.97 1.14e+00 7.69e-01 3.74e+01 angle pdb=" N LEU A 759 " pdb=" CA LEU A 759 " pdb=" C LEU A 759 " ideal model delta sigma weight residual 109.81 122.50 -12.69 2.21e+00 2.05e-01 3.30e+01 angle pdb=" C TRP A1382 " pdb=" N MET A1383 " pdb=" CA MET A1383 " ideal model delta sigma weight residual 121.54 131.79 -10.25 1.91e+00 2.74e-01 2.88e+01 angle pdb=" CA LEU A1636 " pdb=" CB LEU A1636 " pdb=" CG LEU A1636 " ideal model delta sigma weight residual 116.30 134.69 -18.39 3.50e+00 8.16e-02 2.76e+01 ... (remaining 17788 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.67: 7478 21.67 - 43.34: 269 43.34 - 65.01: 32 65.01 - 86.68: 34 86.68 - 108.36: 16 Dihedral angle restraints: 7829 sinusoidal: 2338 harmonic: 5491 Sorted by residual: dihedral pdb=" CA THR A 386 " pdb=" C THR A 386 " pdb=" N PRO A 387 " pdb=" CA PRO A 387 " ideal model delta harmonic sigma weight residual -180.00 -117.05 -62.95 0 5.00e+00 4.00e-02 1.59e+02 dihedral pdb=" CB CYS A 355 " pdb=" SG CYS A 355 " pdb=" SG CYS A 504 " pdb=" CB CYS A 504 " ideal model delta sinusoidal sigma weight residual 93.00 179.44 -86.44 1 1.00e+01 1.00e-02 9.00e+01 dihedral pdb=" CB CYS A 75 " pdb=" SG CYS A 75 " pdb=" SG CYS A 309 " pdb=" CB CYS A 309 " ideal model delta sinusoidal sigma weight residual -86.00 -165.78 79.78 1 1.00e+01 1.00e-02 7.90e+01 ... (remaining 7826 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1894 0.096 - 0.193: 253 0.193 - 0.289: 25 0.289 - 0.386: 6 0.386 - 0.482: 2 Chirality restraints: 2180 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A1637 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.81e+00 chirality pdb=" CG LEU A 367 " pdb=" CB LEU A 367 " pdb=" CD1 LEU A 367 " pdb=" CD2 LEU A 367 " both_signs ideal model delta sigma weight residual False -2.59 -2.14 -0.45 2.00e-01 2.50e+01 5.00e+00 chirality pdb=" CG LEU A1636 " pdb=" CB LEU A1636 " pdb=" CD1 LEU A1636 " pdb=" CD2 LEU A1636 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.28e+00 ... (remaining 2177 not shown) Planarity restraints: 2329 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A1460 " -0.087 5.00e-02 4.00e+02 1.32e-01 2.78e+01 pdb=" N PRO A1461 " 0.228 5.00e-02 4.00e+02 pdb=" CA PRO A1461 " -0.072 5.00e-02 4.00e+02 pdb=" CD PRO A1461 " -0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 386 " -0.075 5.00e-02 4.00e+02 1.12e-01 2.02e+01 pdb=" N PRO A 387 " 0.195 5.00e-02 4.00e+02 pdb=" CA PRO A 387 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO A 387 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A1458 " 0.073 5.00e-02 4.00e+02 1.12e-01 1.99e+01 pdb=" N PRO A1459 " -0.193 5.00e-02 4.00e+02 pdb=" CA PRO A1459 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO A1459 " 0.062 5.00e-02 4.00e+02 ... (remaining 2326 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1642 2.74 - 3.28: 13099 3.28 - 3.82: 20183 3.82 - 4.36: 22398 4.36 - 4.90: 36607 Nonbonded interactions: 93929 Sorted by model distance: nonbonded pdb=" O ASN A1451 " pdb=" OG1 THR A1455 " model vdw 2.200 3.040 nonbonded pdb=" O TRP A 12 " pdb=" OG1 THR A 16 " model vdw 2.206 3.040 nonbonded pdb=" O PRO A 641 " pdb=" OG1 THR A 645 " model vdw 2.231 3.040 nonbonded pdb=" O MET A1456 " pdb=" OG SER A1460 " model vdw 2.233 3.040 nonbonded pdb=" O ILE A1697 " pdb=" OG SER A1701 " model vdw 2.258 3.040 ... (remaining 93924 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: 0.650 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: 0.020 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.210 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 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 : 0.010 0.095 13015 Z= 0.435 Angle : 1.326 18.386 17837 Z= 0.702 Chirality : 0.069 0.482 2180 Planarity : 0.009 0.132 2322 Dihedral : 14.801 108.356 4247 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.16 % Allowed : 14.07 % Favored : 85.77 % Rotamer: Outliers : 1.27 % Allowed : 4.56 % Favored : 94.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.74 % Twisted General : 0.50 % 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 aren not related in a simple way. whole: -6.01 (0.13), residues: 1869 helix: -3.43 (0.11), residues: 936 sheet: -5.20 (0.28), residues: 116 loop : -4.46 (0.17), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.002 ARG A1417 TYR 0.044 0.005 TYR A 754 PHE 0.051 0.004 PHE A 538 TRP 0.065 0.005 TRP A 533 HIS 0.012 0.004 HIS A 52 Details of bonding type rmsd covalent geometry : bond 0.00968 (12999) covalent geometry : angle 1.30908 (17793) SS BOND : bond 0.00784 ( 4) SS BOND : angle 4.01925 ( 8) hydrogen bonds : bond 0.13228 ( 675) hydrogen bonds : angle 11.82289 ( 1989) link_BETA1-3 : bond 0.00253 ( 1) link_BETA1-3 : angle 1.58190 ( 3) link_BETA1-4 : bond 0.01112 ( 3) link_BETA1-4 : angle 3.42576 ( 9) link_BETA1-6 : bond 0.00253 ( 1) link_BETA1-6 : angle 1.55764 ( 3) link_NAG-ASN : bond 0.00722 ( 7) link_NAG-ASN : angle 5.36344 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 333 time to evaluate : 0.344 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: A 101 ILE cc_start: 0.9269 (pt) cc_final: 0.8941 (tp) REVERT: A 282 ARG cc_start: 0.7019 (ptm160) cc_final: 0.5375 (mpt180) REVERT: A 362 LEU cc_start: 0.8338 (mt) cc_final: 0.8053 (mt) REVERT: A 373 LYS cc_start: 0.8958 (mptp) cc_final: 0.8684 (mmmt) REVERT: A 384 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8971 (pp) REVERT: A 511 