Starting phenix.real_space_refine on Thu Jul 31 02:30:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5xjy_6724/07_2025/5xjy_6724.cif Found real_map, /net/cci-nas-00/data/ceres_data/5xjy_6724/07_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_6724/07_2025/5xjy_6724.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5xjy_6724/07_2025/5xjy_6724.map" model { file = "/net/cci-nas-00/data/ceres_data/5xjy_6724/07_2025/5xjy_6724.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5xjy_6724/07_2025/5xjy_6724.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 28, 'ARG:plan': 40, 'TYR:plan': 21, 'ASN:plan1': 34, 'TRP:plan': 9, 'ASP:plan': 39, 'PHE:plan': 41, 'GLU:plan': 50, 'HIS:plan': 23} 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: 7.83, per 1000 atoms: 0.61 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: 4.76 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 1.73 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: 4.52 Time building geometry restraints manager: 4.13 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: 0.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 32.680 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.790 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.065 0.005 TRP A 533 HIS 0.012 0.004 HIS A 52 PHE 0.051 0.004 PHE A 538 TYR 0.044 0.005 TYR A 754 ARG 0.028 0.002 ARG A1417 Details of bonding type rmsd link_NAG-ASN : bond 0.00722 ( 7) link_NAG-ASN : angle 5.36344 ( 21) link_BETA1-4 : bond 0.01112 ( 3) link_BETA1-4 : angle 3.42576 ( 9) hydrogen bonds : bond 0.13228 ( 675) hydrogen bonds : angle 11.82289 ( 1989) link_BETA1-6 : bond 0.00253 ( 1) link_BETA1-6 : angle 1.55764 ( 3) SS BOND : bond 0.00784 ( 4) SS BOND : angle 4.01925 ( 8) link_BETA1-3 : bond 0.00253 ( 1) link_BETA1-3 : angle 1.58190 ( 3) covalent geometry : bond 0.00968 (12999) covalent geometry : angle 1.30908 (17793) *********************** 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 : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 ILE cc_start: 0.9269 (pt) cc_final: 0.8940 (tp) REVERT: A 282 ARG cc_start: 0.7019 (ptm160) cc_final: 0.5376 (mpt180) REVERT: A 354 TYR cc_start: 0.7494 (t80) cc_final: 0.7207 (t80) REVERT: A 362 LEU cc_start: 0.8338 (mt) cc_final: 0.8056 (mt) REVERT: A 373 LYS cc_start: 0.8958 (mptp) cc_final: 0.8683 (mmmt) REVERT: A 384 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8975 (pp) REVERT: A 511 GLU cc_start: 0.8271 (mp0) cc_final: 0.8061 (mp0) REVERT: A 525 GLU cc_start: 0.8440 (tt0) cc_final: 0.7873 (tp30) REVERT: A 533 TRP cc_start: 0.9293 (OUTLIER) cc_final: 0.8346 (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: 0.7550 (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: 0.8357 (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: 0.7235 (tppt) REVERT: A 1556 LYS cc_start: 0.8914 (ttmm) cc_final: 0.8659 (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: 0.8491 (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: 0.8749 (mmp) REVERT: A 1757 SER cc_start: 0.7889 (t) cc_final: 0.7557 (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: 0.2560 time to fit residues: 125.6909 Evaluate side-chains 225 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 220 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 4.9990 chunk 144 optimal weight: 7.9990 chunk 79 optimal weight: 0.4980 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.3980 chunk 76 optimal weight: 4.9990 chunk 148 optimal weight: 7.9990 chunk 57 optimal weight: 0.9980 chunk 90 optimal weight: 10.0000 chunk 110 optimal weight: 7.9990 chunk 172 optimal weight: 20.0000 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.158428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 110)---------------| | r_work = 0.3543 r_free = 0.3543 target = 0.122421 restraints weight = 23812.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.122287 restraints weight = 17797.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.122682 restraints weight = 14876.135| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13015 Z= 0.190 Angle : 0.862 17.384 17837 Z= 0.441 Chirality : 0.052 0.828 2180 Planarity : 0.007 0.108 2322 Dihedral : 11.064 88.149 2211 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.50 % Favored : 88.50 % Rotamer: Outliers : 0.42 % Allowed : 4.77 % Favored : 94.