GLU cc_start: 0.8271 (mp0) cc_final: 0.8062 (mp0) REVERT: A 525 GLU cc_start: 0.8440 (tt0) cc_final: 0.7872 (tp30) REVERT: A 533 TRP cc_start: 0.9293 (OUTLIER) cc_final: 0.8343 (t60) REVERT: A 553 LYS cc_start: 0.8945 (mttt) cc_final: 0.8650 (mttm) REVERT: A 598 ASP cc_start: 0.7808 (t0) cc_final: 0.7551 (t0) REVERT: A 638 ARG cc_start: 0.7598 (mpt-90) cc_final: 0.7024 (ttm110) REVERT: A 664 GLU cc_start: 0.8622 (tt0) cc_final: 0.8358 (tp30) REVERT: A 685 TRP cc_start: 0.8928 (m100) cc_final: 0.8640 (m100) REVERT: A 689 SER cc_start: 0.8408 (t) cc_final: 0.7983 (t) REVERT: A 705 LYS cc_start: 0.7805 (tptt) cc_final: 0.7236 (tppt) REVERT: A 1556 LYS cc_start: 0.8914 (ttmm) cc_final: 0.8658 (tppt) REVERT: A 1654 ASP cc_start: 0.7848 (t70) cc_final: 0.7235 (t0) REVERT: A 1665 MET cc_start: 0.8777 (mmp) cc_final: 0.8492 (mmp) REVERT: A 1726 GLN cc_start: 0.7177 (mt0) cc_final: 0.6707 (pm20) REVERT: A 1753 MET cc_start: 0.9122 (mmm) cc_final: 0.8750 (mmp) REVERT: A 1757 SER cc_start: 0.7889 (t) cc_final: 0.7559 (t) REVERT: A 1825 ASN cc_start: 0.8099 (t0) cc_final: 0.7779 (t0) outliers start: 12 outliers final: 3 residues processed: 343 average time/residue: 0.0955 time to fit residues: 47.2619 Evaluate side-chains 224 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 219 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 40.0000 chunk 77 optimal weight: 30.0000 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 0.9980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 55 HIS A 78 ASN A 621 GLN A1380 GLN A1607 ASN A1610 ASN ** A1611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1626 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1734 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.158177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 109)---------------| | r_work = 0.3551 r_free = 0.3551 target = 0.122953 restraints weight = 23904.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.120847 restraints weight = 18965.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.122085 restraints weight = 16787.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.122186 restraints weight = 14732.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.122244 restraints weight = 14179.603| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 13015 Z= 0.197 Angle : 0.871 15.599 17837 Z= 0.443 Chirality : 0.052 0.802 2180 Planarity : 0.007 0.109 2322 Dihedral : 10.867 87.418 2211 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.88 % Favored : 88.12 % Rotamer: Outliers : 0.53 % Allowed : 4.56 % Favored : 94.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.37 % Twisted General : 0.11 % 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 aren not related in a simple way. whole: -4.50 (0.16), residues: 1869 helix: -1.77 (0.14), residues: 967 sheet: -5.06 (0.31), residues: 108 loop : -4.30 (0.18), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1531 TYR 0.037 0.003 TYR A1532 PHE 0.030 0.002 PHE A1721 TRP 0.039 0.003 TRP A 533 HIS 0.006 0.001 HIS A1600 Details of bonding type rmsd covalent geometry : bond 0.00427 (12999) covalent geometry : angle 0.84889 (17793) SS BOND : bond 0.00566 ( 4) SS BOND : angle 2.19461 ( 8) hydrogen bonds : bond 0.05385 ( 675) hydrogen bonds : angle 6.94952 ( 1989) link_BETA1-3 : bond 0.00291 ( 1) link_BETA1-3 : angle 2.77905 ( 3) link_BETA1-4 : bond 0.00317 ( 3) link_BETA1-4 : angle 2.12197 ( 9) link_BETA1-6 : bond 0.00333 ( 1) link_BETA1-6 : angle 2.84533 ( 3) link_NAG-ASN : bond 0.00707 ( 7) link_NAG-ASN : angle 5.26223 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 283 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 LEU cc_start: 0.9064 (pp) cc_final: 0.8860 (pp) REVERT: A 362 LEU cc_start: 0.8235 (mt) cc_final: 0.7942 (mt) REVERT: A 511 GLU cc_start: 0.8220 (mp0) cc_final: 0.7932 (mp0) REVERT: A 525 GLU cc_start: 0.8137 (tt0) cc_final: 0.7754 (tp30) REVERT: A 529 GLU cc_start: 0.7379 (tp30) cc_final: 0.7129 (tp30) REVERT: A 533 TRP cc_start: 0.8412 (OUTLIER) cc_final: 0.7392 (t60) REVERT: A 598 ASP cc_start: 0.7431 (t0) cc_final: 0.7207 (t0) REVERT: A 631 ILE cc_start: 0.7888 (pt) cc_final: 0.7356 (tp) REVERT: A 638 ARG cc_start: 0.8258 (mpt-90) cc_final: 0.8034 (mmt-90) REVERT: A 689 SER cc_start: 0.8406 (t) cc_final: 0.7837 (t) REVERT: A 705 LYS cc_start: 0.7613 (tptt) cc_final: 0.6952 (tppt) REVERT: A 735 LEU cc_start: 0.8731 (tt) cc_final: 0.8492 (tt) REVERT: A 796 LEU cc_start: 0.7915 (tt) cc_final: 0.7601 (mm) REVERT: A 1335 LYS cc_start: 0.7854 (tttm) cc_final: 0.7087 (tptp) REVERT: A 1469 LYS cc_start: 0.8516 (pttm) cc_final: 0.7994 (mmmt) REVERT: A 1587 LYS cc_start: 0.8245 (mmtt) cc_final: 0.7735 (ptmm) REVERT: A 1654 ASP cc_start: 0.8119 (t70) cc_final: 0.7358 (t0) REVERT: A 1679 GLU cc_start: 0.8357 (mt-10) cc_final: 0.7917 (pt0) REVERT: A 1726 GLN cc_start: 0.7095 (mt0) cc_final: 0.6701 (pm20) REVERT: A 1753 MET cc_start: 0.9175 (mmm) cc_final: 0.8859 (mmp) REVERT: A 1757 SER cc_start: 0.7668 (t) cc_final: 0.7369 (m) REVERT: A 1822 MET cc_start: 0.6772 (mmm) cc_final: 0.6083 (mmm) outliers start: 5 outliers final: 1 residues processed: 286 average time/residue: 0.0802 time to fit residues: 35.1665 Evaluate side-chains 209 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 207 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 88 optimal weight: 0.0980 chunk 83 optimal weight: 7.9990 chunk 151 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 17 optimal weight: 40.0000 chunk 71 optimal weight: 6.9990 chunk 79 optimal weight: 7.9990 chunk 168 optimal weight: 30.0000 chunk 33 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 52 optimal weight: 0.0070 overall best weight: 2.4204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS A 134 GLN A 506 ASN A 508 ASN A1557 GLN A1607 ASN ** A1626 HIS ** 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 = 0.3970 r_free = 0.3970 target = 0.156307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.123147 restraints weight = 24322.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.122621 restraints weight = 24941.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.124265 restraints weight = 21704.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.124180 restraints weight = 17714.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.124271 restraints weight = 17076.859| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 13015 Z= 0.215 Angle : 0.831 13.878 17837 Z= 0.424 Chirality : 0.050 0.578 2180 Planarity : 0.006 0.101 2322 Dihedral : 9.138 77.107 2211 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.95 % Favored : 87.05 % Rotamer: Outliers : 0.32 % Allowed : 5.41 % Favored : 94.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.06 % 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 aren not related in a simple way. whole: -3.71 (0.17), residues: 1869 helix: -0.87 (0.15), residues: 989 sheet: -5.34 (0.32), residues: 99 loop : -4.29 (0.18), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 579 TYR 0.042 0.003 TYR A1532 PHE 0.039 0.002 PHE A 36 TRP 0.044 0.003 TRP A 533 HIS 0.004 0.001 HIS A 52 Details of bonding type rmsd covalent geometry : bond 0.00470 (12999) covalent geometry : angle 0.80936 (17793) SS BOND : bond 0.00474 ( 4) SS BOND : angle 1.93359 ( 8) hydrogen bonds : bond 0.05027 ( 675) hydrogen bonds : angle 6.18111 ( 1989) link_BETA1-3 : bond 0.00522 ( 1) link_BETA1-3 : angle 1.95580 ( 3) link_BETA1-4 : bond 0.00534 ( 3) link_BETA1-4 : angle 2.29752 ( 9) link_BETA1-6 : bond 0.00453 ( 1) link_BETA1-6 : angle 2.10400 ( 3) link_NAG-ASN : bond 0.01009 ( 7) link_NAG-ASN : angle 5.14049 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 264 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 525 GLU cc_start: 0.8200 (tt0) cc_final: 0.7863 (tp30) REVERT: A 529 GLU cc_start: 0.7512 (tp30) cc_final: 0.7234 (tp30) REVERT: A 598 ASP cc_start: 0.7966 (t0) cc_final: 0.7759 (t0) REVERT: A 622 MET cc_start: 0.8702 (mpp) cc_final: 0.8422 (mpp) REVERT: A 631 ILE cc_start: 0.7938 (pt) cc_final: 0.7499 (tp) REVERT: A 638 ARG cc_start: 0.8223 (mpt-90) cc_final: 0.7807 (mmt-90) REVERT: A 705 LYS cc_start: 0.7694 (tptt) cc_final: 0.7032 (tppt) REVERT: A 735 LEU cc_start: 0.8915 (tt) cc_final: 0.8710 (tt) REVERT: A 761 TYR cc_start: 0.7563 (t80) cc_final: 0.7261 (t80) REVERT: A 796 LEU cc_start: 0.8098 (tt) cc_final: 0.7702 (mm) REVERT: A 1335 LYS cc_start: 0.7801 (tttm) cc_final: 0.7186 (tptp) REVERT: A 1364 PHE cc_start: 0.7308 (t80) cc_final: 0.6791 (m-80) REVERT: A 1469 LYS cc_start: 0.8422 (pttm) cc_final: 0.8182 (mmmt) REVERT: A 1587 LYS cc_start: 0.8394 (mmtt) cc_final: 0.7798 (ptmm) REVERT: A 1599 TRP cc_start: 0.8885 (m100) cc_final: 0.8522 (m-10) REVERT: A 1654 ASP cc_start: 0.7802 (t70) cc_final: 0.7081 (t0) REVERT: A 1673 VAL cc_start: 0.9575 (t) cc_final: 0.9304 (t) REVERT: A 1679 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7564 (mm-30) REVERT: A 1726 GLN cc_start: 0.7400 (mt0) cc_final: 0.6891 (pm20) REVERT: A 1753 MET cc_start: 0.9076 (mmm) cc_final: 0.8770 (mmp) REVERT: A 1822 MET cc_start: 0.6490 (mmm) cc_final: 0.5797 (mmm) outliers start: 3 outliers final: 0 residues processed: 265 average time/residue: 0.0753 time to fit residues: 30.4530 Evaluate side-chains 210 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 118 optimal weight: 7.9990 chunk 165 optimal weight: 40.0000 chunk 27 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 158 optimal weight: 20.0000 chunk 54 optimal weight: 0.2980 chunk 91 optimal weight: 20.0000 chunk 8 optimal weight: 8.9990 chunk 1 optimal weight: 0.2980 chunk 47 optimal weight: 0.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 ASN A1607 ASN ** A1611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1626 HIS A1734 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.157219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.132521 restraints weight = 24212.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 74)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.122700 restraints weight = 25567.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.121994 restraints weight = 24827.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.122532 restraints weight = 18956.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.122701 restraints weight = 14275.862| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13015 Z= 0.191 Angle : 0.793 12.701 17837 Z= 0.401 Chirality : 0.049 0.496 2180 Planarity : 0.006 0.096 2322 Dihedral : 8.290 68.532 2211 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.63 % Favored : 87.37 % Rotamer: Outliers : 0.21 % Allowed : 4.77 % Favored : 95.