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.37 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.54 (0.16), residues: 1869 helix: -1.80 (0.14), residues: 966 sheet: -5.12 (0.30), residues: 114 loop : -4.28 (0.18), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP A 533 HIS 0.005 0.001 HIS A1600 PHE 0.030 0.002 PHE A1721 TYR 0.036 0.003 TYR A1532 ARG 0.005 0.001 ARG A 557 Details of bonding type rmsd link_NAG-ASN : bond 0.00379 ( 7) link_NAG-ASN : angle 5.58935 ( 21) link_BETA1-4 : bond 0.00266 ( 3) link_BETA1-4 : angle 2.14745 ( 9) hydrogen bonds : bond 0.05420 ( 675) hydrogen bonds : angle 7.04968 ( 1989) link_BETA1-6 : bond 0.00199 ( 1) link_BETA1-6 : angle 2.52522 ( 3) SS BOND : bond 0.01154 ( 4) SS BOND : angle 1.93183 ( 8) link_BETA1-3 : bond 0.00486 ( 1) link_BETA1-3 : angle 2.69498 ( 3) covalent geometry : bond 0.00403 (12999) covalent geometry : angle 0.83718 (17793) *********************** 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 283 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 279 time to evaluate : 1.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 362 LEU cc_start: 0.8289 (mt) cc_final: 0.8046 (mt) REVERT: A 511 GLU cc_start: 0.8203 (mp0) cc_final: 0.7918 (mp0) REVERT: A 525 GLU cc_start: 0.8079 (tt0) cc_final: 0.7688 (tp30) REVERT: A 529 GLU cc_start: 0.7322 (tp30) cc_final: 0.7077 (tp30) REVERT: A 598 ASP cc_start: 0.7461 (t0) cc_final: 0.7189 (t0) REVERT: A 631 ILE cc_start: 0.7867 (pt) cc_final: 0.7321 (tp) REVERT: A 650 TYR cc_start: 0.7535 (t80) cc_final: 0.7311 (t80) REVERT: A 689 SER cc_start: 0.8404 (t) cc_final: 0.7870 (t) REVERT: A 705 LYS cc_start: 0.7621 (tptt) cc_final: 0.6961 (tppt) REVERT: A 735 LEU cc_start: 0.8717 (tt) cc_final: 0.8475 (tt) REVERT: A 796 LEU cc_start: 0.7934 (tt) cc_final: 0.7608 (mm) REVERT: A 1335 LYS cc_start: 0.7846 (tttm) cc_final: 0.7102 (tptp) REVERT: A 1469 LYS cc_start: 0.8562 (pttm) cc_final: 0.7955 (mmmt) REVERT: A 1587 LYS cc_start: 0.8316 (mmtt) cc_final: 0.7785 (ptmm) REVERT: A 1654 ASP cc_start: 0.7988 (t70) cc_final: 0.7230 (t0) REVERT: A 1726 GLN cc_start: 0.7067 (mt0) cc_final: 0.6690 (pm20) REVERT: A 1753 MET cc_start: 0.9171 (mmm) cc_final: 0.8955 (mmp) REVERT: A 1822 MET cc_start: 0.6831 (mmm) cc_final: 0.6157 (mmm) outliers start: 4 outliers final: 1 residues processed: 281 average time/residue: 0.2217 time to fit residues: 94.5976 Evaluate side-chains 207 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 206 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 147 optimal weight: 0.0470 chunk 173 optimal weight: 7.9990 chunk 99 optimal weight: 30.0000 chunk 146 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 123 optimal weight: 7.9990 chunk 118 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 103 optimal weight: 20.0000 overall best weight: 4.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1607 ASN ** A1626 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.151583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 113)---------------| | r_work = 0.3471 r_free = 0.3471 target = 0.116890 restraints weight = 24242.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.114990 restraints weight = 20701.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.115593 restraints weight = 19370.262| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 13015 Z= 0.334 Angle : 0.948 14.366 17837 Z= 0.489 Chirality : 0.053 0.608 2180 Planarity : 0.007 0.109 2322 Dihedral : 9.790 82.746 2211 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.05 % Allowed : 14.87 % Favored : 85.07 % Rotamer: Outliers : 0.53 % Allowed : 4.88 % Favored : 94.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.95 (0.17), residues: 1869 helix: -1.12 (0.15), residues: 984 sheet: -5.40 (0.33), residues: 93 loop : -4.35 (0.18), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.003 TRP A 533 HIS 0.005 0.002 HIS A 410 PHE 0.041 0.003 PHE A1721 TYR 0.041 0.003 TYR A1532 ARG 0.007 0.001 ARG A 579 Details of bonding type rmsd link_NAG-ASN : bond 0.01069 ( 7) link_NAG-ASN : angle 5.52531 ( 21) link_BETA1-4 : bond 0.00664 ( 3) link_BETA1-4 : angle 2.51988 ( 9) hydrogen bonds : bond 0.05596 ( 675) hydrogen bonds : angle 6.51907 ( 1989) link_BETA1-6 : bond 0.00602 ( 1) link_BETA1-6 : angle 2.46593 ( 3) SS BOND : bond 0.00762 ( 4) SS BOND : angle 2.02297 ( 8) link_BETA1-3 : bond 0.00986 ( 1) link_BETA1-3 : angle 2.19685 ( 3) covalent geometry : bond 0.00737 (12999) covalent geometry : angle 0.92587 (17793) *********************** 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 258 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 253 time to evaluate : 1.