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.13 (0.18), residues: 1869 helix: -0.27 (0.16), residues: 983 sheet: -5.09 (0.36), residues: 92 loop : -4.19 (0.18), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 485 TYR 0.043 0.003 TYR A 650 PHE 0.030 0.002 PHE A1721 TRP 0.037 0.002 TRP A 533 HIS 0.003 0.001 HIS A1626 Details of bonding type rmsd covalent geometry : bond 0.00421 (12999) covalent geometry : angle 0.77642 (17793) SS BOND : bond 0.00480 ( 4) SS BOND : angle 1.59009 ( 8) hydrogen bonds : bond 0.04709 ( 675) hydrogen bonds : angle 5.78444 ( 1989) link_BETA1-3 : bond 0.00443 ( 1) link_BETA1-3 : angle 2.25914 ( 3) link_BETA1-4 : bond 0.00573 ( 3) link_BETA1-4 : angle 2.21114 ( 9) link_BETA1-6 : bond 0.00883 ( 1) link_BETA1-6 : angle 1.96677 ( 3) link_NAG-ASN : bond 0.00782 ( 7) link_NAG-ASN : angle 4.42022 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 277 time to evaluate : 0.387 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: A 26 LEU cc_start: 0.8744 (mm) cc_final: 0.8472 (mt) REVERT: A 278 TRP cc_start: 0.2986 (t-100) cc_final: 0.2491 (t-100) REVERT: A 417 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7809 (tm-30) REVERT: A 525 GLU cc_start: 0.8283 (tt0) cc_final: 0.8034 (tp30) REVERT: A 529 GLU cc_start: 0.7380 (tp30) cc_final: 0.7153 (tp30) REVERT: A 533 TRP cc_start: 0.6922 (t60) cc_final: 0.6713 (t60) REVERT: A 631 ILE cc_start: 0.7843 (pt) cc_final: 0.7443 (tp) REVERT: A 669 GLU cc_start: 0.8209 (mp0) cc_final: 0.7997 (mp0) REVERT: A 689 SER cc_start: 0.8322 (t) cc_final: 0.7754 (t) REVERT: A 705 LYS cc_start: 0.7618 (tptt) cc_final: 0.6911 (tppt) REVERT: A 761 TYR cc_start: 0.7494 (t80) cc_final: 0.7147 (t80) REVERT: A 1335 LYS cc_start: 0.7836 (tttm) cc_final: 0.7136 (tptp) REVERT: A 1364 PHE cc_start: 0.7168 (t80) cc_final: 0.6677 (m-80) REVERT: A 1577 LEU cc_start: 0.9480 (tp) cc_final: 0.9268 (tp) REVERT: A 1587 LYS cc_start: 0.8363 (mmtt) cc_final: 0.7797 (ptmm) REVERT: A 1599 TRP cc_start: 0.8922 (m100) cc_final: 0.8571 (m-10) REVERT: A 1654 ASP cc_start: 0.7912 (t70) cc_final: 0.7195 (t0) REVERT: A 1673 VAL cc_start: 0.9508 (t) cc_final: 0.9262 (t) REVERT: A 1707 MET cc_start: 0.8456 (tpt) cc_final: 0.8250 (mmm) REVERT: A 1710 TYR cc_start: 0.8557 (t80) cc_final: 0.8259 (t80) REVERT: A 1726 GLN cc_start: 0.7112 (mt0) cc_final: 0.6801 (pm20) REVERT: A 1753 MET cc_start: 0.9128 (mmm) cc_final: 0.8857 (mmp) REVERT: A 1822 MET cc_start: 0.6544 (mmm) cc_final: 0.5907 (mmm) outliers start: 2 outliers final: 0 residues processed: 277 average time/residue: 0.0759 time to fit residues: 32.3844 Evaluate side-chains 212 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 53 optimal weight: 0.7980 chunk 102 optimal weight: 0.4980 chunk 18 optimal weight: 7.9990 chunk 177 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 80 optimal weight: 20.0000 chunk 26 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 119 optimal weight: 7.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1557 GLN A1607 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.159426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.126981 restraints weight = 24300.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.125606 restraints weight = 23800.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.127377 restraints weight = 20025.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.127182 restraints weight = 14589.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.127447 restraints weight = 14773.555| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13015 Z= 0.164 Angle : 0.774 11.875 17837 Z= 0.387 Chirality : 0.048 0.461 2180 Planarity : 0.006 0.087 2322 Dihedral : 7.704 61.638 2211 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.40 % Favored : 88.60 % Rotamer: Outliers : 0.11 % Allowed : 3.08 % Favored : 96.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.67 (0.19), residues: 1869 helix: 0.18 (0.17), residues: 985 sheet: -4.86 (0.39), residues: 91 loop : -4.11 (0.18), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 587 TYR 0.026 0.002 TYR A 385 PHE 0.025 0.002 PHE A1721 TRP 0.045 0.002 TRP A 533 HIS 0.003 0.001 HIS A1626 Details of bonding type rmsd covalent geometry : bond 0.00357 (12999) covalent geometry : angle 0.75361 (17793) SS BOND : bond 0.00366 ( 4) SS BOND : angle 2.01781 ( 8) hydrogen bonds : bond 0.04465 ( 675) hydrogen bonds : angle 5.46300 ( 1989) link_BETA1-3 : bond 0.00523 ( 1) link_BETA1-3 : angle 2.17984 ( 3) link_BETA1-4 : bond 0.00352 ( 3) link_BETA1-4 : angle 2.14987 ( 9) link_BETA1-6 : bond 0.01124 ( 1) link_BETA1-6 : angle 1.80752 ( 3) link_NAG-ASN : bond 0.00784 ( 7) link_NAG-ASN : angle 4.74809 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 275 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.8831 (mpt-90) cc_final: 0.8608 (mmt90) REVERT: A 63 SER cc_start: 0.8977 (t) cc_final: 0.8758 (t) REVERT: A 278 TRP cc_start: 0.2758 (t-100) cc_final: 0.2377 (t-100) REVERT: A 417 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7736 (tm-30) REVERT: A 529 GLU cc_start: 0.7230 (tp30) cc_final: 0.7005 (tp30) REVERT: A 613 LYS cc_start: 0.7674 (tppt) cc_final: 0.7465 (tppt) REVERT: A 631 ILE cc_start: 0.7946 (pt) cc_final: 0.7465 (tp) REVERT: A 638 ARG cc_start: 0.7910 (mpt-90) cc_final: 0.7136 (mmm160) REVERT: A 689 SER cc_start: 0.8210 (t) cc_final: 0.7510 (t) REVERT: A 705 LYS cc_start: 0.7701 (tptt) cc_final: 0.6912 (tppt) REVERT: A 735 LEU cc_start: 0.8946 (tt) cc_final: 0.8739 (tt) REVERT: A 1364 PHE cc_start: 