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LYS cc_start: 0.8549 (ttpt) cc_final: 0.7766 (tttt) REVERT: A 126 ARG cc_start: 0.8521 (ttm170) cc_final: 0.8298 (ttm170) REVERT: A 362 LEU cc_start: 0.8355 (mt) cc_final: 0.7950 (mt) REVERT: A 417 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7887 (tm-30) REVERT: A 486 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7216 (pt0) REVERT: A 511 GLU cc_start: 0.8289 (mp0) cc_final: 0.7786 (mp0) REVERT: A 525 GLU cc_start: 0.8356 (tt0) cc_final: 0.8013 (tp30) REVERT: A 529 GLU cc_start: 0.7574 (tp30) cc_final: 0.7323 (tp30) REVERT: A 547 GLU cc_start: 0.7494 (pm20) cc_final: 0.7268 (pm20) REVERT: A 598 ASP cc_start: 0.7996 (t0) cc_final: 0.7769 (t0) REVERT: A 631 ILE cc_start: 0.7948 (pt) cc_final: 0.7472 (tp) REVERT: A 669 GLU cc_start: 0.8260 (mp0) cc_final: 0.8052 (mp0) REVERT: A 705 LYS cc_start: 0.7901 (tptt) cc_final: 0.7335 (tppt) REVERT: A 733 CYS cc_start: 0.8960 (t) cc_final: 0.8694 (t) REVERT: A 735 LEU cc_start: 0.8987 (tt) cc_final: 0.8774 (tt) REVERT: A 761 TYR cc_start: 0.7558 (t80) cc_final: 0.7293 (t80) REVERT: A 796 LEU cc_start: 0.8176 (tt) cc_final: 0.7751 (mm) REVERT: A 1335 LYS cc_start: 0.8024 (tttm) cc_final: 0.7384 (tptp) REVERT: A 1364 PHE cc_start: 0.7317 (t80) cc_final: 0.6711 (m-80) REVERT: A 1587 LYS cc_start: 0.8428 (mmtt) cc_final: 0.7815 (ptmm) REVERT: A 1599 TRP cc_start: 0.8949 (m100) cc_final: 0.8589 (m-10) REVERT: A 1607 ASN cc_start: 0.9041 (t160) cc_final: 0.8821 (t0) REVERT: A 1654 ASP cc_start: 0.8028 (t70) cc_final: 0.7325 (t0) REVERT: A 1673 VAL cc_start: 0.9571 (t) cc_final: 0.9327 (t) REVERT: A 1726 GLN cc_start: 0.7072 (mt0) cc_final: 0.6610 (pm20) REVERT: A 1753 MET cc_start: 0.9221 (mmm) cc_final: 0.8851 (mmp) REVERT: A 1757 SER cc_start: 0.8034 (t) cc_final: 0.7736 (p) REVERT: A 1822 MET cc_start: 0.6735 (mmm) cc_final: 0.6056 (mmm) outliers start: 5 outliers final: 1 residues processed: 256 average time/residue: 0.2206 time to fit residues: 86.7244 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 : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 69 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 172 optimal weight: 0.7980 chunk 171 optimal weight: 5.9990 chunk 183 optimal weight: 30.0000 chunk 25 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS A1557 GLN A1607 ASN ** A1611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1626 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.159222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 112)---------------| | r_work = 0.3500 r_free = 0.3500 target = 0.120498 restraints weight = 23825.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.122484 restraints weight = 17766.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.123576 restraints weight = 14074.277| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13015 Z= 0.152 Angle : 0.769 12.744 17837 Z= 0.387 Chirality : 0.048 0.502 2180 Planarity : 0.005 0.091 2322 Dihedral : 8.239 67.269 2211 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.49 % Favored : 89.51 % Rotamer: Outliers : 0.21 % Allowed : 4.35 % Favored : 95.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.12 (0.18), residues: 1869 helix: -0.27 (0.16), residues: 984 sheet: -5.14 (0.36), residues: 94 loop : -4.18 (0.18), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 533 HIS 0.003 0.001 HIS A 410 PHE 0.025 0.002 PHE A 36 TYR 0.029 0.003 TYR A1767 ARG 0.007 0.001 ARG A1680 Details of bonding type rmsd link_NAG-ASN : bond 0.00806 ( 7) link_NAG-ASN : angle 4.46650 ( 21) link_BETA1-4 : bond 0.00362 ( 3) link_BETA1-4 : angle 2.18879 ( 9) hydrogen bonds : bond 0.04562 ( 675) hydrogen bonds : angle 5.75927 ( 1989) link_BETA1-6 : bond 0.01153 ( 1) link_BETA1-6 : angle 2.24172 ( 3) SS BOND : bond 0.01156 ( 4) SS BOND : angle 1.79401 ( 8) link_BETA1-3 : bond 0.00506 ( 1) link_BETA1-3 : angle 2.59476 ( 3) covalent geometry : bond 0.00323 (12999) covalent geometry : angle 0.75100 (17793) *********************** 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 295 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 293 time to evaluate : 1.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LYS cc_start: 0.8284 (ttpt) cc_final: 0.8070 (ttpt) REVERT: A 26 LEU cc_start: 0.8732 (mm) cc_final: 0.8470 (mt) REVERT: A 417 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7732 (tm-30) REVERT: A 525 GLU cc_start: 0.8244 (tt0) cc_final: 0.7972 (tp30) REVERT: A 529 GLU cc_start: 0.7345 (tp30) cc_final: 0.7113 (tp30) REVERT: A 598 ASP cc_start: 0.7492 (t0) cc_final: 0.7061 (t0) REVERT: A 631 ILE cc_start: 0.7825 (pt) cc_final: 0.7330 (tp) REVERT: A 689 SER cc_start: 0.8395 (t) cc_final: 0.7789 (t) REVERT: A 705 LYS cc_start: 0.7648 (tptt) cc_final: 0.6931 (tppt) REVERT: A 735 LEU cc_start: 0.8851 (tt) cc_final: 0.8650 (tt) REVERT: A 796 LEU cc_start: 0.7731 (tt) cc_final: 0.7470 (mm) REVERT: A 1335 LYS cc_start: 0.7847 (tttm) cc_final: 0.7132 (tptp) REVERT: A 1364 PHE cc_start: 0.7270 (t80) cc_final: 0.6705 (m-80) REVERT: A 1469 LYS cc_start: 0.8424 (pttm) cc_final: 0.8098 (mmmt) REVERT: A 1587 LYS cc_start: 0.8374 (mmtt) cc_final: 0.7774 (ptmm) REVERT: A 1603 SER cc_start: 0.9151 (m) cc_final: 0.8902 (t) REVERT: A 1673 VAL cc_start: 0.9421 (t) cc_final: 0.9194 (t) REVERT: A 1678 GLN cc_start: 0.8332 (mt0) cc_final: 0.8120 (tt0) REVERT: A 1710 TYR cc_start: 0.8571 (t80) cc_final: 0.8211 (t80) REVERT: A 1712 VAL cc_start: 0.8247 (t) cc_final: 0.8012 (t) REVERT: A 1726 GLN cc_start: 0.6957 (mt0) cc_final: 0.6698 (pm20) REVERT: A 1753 MET cc_start: 0.9187 (mmm) cc_final: 0.8925 (mmp) outliers start: 2 outliers final: 0 residues processed: 293 average time/residue: 0.2139 time to fit residues: 96.6555 Evaluate side-chains 219 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 24 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 122 optimal weight: 9.9990 chunk 106 optimal weight: 20.0000 chunk 118 optimal weight: 8.9990 chunk 25 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 161 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 188 optimal weight: 0.3980 chunk 38 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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** A1607 ASN A1610 ASN A1611 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.160629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.137731 restraints weight = 23785.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.129447 restraints weight = 25302.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.127570 restraints weight = 29170.630| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13015 Z= 0.152 Angle : 0.757 11.769 17837 Z= 0.381 Chirality : 0.047 0.455 2180 Planarity : 0.006 0.083 2322 Dihedral : 7.686 61.965 2211 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.75 % Favored : 89.25 % Rotamer: Outliers : 0.11 % Allowed : 3.39 % Favored : 96.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.19), residues: 1869 helix: 0.21 (0.17), residues: 984 sheet: -4.84 (0.40), residues: 92 loop : -4.09 (0.18), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 533 HIS 0.005 0.001 HIS A1600 PHE 0.026 0.002 PHE A1721 TYR 0.025 0.002 TYR A 385 ARG 0.007 0.001 ARG A 587 Details of bonding type rmsd link_NAG-ASN : bond 0.00833 ( 7) link_NAG-ASN : angle 4.70878 ( 21) link_BETA1-4 : bond 0.00317 ( 3) link_BETA1-4 : angle 2.15859 ( 9) hydrogen bonds : bond 0.04394 ( 675) hydrogen bonds : angle 5.42518 ( 1989) link_BETA1-6 : bond 0.01139 ( 1) link_BETA1-6 : angle 1.72768 ( 3) SS BOND : bond 0.00355 ( 4) SS BOND : angle 2.06140 ( 8) link_BETA1-3 : bond 0.00617 ( 1) link_BETA1-3 : angle 2.06031 ( 3) covalent geometry : bond 0.00328 (12999) covalent geometry : angle 0.73713 (17793) *********************** 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 277 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 276 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 TRP cc_start: 0.2599 (t-100) cc_final: 0.2338 (t-100) REVERT: A 417 GLU cc_start: 0.7990 (tm-30) cc_final: 0.7710 (tm-30) REVERT: A 502 MET cc_start: 0.8455 (tmm) cc_final: 0.8202 (tmm) REVERT: A 524 MET cc_start: 0.7959 (mmm) cc_final: 0.7179 (mmm) REVERT: A 598 ASP cc_start: 0.7268 (t0) cc_final: 0.6935 (t0) REVERT: A 622 MET cc_start: 0.8577 (mpp) cc_final: 0.8357 (mpp) REVERT: A 631 ILE cc_start: 0.7903 (pt) cc_final: 0.7520 (tp) REVERT: A 689 SER cc_start: 0.8200 (t) cc_final: 0.7490 (t) REVERT: A 705 LYS cc_start: 0.7743 (tptt) cc_final: 0.7019 (tppt) REVERT: A 796 LEU cc_start: 0.7842 (tt) cc_final: 0.7470 (mm) REVERT: A 1364 PHE cc_start: 0.7007 (t80) cc_final: 0.6792 (m-80) REVERT: A 1469 LYS cc_start: 0.8394 (pttm) cc_final: 0.8078 (mmmt) REVERT: A 1587 LYS cc_start: 0.8213 (mmtt) cc_final: 0.7727 (ptmm) REVERT: A 1654 ASP cc_start: 0.7986 (t70) cc_final: 0.7755 (t0) REVERT: A 1673 VAL cc_start: 0.9608 (t) cc_final: 0.9352 (t) REVERT: A 1726 GLN cc_start: 0.7294 (mt0) cc_final: 0.7048 (pm20) outliers start: 1 outliers final: 1 residues processed: 277 average time/residue: 0.2137 time to fit residues: 90.5804 Evaluate side-chains 214 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 213 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 86 optimal weight: 20.0000 chunk 50 optimal weight: 0.5980 chunk 173 optimal weight: 0.0870 chunk 107 optimal weight: 10.0000 chunk 36 optimal weight: 7.9990 chunk 140 optimal weight: 0.8980 chunk 171 optimal weight: 5.9990 chunk 76 optimal weight: 20.0000 chunk 92 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 135 optimal weight: 0.8980 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1557 GLN A1607 ASN ** A1611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1678 GLN A1774 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.162129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.130315 restraints weight = 24436.