0.7122 (t80) cc_final: 0.6732 (m-80) REVERT: A 1587 LYS cc_start: 0.8280 (mmtt) cc_final: 0.7635 (ptmm) REVERT: A 1607 ASN cc_start: 0.8938 (t160) cc_final: 0.8652 (t0) REVERT: A 1629 ILE cc_start: 0.9286 (tt) cc_final: 0.8771 (tt) REVERT: A 1654 ASP cc_start: 0.7838 (t70) cc_final: 0.6951 (t0) REVERT: A 1665 MET cc_start: 0.8740 (mmp) cc_final: 0.8531 (mmp) REVERT: A 1673 VAL cc_start: 0.9522 (t) cc_final: 0.9262 (t) REVERT: A 1710 TYR cc_start: 0.8578 (t80) cc_final: 0.8238 (t80) REVERT: A 1726 GLN cc_start: 0.7246 (mt0) cc_final: 0.6864 (pm20) REVERT: A 1825 ASN cc_start: 0.8024 (t0) cc_final: 0.7485 (t0) outliers start: 1 outliers final: 1 residues processed: 276 average time/residue: 0.0767 time to fit residues: 32.1728 Evaluate side-chains 217 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 216 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 175 optimal weight: 40.0000 chunk 11 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 68 optimal weight: 7.9990 chunk 91 optimal weight: 0.0470 chunk 50 optimal weight: 2.9990 chunk 144 optimal weight: 6.9990 chunk 88 optimal weight: 8.9990 chunk 96 optimal weight: 0.0060 chunk 178 optimal weight: 20.0000 chunk 27 optimal weight: 8.9990 overall best weight: 1.0100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1607 ASN A1611 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.160959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 112)---------------| | r_work = 0.3618 r_free = 0.3618 target = 0.127318 restraints weight = 24014.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.125391 restraints weight = 19332.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.126166 restraints weight = 18194.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.126386 restraints weight = 14815.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.126540 restraints weight = 13903.717| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.3912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13015 Z= 0.147 Angle : 0.741 11.377 17837 Z= 0.369 Chirality : 0.047 0.436 2180 Planarity : 0.005 0.076 2322 Dihedral : 7.164 55.490 2211 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.49 % Favored : 89.51 % Rotamer: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.26 (0.19), residues: 1869 helix: 0.52 (0.17), residues: 991 sheet: -4.75 (0.39), residues: 92 loop : -3.96 (0.19), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1680 TYR 0.028 0.002 TYR A 650 PHE 0.021 0.002 PHE A1721 TRP 0.034 0.002 TRP A 533 HIS 0.004 0.001 HIS A1600 Details of bonding type rmsd covalent geometry : bond 0.00319 (12999) covalent geometry : angle 0.72307 (17793) SS BOND : bond 0.00526 ( 4) SS BOND : angle 1.77063 ( 8) hydrogen bonds : bond 0.04181 ( 675) hydrogen bonds : angle 5.16843 ( 1989) link_BETA1-3 : bond 0.00575 ( 1) link_BETA1-3 : angle 2.25808 ( 3) link_BETA1-4 : bond 0.00372 ( 3) link_BETA1-4 : angle 2.09897 ( 9) link_BETA1-6 : bond 0.01306 ( 1) link_BETA1-6 : angle 1.73512 ( 3) link_NAG-ASN : bond 0.00782 ( 7) link_NAG-ASN : angle 4.42772 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.8901 (mpt-90) cc_final: 0.8654 (mmt90) REVERT: A 278 TRP cc_start: 0.3029 (t-100) cc_final: 0.2741 (t-100) REVERT: A 301 TYR cc_start: 0.6917 (m-10) cc_final: 0.6617 (m-80) REVERT: A 417 GLU cc_start: 0.8165 (tm-30) cc_final: 0.7790 (tm-30) REVERT: A 631 ILE cc_start: 0.7696 (pt) cc_final: 0.7246 (tp) REVERT: A 689 SER cc_start: 0.8207 (t) cc_final: 0.7562 (t) REVERT: A 705 LYS cc_start: 0.7565 (tptt) cc_final: 0.6759 (ttmt) REVERT: A 1364 PHE cc_start: 0.7028 (t80) cc_final: 0.6546 (m-80) REVERT: A 1587 LYS cc_start: 0.8285 (mmtt) cc_final: 0.7599 (ptmm) REVERT: A 1599 TRP cc_start: 0.8618 (m-10) cc_final: 0.8394 (m-10) REVERT: A 1607 ASN cc_start: 0.8913 (t160) cc_final: 0.8467 (t0) REVERT: A 1611 ASN cc_start: 0.8263 (m-40) cc_final: 0.7810 (m110) REVERT: A 1654 ASP cc_start: 0.7861 (t70) cc_final: 0.6933 (t0) REVERT: A 1673 VAL cc_start: 0.9456 (t) cc_final: 0.9196 (t) REVERT: A 1710 TYR cc_start: 0.8509 (t80) cc_final: 0.8176 (t80) REVERT: A 1726 GLN cc_start: 0.7120 (mt0) cc_final: 0.6739 (pm20) REVERT: A 1825 ASN cc_start: 0.8121 (t0) cc_final: 0.7553 (t0) outliers start: 0 outliers final: 0 residues processed: 265 average time/residue: 0.0753 time to fit residues: 30.9835 Evaluate side-chains 211 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 41 optimal weight: 9.9990 chunk 117 optimal weight: 5.9990 chunk 99 optimal weight: 40.0000 chunk 44 optimal weight: 0.9990 chunk 165 optimal weight: 0.5980 chunk 158 optimal weight: 0.0970 chunk 103 optimal weight: 30.0000 chunk 129 optimal weight: 5.9990 chunk 123 optimal weight: 0.9990 chunk 7 optimal weight: 0.0570 chunk 16 optimal weight: 0.1980 overall best weight: 0.3898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 621 GLN A1443 GLN A1607 ASN A1686 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.163812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 101)---------------| | r_work = 0.3585 r_free = 0.3585 target = 0.126580 restraints weight = 24066.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.127265 restraints weight = 19217.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.128005 restraints weight = 15843.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.127975 restraints weight = 13790.