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.129059 restraints weight = 23874.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.130310 restraints weight = 21546.535| |-----------------------------------------------------------------------------| r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.3981 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= 0.144 Angle : 0.754 14.538 17837 Z= 0.373 Chirality : 0.048 0.436 2180 Planarity : 0.005 0.073 2322 Dihedral : 7.169 55.319 2211 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer: Outliers : 0.00 % Allowed : 3.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.19), residues: 1869 helix: 0.40 (0.17), residues: 990 sheet: -4.70 (0.41), residues: 92 loop : -3.98 (0.19), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 533 HIS 0.003 0.001 HIS A1626 PHE 0.023 0.001 PHE A1721 TYR 0.034 0.002 TYR A 650 ARG 0.007 0.001 ARG A1336 Details of bonding type rmsd link_NAG-ASN : bond 0.00788 ( 7) link_NAG-ASN : angle 4.34778 ( 21) link_BETA1-4 : bond 0.00335 ( 3) link_BETA1-4 : angle 2.08789 ( 9) hydrogen bonds : bond 0.04167 ( 675) hydrogen bonds : angle 5.16971 ( 1989) link_BETA1-6 : bond 0.01364 ( 1) link_BETA1-6 : angle 1.73212 ( 3) SS BOND : bond 0.00287 ( 4) SS BOND : angle 1.71349 ( 8) link_BETA1-3 : bond 0.00635 ( 1) link_BETA1-3 : angle 2.31495 ( 3) covalent geometry : bond 0.00310 (12999) covalent geometry : angle 0.73697 (17793) *********************** 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 256 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 1.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ASP cc_start: 0.8689 (m-30) cc_final: 0.8470 (m-30) REVERT: A 278 TRP cc_start: 0.2767 (t-100) cc_final: 0.2548 (t-100) REVERT: A 301 TYR cc_start: 0.6885 (m-10) cc_final: 0.6637 (m-80) REVERT: A 354 TYR cc_start: 0.7416 (t80) cc_final: 0.7087 (t80) REVERT: A 358 LEU cc_start: 0.8700 (pp) cc_final: 0.8338 (pp) REVERT: A 386 THR cc_start: 0.8850 (p) cc_final: 0.8072 (p) REVERT: A 392 THR cc_start: 0.8654 (p) cc_final: 0.7954 (p) REVERT: A 417 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7748 (tm-30) REVERT: A 524 MET cc_start: 0.7717 (mmm) cc_final: 0.7149 (mmm) REVERT: A 598 ASP cc_start: 0.7385 (t0) cc_final: 0.7015 (t0) REVERT: A 622 MET cc_start: 0.8616 (mpp) cc_final: 0.8274 (mpp) REVERT: A 631 ILE cc_start: 0.7939 (pt) cc_final: 0.7547 (tp) REVERT: A 640 MET cc_start: 0.8171 (ttt) cc_final: 0.7557 (tpp) REVERT: A 660 VAL cc_start: 0.8753 (p) cc_final: 0.8522 (p) REVERT: A 689 SER cc_start: 0.8180 (t) cc_final: 0.7431 (t) REVERT: A 705 LYS cc_start: 0.7628 (tptt) cc_final: 0.6910 (tppt) REVERT: A 796 LEU cc_start: 0.7643 (tt) cc_final: 0.7312 (mm) REVERT: A 1364 PHE cc_start: 0.6955 (t80) cc_final: 0.6668 (m-80) REVERT: A 1469 LYS cc_start: 0.8479 (pttm) cc_final: 0.8125 (mmmt) REVERT: A 1587 LYS cc_start: 0.8229 (mmtt) cc_final: 0.7605 (ptmm) REVERT: A 1599 TRP cc_start: 0.8739 (m100) cc_final: 0.8405 (m-10) REVERT: A 1654 ASP cc_start: 0.8344 (t70) cc_final: 0.7977 (t0) REVERT: A 1710 TYR cc_start: 0.8595 (t80) cc_final: 0.8389 (t80) REVERT: A 1726 GLN cc_start: 0.7330 (mt0) cc_final: 0.6972 (pm20) outliers start: 0 outliers final: 0 residues processed: 256 average time/residue: 0.2023 time to fit residues: 81.1379 Evaluate side-chains 214 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 83 optimal weight: 0.0010 chunk 46 optimal weight: 2.9990 chunk 188 optimal weight: 0.0570 chunk 13 optimal weight: 20.0000 chunk 128 optimal weight: 0.7980 chunk 132 optimal weight: 0.7980 chunk 174 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 149 optimal weight: 0.5980 chunk 75 optimal weight: 6.9990 chunk 171 optimal weight: 0.0970 overall best weight: 0.3102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1443 GLN A1607 ASN ** A1611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1774 ASN A1825 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.164421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.130649 restraints weight = 24184.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.129298 restraints weight = 18340.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.130361 restraints weight = 16368.387| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.4349 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= 0.138 Angle : 0.740 13.413 17837 Z= 0.362 Chirality : 0.046 0.415 2180 Planarity : 0.005 0.067 2322 Dihedral : 6.805 54.717 2211 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.58 % Favored : 90.42 % Rotamer: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.20), residues: 1869 helix: 0.69 (0.17), residues: 995 sheet: -4.43 (0.41), residues: 97 loop : -3.86 (0.19), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 533 HIS 0.003 0.001 HIS A1634 PHE 0.024 0.001 PHE A1721 TYR 0.036 0.002 TYR A1767 ARG 0.006 0.001 ARG A1336 Details of bonding type rmsd link_NAG-ASN : bond 0.00773 ( 7) link_NAG-ASN : angle 4.93989 ( 21) link_BETA1-4 : bond 0.00312 ( 3) link_BETA1-4 : angle 2.13389 ( 9) hydrogen bonds : bond 0.04027 ( 675) hydrogen bonds : angle 4.91043 ( 1989) link_BETA1-6 : bond 0.01482 ( 1) link_BETA1-6 : angle 1.70643 ( 3) SS BOND : bond 0.00298 ( 4) SS BOND : angle 1.36238 ( 8) link_BETA1-3 : bond 0.00660 ( 1) link_BETA1-3 : angle 2.23219 ( 3) covalent geometry : bond 0.00293 (12999) covalent geometry : angle 0.71796 (17793) *********************** 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 260 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 1.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.7522 (tp) cc_final: 0.7084 (tt) REVERT: A 124 ASP cc_start: 0.8725 (m-30) cc_final: 0.8423 (m-30) REVERT: A 278 TRP cc_start: 0.2723 (t-100) cc_final: 0.2517 (t-100) REVERT: A 354 TYR cc_start: 0.7351 (t80) cc_final: 0.6929 (t80) REVERT: A 358 LEU cc_start: 0.8813 (pp) cc_final: 0.8416 (pp) REVERT: A 359 MET cc_start: 0.8619 (ppp) cc_final: 0.8333 (ppp) REVERT: A 417 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7690 (tm-30) REVERT: A 419 LEU cc_start: 0.9028 (mp) cc_final: 0.8671 (mp) REVERT: A 598 ASP cc_start: 0.7259 (t0) cc_final: 0.6862 (t0) REVERT: A 622 MET cc_start: 0.8689 (mpp) cc_final: 0.8354 (mpp) REVERT: A 631 ILE cc_start: 0.7713 (pt) cc_final: 0.7358 (tp) REVERT: A 644 MET cc_start: 0.8693 (tpp) cc_final: 0.8413 (tpp) REVERT: A 689 SER cc_start: 0.8146 (t) cc_final: 0.7442 (t) REVERT: A 705 LYS cc_start: 0.7452 (tptt) cc_final: 0.6673 (ttmt) REVERT: A 1587 LYS cc_start: 0.8138 (mmtt) cc_final: 0.7527 (ptmm) REVERT: A 1594 PHE cc_start: 0.9206 (p90) cc_final: 0.8804 (p90) REVERT: A 1707 MET cc_start: 0.8534 (tpp) cc_final: 0.8184 (mmm) REVERT: A 1710 TYR cc_start: 0.8720 (t80) cc_final: 0.8435 (t80) REVERT: A 1726 GLN cc_start: 0.7245 (mt0) cc_final: 0.6906 (pm20) REVERT: A 1825 ASN cc_start: 0.7994 (t160) cc_final: 0.7760 (t0) outliers start: 0 outliers final: 0 residues processed: 260 average time/residue: 0.2051 time to fit residues: 83.6883 Evaluate side-chains 216 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 149 optimal weight: 0.6980 chunk 129 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 16 optimal weight: 40.0000 chunk 83 optimal weight: 20.0000 chunk 65 optimal weight: 0.8980 chunk 148 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 165 optimal weight: 30.0000 chunk 4 optimal weight: 5.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1422 ASN A1607 ASN ** A1611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1686 HIS A1825 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.161170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 102)---------------| | r_work = 0.3585 r_free = 0.3585 target = 0.124998 restraints weight = 24303.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.124359 restraints weight = 17932.