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.128179 restraints weight = 14456.538| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.4246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13015 Z= 0.137 Angle : 0.745 12.983 17837 Z= 0.365 Chirality : 0.046 0.417 2180 Planarity : 0.005 0.070 2322 Dihedral : 6.846 54.276 2211 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.97 (0.20), residues: 1869 helix: 0.76 (0.17), residues: 994 sheet: -4.63 (0.40), residues: 91 loop : -3.84 (0.19), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 638 TYR 0.043 0.002 TYR A 650 PHE 0.023 0.001 PHE A1721 TRP 0.039 0.002 TRP A 533 HIS 0.005 0.001 HIS A1600 Details of bonding type rmsd covalent geometry : bond 0.00294 (12999) covalent geometry : angle 0.72390 (17793) SS BOND : bond 0.00328 ( 4) SS BOND : angle 1.42171 ( 8) hydrogen bonds : bond 0.04044 ( 675) hydrogen bonds : angle 4.96494 ( 1989) link_BETA1-3 : bond 0.00706 ( 1) link_BETA1-3 : angle 2.31474 ( 3) link_BETA1-4 : bond 0.00331 ( 3) link_BETA1-4 : angle 2.12102 ( 9) link_BETA1-6 : bond 0.01533 ( 1) link_BETA1-6 : angle 1.75667 ( 3) link_NAG-ASN : bond 0.00805 ( 7) link_NAG-ASN : angle 4.90892 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.8945 (mpt-90) cc_final: 0.8685 (mmt90) REVERT: A 39 LEU cc_start: 0.7414 (tp) cc_final: 0.6969 (tt) REVERT: A 278 TRP cc_start: 0.2747 (t-100) cc_final: 0.2536 (t-100) REVERT: A 360 LYS cc_start: 0.9122 (tttt) cc_final: 0.8611 (tttm) REVERT: A 417 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7816 (tm-30) REVERT: A 419 LEU cc_start: 0.9082 (mp) cc_final: 0.8692 (mp) REVERT: A 554 TYR cc_start: 0.8649 (p90) cc_final: 0.8358 (p90) REVERT: A 631 ILE cc_start: 0.7682 (pt) cc_final: 0.7295 (tp) REVERT: A 643 PHE cc_start: 0.6856 (p90) cc_final: 0.6655 (p90) REVERT: A 650 TYR cc_start: 0.7807 (t80) cc_final: 0.7581 (t80) REVERT: A 689 SER cc_start: 0.8257 (t) cc_final: 0.7597 (t) REVERT: A 705 LYS cc_start: 0.7446 (tptt) cc_final: 0.6656 (ttmt) REVERT: A 712 TYR cc_start: 0.4168 (m-80) cc_final: 0.3965 (m-80) REVERT: A 796 LEU cc_start: 0.7653 (tt) cc_final: 0.7333 (mm) REVERT: A 1401 THR cc_start: 0.8876 (m) cc_final: 0.8673 (m) REVERT: A 1571 ASP cc_start: 0.7205 (t0) cc_final: 0.6910 (t0) REVERT: A 1587 LYS cc_start: 0.8198 (mmtt) cc_final: 0.7574 (ptmm) REVERT: A 1607 ASN cc_start: 0.8977 (t160) cc_final: 0.8643 (t0) REVERT: A 1611 ASN cc_start: 0.8191 (m-40) cc_final: 0.7681 (m110) REVERT: A 1673 VAL cc_start: 0.9344 (t) cc_final: 0.9103 (t) REVERT: A 1710 TYR cc_start: 0.8530 (t80) cc_final: 0.8100 (t80) REVERT: A 1726 GLN cc_start: 0.7073 (mt0) cc_final: 0.6722 (pm20) REVERT: A 1825 ASN cc_start: 0.8165 (t0) cc_final: 0.7636 (t0) outliers start: 0 outliers final: 0 residues processed: 264 average time/residue: 0.0782 time to fit residues: 31.4995 Evaluate side-chains 211 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 0 optimal weight: 8.9990 chunk 9 optimal weight: 0.6980 chunk 132 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 83 optimal weight: 20.0000 chunk 89 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 70 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 37 optimal weight: 9.9990 chunk 76 optimal weight: 0.0010 overall best weight: 1.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 621 GLN ** A1607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1610 ASN A1812 HIS A1825 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.162169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.135487 restraints weight = 23895.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.129988 restraints weight = 28419.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.128946 restraints weight = 23922.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.129575 restraints weight = 18417.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.129877 restraints weight = 16457.979| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.4341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13015 Z= 0.148 Angle : 0.746 12.607 17837 Z= 0.367 Chirality : 0.047 0.413 2180 Planarity : 0.005 0.068 2322 Dihedral : 6.696 54.854 2211 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.33 % Favored : 89.67 % Rotamer: Outliers : 0.11 % Allowed : 1.91 % Favored : 97.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.78 (0.20), residues: 1869 helix: 0.93 (0.17), residues: 991 sheet: -4.55 (0.41), residues: 91 loop : -3.75 (0.19), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 579 TYR 0.040 0.002 TYR A 650 PHE 0.026 0.002 PHE A1721 TRP 0.052 0.002 TRP A1599 HIS 0.003 0.001 HIS A1626 Details of bonding type rmsd covalent geometry : bond 0.00325 (12999) covalent geometry : angle 0.72960 (17793) SS BOND : bond 0.00322 ( 4) SS BOND : angle 2.28647 ( 8) hydrogen bonds : bond 0.03956 ( 675) hydrogen bonds : angle 4.90245 ( 1989) link_BETA1-3 : bond 0.00596 ( 1) link_BETA1-3 : angle 2.21048 ( 3) link_BETA1-4 : bond 0.00374 ( 3) link_BETA1-4 : angle 2.15125 ( 9) link_BETA1-6 : bond 0.01335 ( 1) link_BETA1-6 : angle 1.72087 ( 3) link_NAG-ASN : bond 0.00759 ( 7) link_NAG-ASN : angle 4.14385 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 247 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.8863 (mpt-90) cc_final: 0.8619 (mmt90) REVERT: A 39 LEU cc_start: 0.7577 (tp) cc_final: 0.7129 (tt) REVERT: A 278 TRP cc_start: 0.2920 (t-100) cc_final: 0.2706 (t-100) REVERT: A 360 LYS cc_start: 