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.124704 restraints weight = 15885.148| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.4305 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= 0.182 Angle : 0.756 11.715 17837 Z= 0.377 Chirality : 0.048 0.418 2180 Planarity : 0.005 0.083 2322 Dihedral : 6.774 55.380 2211 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.86 % Favored : 89.14 % Rotamer: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.20), residues: 1869 helix: 0.85 (0.17), residues: 990 sheet: -4.52 (0.41), residues: 102 loop : -3.76 (0.19), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP A 533 HIS 0.005 0.001 HIS A1626 PHE 0.027 0.002 PHE A1721 TYR 0.028 0.002 TYR A 385 ARG 0.005 0.001 ARG A1680 Details of bonding type rmsd link_NAG-ASN : bond 0.00754 ( 7) link_NAG-ASN : angle 4.25098 ( 21) link_BETA1-4 : bond 0.00432 ( 3) link_BETA1-4 : angle 2.16018 ( 9) hydrogen bonds : bond 0.04040 ( 675) hydrogen bonds : angle 4.91455 ( 1989) link_BETA1-6 : bond 0.01245 ( 1) link_BETA1-6 : angle 1.73048 ( 3) SS BOND : bond 0.01857 ( 4) SS BOND : angle 2.32008 ( 8) link_BETA1-3 : bond 0.00548 ( 1) link_BETA1-3 : angle 2.19075 ( 3) covalent geometry : bond 0.00403 (12999) covalent geometry : angle 0.73910 (17793) *********************** 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 258 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 1.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.7468 (tp) cc_final: 0.7051 (tt) REVERT: A 359 MET cc_start: 0.8626 (ppp) cc_final: 0.8358 (ppp) REVERT: A 417 GLU cc_start: 0.8081 (tm-30) cc_final: 0.7775 (tm-30) REVERT: A 553 LYS cc_start: 0.9035 (mttt) cc_final: 0.8712 (mttm) REVERT: A 598 ASP cc_start: 0.7442 (t0) cc_final: 0.7011 (t0) REVERT: A 613 LYS cc_start: 0.8311 (tppt) cc_final: 0.8107 (tppt) REVERT: A 622 MET cc_start: 0.8668 (mpp) cc_final: 0.8254 (mpp) REVERT: A 631 ILE cc_start: 0.7877 (pt) cc_final: 0.7486 (tp) REVERT: A 640 MET cc_start: 0.8186 (ttt) cc_final: 0.7621 (tpp) REVERT: A 644 MET cc_start: 0.8768 (tpp) cc_final: 0.8445 (tpp) REVERT: A 689 SER cc_start: 0.8065 (t) cc_final: 0.7299 (t) REVERT: A 705 LYS cc_start: 0.7430 (tptt) cc_final: 0.6704 (ttmt) REVERT: A 1587 LYS cc_start: 0.8241 (mmtt) cc_final: 0.7568 (ptmm) REVERT: A 1599 TRP cc_start: 0.8813 (m100) cc_final: 0.8517 (m-10) REVERT: A 1654 ASP cc_start: 0.8606 (t70) cc_final: 0.8034 (t0) REVERT: A 1710 TYR cc_start: 0.8841 (t80) cc_final: 0.8554 (t80) REVERT: A 1726 GLN cc_start: 0.7202 (mt0) cc_final: 0.6780 (pm20) REVERT: A 1825 ASN cc_start: 0.8058 (t160) cc_final: 0.7731 (t0) outliers start: 0 outliers final: 0 residues processed: 258 average time/residue: 0.2040 time to fit residues: 82.8723 Evaluate side-chains 219 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 27 optimal weight: 0.6980 chunk 121 optimal weight: 0.0050 chunk 165 optimal weight: 6.9990 chunk 102 optimal weight: 50.0000 chunk 99 optimal weight: 20.0000 chunk 169 optimal weight: 6.9990 chunk 32 optimal weight: 0.8980 chunk 174 optimal weight: 5.9990 chunk 186 optimal weight: 50.0000 chunk 134 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1607 ASN ** A1611 ASN ** 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 = 0.4061 r_free = 0.4061 target = 0.163638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.127877 restraints weight = 24136.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.128818 restraints weight = 17636.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.129000 restraints weight = 14811.488| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.4577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13015 Z= 0.139 Angle : 0.751 12.245 17837 Z= 0.367 Chirality : 0.046 0.402 2180 Planarity : 0.005 0.083 2322 Dihedral : 6.519 54.467 2211 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.20), residues: 1869 helix: 0.98 (0.17), residues: 995 sheet: -4.42 (0.42), residues: 93 loop : -3.65 (0.20), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 533 HIS 0.002 0.001 HIS A1600 PHE 0.026 0.001 PHE A1721 TYR 0.036 0.002 TYR A 650 ARG 0.004 0.001 ARG A1336 Details of bonding type rmsd link_NAG-ASN : bond 0.00728 ( 7) link_NAG-ASN : angle 3.86010 ( 21) link_BETA1-4 : bond 0.00447 ( 3) link_BETA1-4 : angle 2.14470 ( 9) hydrogen bonds : bond 0.03879 ( 675) hydrogen bonds : angle 4.79706 ( 1989) link_BETA1-6 : bond 0.01529 ( 1) link_BETA1-6 : angle 1.93823 ( 3) SS BOND : bond 0.00239 ( 4) SS BOND : angle 2.02467 ( 8) link_BETA1-3 : bond 0.00624 ( 1) link_BETA1-3 : angle 2.28981 ( 3) covalent geometry : bond 0.00304 (12999) covalent geometry : angle 0.73598 (17793) *********************** 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 255 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 1.