0.9072 (tttt) cc_final: 0.8563 (tttm) REVERT: A 417 GLU cc_start: 0.8047 (tm-30) cc_final: 0.7748 (tm-30) REVERT: A 524 MET cc_start: 0.8631 (mpp) cc_final: 0.8418 (mpp) REVERT: A 553 LYS cc_start: 0.8947 (mttt) cc_final: 0.8566 (mttm) REVERT: A 554 TYR cc_start: 0.8691 (p90) cc_final: 0.8203 (p90) REVERT: A 631 ILE cc_start: 0.7785 (pt) cc_final: 0.7402 (tp) REVERT: A 640 MET cc_start: 0.7546 (tpp) cc_final: 0.7098 (tpp) REVERT: A 689 SER cc_start: 0.7938 (t) cc_final: 0.7159 (t) REVERT: A 705 LYS cc_start: 0.7350 (tptt) cc_final: 0.6617 (ttmt) REVERT: A 796 LEU cc_start: 0.7767 (tt) cc_final: 0.7383 (mm) REVERT: A 1587 LYS cc_start: 0.8192 (mmtt) cc_final: 0.7572 (ptmm) REVERT: A 1607 ASN cc_start: 0.8997 (t0) cc_final: 0.8712 (t0) REVERT: A 1710 TYR cc_start: 0.8533 (t80) cc_final: 0.8242 (t80) REVERT: A 1726 GLN cc_start: 0.7331 (mt0) cc_final: 0.6950 (pm20) REVERT: A 1737 VAL cc_start: 0.9255 (m) cc_final: 0.8795 (p) REVERT: A 1825 ASN cc_start: 0.7943 (OUTLIER) cc_final: 0.7358 (t0) outliers start: 1 outliers final: 0 residues processed: 247 average time/residue: 0.0690 time to fit residues: 27.0779 Evaluate side-chains 209 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 208 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 98 optimal weight: 30.0000 chunk 42 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 91 optimal weight: 9.9990 chunk 118 optimal weight: 8.9990 chunk 177 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 136 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 82 optimal weight: 0.0060 chunk 29 optimal weight: 7.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1678 GLN A1686 HIS ** A1812 HIS ** 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 = 0.4062 r_free = 0.4062 target = 0.163725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.127852 restraints weight = 24374.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.128743 restraints weight = 20817.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.128961 restraints weight = 15247.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.129029 restraints weight = 14347.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.129255 restraints weight = 13829.583| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.4569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 13015 Z= 0.139 Angle : 0.744 13.348 17837 Z= 0.364 Chirality : 0.047 0.400 2180 Planarity : 0.005 0.071 2322 Dihedral : 6.501 54.572 2211 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.62 (0.20), residues: 1869 helix: 1.02 (0.17), residues: 996 sheet: -4.45 (0.39), residues: 98 loop : -3.62 (0.20), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 638 TYR 0.027 0.002 TYR A 354 PHE 0.028 0.001 PHE A1721 TRP 0.038 0.002 TRP A1599 HIS 0.003 0.001 HIS A1812 Details of bonding type rmsd covalent geometry : bond 0.00302 (12999) covalent geometry : angle 0.72898 (17793) SS BOND : bond 0.00325 ( 4) SS BOND : angle 2.03881 ( 8) hydrogen bonds : bond 0.03906 ( 675) hydrogen bonds : angle 4.82361 ( 1989) link_BETA1-3 : bond 0.00626 ( 1) link_BETA1-3 : angle 2.25756 ( 3) link_BETA1-4 : bond 0.00348 ( 3) link_BETA1-4 : angle 2.17592 ( 9) link_BETA1-6 : bond 0.01472 ( 1) link_BETA1-6 : angle 1.84184 ( 3) link_NAG-ASN : bond 0.00744 ( 7) link_NAG-ASN : angle 3.81407 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 247 time to evaluate : 0.279 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: A 18 ARG cc_start: 0.8894 (mpt-90) cc_final: 0.8628 (mmt90) REVERT: A 39 LEU cc_start: 0.7515 (tp) cc_final: 0.7077 (tt) REVERT: A 360 LYS cc_start: 0.9093 (tttt) cc_final: 0.8587 (tttm) REVERT: A 417 GLU cc_start: 0.8038 (tm-30) cc_final: 0.7737 (tm-30) REVERT: A 508 ASN cc_start: 0.6513 (p0) cc_final: 0.6306 (p0) REVERT: A 554 TYR cc_start: 0.8637 (p90) cc_final: 0.8127 (p90) REVERT: A 631 ILE cc_start: 0.7739 (pt) cc_final: 0.7353 (tp) REVERT: A 640 MET cc_start: 0.7413 (tpp) cc_final: 0.6835 (tpp) REVERT: A 689 SER cc_start: 0.7992 (t) cc_final: 0.7225 (t) REVERT: A 705 LYS cc_start: 0.7278 (tptt) cc_final: 0.6551 (ttmt) REVERT: A 712 TYR cc_start: 0.4057 (m-80) cc_final: 0.3729 (m-80) REVERT: A 796 LEU cc_start: 0.7677 (tt) cc_final: 0.7361 (mm) REVERT: A 1401 THR cc_start: 0.8858 (m) cc_final: 0.8642 (m) REVERT: A 1473 MET cc_start: 0.8635 (mpp) cc_final: 0.8401 (mtt) REVERT: A 1587 LYS cc_start: 0.8183 (mmtt) cc_final: 0.7624 (ptmm) REVERT: A 1654 ASP cc_start: 0.8236 (t0) cc_final: 0.7810 (t0) REVERT: A 1710 TYR cc_start: 0.8579 (t80) cc_final: 0.8207 (t80) REVERT: A 1726 GLN cc_start: 0.7556 (mt0) cc_final: 0.7042 (pm20) REVERT: A 1737 VAL cc_start: 0.9290 (m) cc_final: 0.8845 (p) outliers start: 0 outliers final: 0 residues processed: 247 average time/residue: 0.0627 time to fit residues: 24.7309 Evaluate side-chains 210 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 152 optimal weight: 6.9990 chunk 153 optimal weight: 0.8980 chunk 122 optimal weight: 0.0470 chunk 25 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 133 optimal weight: 0.3980 chunk 58 optimal weight: 0.7980 chunk 85 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1686 HIS A1812 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.164677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.137069 restraints weight = 24402.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.132264 restraints weight = 26773.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.130423 restraints weight = 22833.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.130416 restraints weight = 20723.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.130732 restraints weight = 20183.803| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.4718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 13015 Z= 0.136 Angle : 0.741 12.695 17837 Z= 0.362 Chirality : 0.046 0.394 2180 Planarity : 0.005 0.071 2322 Dihedral : 6.359 54.557 2211 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.51 (0.20), residues: 1869 helix: 1.09 (0.17), residues: 997 sheet: -4.32 (0.42), residues: 96 loop : -3.56 (0.20), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 579 TYR 0.027 0.002 TYR A 650 PHE 0.030 0.001 PHE A1721 TRP 0.037 0.002 TRP A 533 HIS 0.003 0.001 HIS A1626 Details of bonding type rmsd covalent geometry : bond 0.00297 (12999) covalent geometry : angle 0.72765 (17793) SS BOND : bond 0.00273 ( 4) SS BOND : angle 1.79772 ( 8) hydrogen bonds : bond 0.03792 ( 675) hydrogen bonds : angle 4.77407 ( 1989) link_BETA1-3 : bond 0.00631 ( 1) link_BETA1-3 : angle 2.19929 ( 3) link_BETA1-4 : bond 0.00346 ( 3) link_BETA1-4 : angle 2.18341 ( 9) link_BETA1-6 : bond 0.01473 ( 1) link_BETA1-6 : angle 1.84755 ( 3) link_NAG-ASN : bond 0.00731 ( 7) link_NAG-ASN : angle 3.66380 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.8842 (mpt-90) cc_final: 0.8583 (mmt90) REVERT: A 39 LEU cc_start: 0.7515 (tp) cc_final: 0.7059 (tt) REVERT: A 360 LYS cc_start: 0.9063 (tttt) cc_final: 0.8590 (tttm) REVERT: A 413 GLU cc_start: 0.6701 (tm-30) cc_final: 0.5629 (tm-30) REVERT: A 508 ASN cc_start: 0.6510 (p0) cc_final: 0.6305 (p0) REVERT: A 524 MET cc_start: 0.8600 (mpp) cc_final: 0.8373 (mpp) REVERT: A 553 LYS cc_start: 0.8650 (mttt) cc_final: 0.8442 (mtpt) REVERT: A 554 TYR cc_start: 0.8601 (p90) cc_final: 0.8263 (p90) REVERT: A 613 LYS cc_start: 0.8355 (tppt) cc_final: 0.8123 (tppt) REVERT: A 631 ILE cc_start: 0.7754 (pt) cc_final: 0.7402 (tp) REVERT: A 689 SER cc_start: 0.7989 (t) cc_final: 0.7267 (t) REVERT: A 705 LYS cc_start: 0.7272 (tptt) cc_final: 0.6612 (ttmt) REVERT: A 712 TYR cc_start: 0.4033 (m-80) cc_final: 0.3738 (m-80) REVERT: A 796 LEU cc_start: 0.7652 (tt) cc_final: 0.7350 (mm) REVERT: A 1401 THR cc_start: 0.8855 (m) cc_final: 0.8641 (m) REVERT: A 1422 ASN cc_start: 0.8182 (m110) cc_final: 0.7843 (t0) REVERT: A 1473 MET cc_start: 0.8686 (mpp) cc_final: 0.8470 (mtt) REVERT: A 1587 LYS cc_start: 0.8230 (mmtt) cc_final: 0.7584 (ptmm) REVERT: A 1607 ASN cc_start: 0.8952 (t0) cc_final: 0.8651 (t0) REVERT: A 1611 ASN cc_start: 0.8458 (m-40) cc_final: 0.8020 (m110) REVERT: A 1662 ILE cc_start: 0.8725 (tp) cc_final: 0.7170 (tp) REVERT: A 1710 TYR cc_start: 0.8607 (t80) cc_final: 0.8256 (t80) REVERT: A 1726 GLN cc_start: 0.7624 (mt0) cc_final: 0.7119 (pm20) REVERT: A 1737 VAL cc_start: 0.9214 (m) cc_final: 0.8833 (p) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.0742 time to fit residues: 28.2904 Evaluate side-chains 207 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 174 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 162 optimal weight: 40.0000 chunk 136 optimal weight: 0.3980 chunk 25 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 98 optimal weight: 30.0000 chunk 137 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 17 optimal weight: 20.0000 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1686 HIS ** A1812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1825 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.163642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 111)---------------| | r_work = 0.3628 r_free = 0.3628 target = 0.128083 restraints weight = 24251.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.127581 restraints weight = 18075.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.127415 restraints weight = 15972.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.127486 restraints weight = 17634.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.127998 restraints weight = 15522.096| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.4789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 13015 Z= 0.153 Angle : 0.763 12.058 17837 Z= 0.376 Chirality : 0.047 0.395 2180 Planarity : 0.006 0.176 2322 Dihedral : 6.352 54.847 2211 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.58 % Favored : 90.42 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.46 (0.21), residues: 1869 helix: 1.11 (0.17), residues: 1001 sheet: -4.36 (0.41), residues: 96 loop : -3.52 (0.20), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 579 TYR 0.028 0.002 TYR A 573 PHE 0.031 0.002 PHE A1721 TRP 0.041 0.002 TRP A 533 HIS 0.004 0.001 HIS A1626 Details of bonding type rmsd covalent geometry : bond 0.00347 (12999) covalent geometry : angle 0.75083 (17793) SS BOND : bond 0.00280 ( 4) SS BOND : angle 1.74203 ( 8) hydrogen bonds : bond 0.03891 ( 675) hydrogen bonds : angle 4.74186 ( 1989) link_BETA1-3 : bond 0.00572 ( 1) link_BETA1-3 : angle 2.14700 ( 3) link_BETA1-4 : bond 0.00424 ( 3) link_BETA1-4 : angle 2.17707 ( 9) link_BETA1-6 : bond 0.01425 ( 1) link_BETA1-6 : angle 1.86339 ( 3) link_NAG-ASN : bond 0.00722 ( 7) link_NAG-ASN : angle 3.62094 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1790.56 seconds wall clock time: 31 minutes 35.17 seconds (1895.17 seconds total)