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.7405 (tp) cc_final: 0.6891 (tt) REVERT: A 366 PRO cc_start: 0.7735 (Cg_exo) cc_final: 0.7518 (Cg_endo) REVERT: A 417 GLU cc_start: 0.8026 (tm-30) cc_final: 0.7702 (tm-30) REVERT: A 524 MET cc_start: 0.8804 (mpp) cc_final: 0.8566 (mpp) REVERT: A 553 LYS cc_start: 0.8909 (mttt) cc_final: 0.8391 (mttm) REVERT: A 622 MET cc_start: 0.8691 (mpp) cc_final: 0.8346 (mpp) REVERT: A 631 ILE cc_start: 0.8164 (pt) cc_final: 0.7791 (tp) REVERT: A 640 MET cc_start: 0.8154 (ttt) cc_final: 0.7593 (tpp) REVERT: A 644 MET cc_start: 0.8685 (tpp) cc_final: 0.8354 (tpp) REVERT: A 650 TYR cc_start: 0.7799 (t80) cc_final: 0.7585 (t80) REVERT: A 689 SER cc_start: 0.8007 (t) cc_final: 0.7219 (t) REVERT: A 705 LYS cc_start: 0.7356 (tptt) cc_final: 0.6625 (ttmt) REVERT: A 1401 THR cc_start: 0.8993 (m) cc_final: 0.8785 (m) REVERT: A 1473 MET cc_start: 0.8749 (mpp) cc_final: 0.8476 (mtt) REVERT: A 1587 LYS cc_start: 0.8163 (mmtt) cc_final: 0.7566 (ptmm) REVERT: A 1594 PHE cc_start: 0.9195 (p90) cc_final: 0.8854 (p90) REVERT: A 1654 ASP cc_start: 0.8407 (t70) cc_final: 0.7949 (t0) REVERT: A 1726 GLN cc_start: 0.7649 (mt0) cc_final: 0.7117 (pm20) REVERT: A 1737 VAL cc_start: 0.9338 (m) cc_final: 0.8854 (p) REVERT: A 1825 ASN cc_start: 0.8061 (t160) cc_final: 0.7783 (t0) outliers start: 0 outliers final: 0 residues processed: 255 average time/residue: 0.2375 time to fit residues: 96.2795 Evaluate side-chains 221 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 104 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 153 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 141 optimal weight: 0.4980 chunk 27 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 151 optimal weight: 5.9990 chunk 165 optimal weight: 40.0000 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1607 ASN ** A1611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1812 HIS A1825 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.159496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.122636 restraints weight = 24185.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.123871 restraints weight = 19871.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.123113 restraints weight = 15625.426| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.4498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 13015 Z= 0.196 Angle : 0.785 10.494 17837 Z= 0.391 Chirality : 0.048 0.413 2180 Planarity : 0.005 0.086 2322 Dihedral : 6.660 55.256 2211 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.97 % Favored : 89.03 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.20), residues: 1869 helix: 0.92 (0.17), residues: 996 sheet: -4.42 (0.42), residues: 102 loop : -3.63 (0.20), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.003 TRP A 533 HIS 0.004 0.001 HIS A1626 PHE 0.030 0.002 PHE A1721 TYR 0.035 0.003 TYR A 385 ARG 0.006 0.001 ARG A1680 Details of bonding type rmsd link_NAG-ASN : bond 0.00746 ( 7) link_NAG-ASN : angle 3.88914 ( 21) link_BETA1-4 : bond 0.00429 ( 3) link_BETA1-4 : angle 2.16480 ( 9) hydrogen bonds : bond 0.04121 ( 675) hydrogen bonds : angle 4.88948 ( 1989) link_BETA1-6 : bond 0.01207 ( 1) link_BETA1-6 : angle 1.87392 ( 3) SS BOND : bond 0.00481 ( 4) SS BOND : angle 1.78159 ( 8) link_BETA1-3 : bond 0.00488 ( 1) link_BETA1-3 : angle 2.18997 ( 3) covalent geometry : bond 0.00439 (12999) covalent geometry : angle 0.77129 (17793) ********************** 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 246 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 1.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LEU cc_start: 0.8881 (mm) cc_final: 0.8666 (mt) REVERT: A 39 LEU cc_start: 0.7415 (tp) cc_final: 0.6931 (tt) REVERT: A 417 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7723 (tm-30) REVERT: A 524 MET cc_start: 0.8789 (mpp) cc_final: 0.8358 (mpp) REVERT: A 553 LYS cc_start: 0.8950 (mttt) cc_final: 0.8741 (mtpt) REVERT: A 622 MET cc_start: 0.8653 (mpp) cc_final: 0.8160 (mpp) REVERT: A 631 ILE cc_start: 0.8003 (pt) cc_final: 0.7663 (tp) REVERT: A 644 MET cc_start: 0.8740 (tpp) cc_final: 0.8472 (tpp) REVERT: A 689 SER cc_start: 0.8082 (t) cc_final: 0.7346 (t) REVERT: A 705 LYS cc_start: 0.7409 (tptt) cc_final: 0.6666 (ttmt) REVERT: A 796 LEU cc_start: 0.7803 (tt) cc_final: 0.7462 (mm) REVERT: A 1473 MET cc_start: 0.8783 (mpp) cc_final: 0.8537 (mtt) REVERT: A 1587 LYS cc_start: 0.8239 (mmtt) cc_final: 0.7609 (ptmm) REVERT: A 1599 TRP cc_start: 0.8886 (m100) cc_final: 0.8606 (m-10) REVERT: A 1654 ASP cc_start: 0.8462 (t70) cc_final: 0.8089 (t0) REVERT: A 1662 ILE cc_start: 0.8664 (tp) cc_final: 0.6876 (tp) REVERT: A 1710 TYR cc_start: 0.8668 (t80) cc_final: 0.8197 (t80) REVERT: A 1726 GLN cc_start: 0.7722 (mt0) cc_final: 0.7105 (pm20) REVERT: A 1825 ASN cc_start: 0.8190 (t160) cc_final: 0.7932 (t0) outliers start: 0 outliers final: 0 residues processed: 246 average time/residue: 0.1952 time to fit residues: 76.8696 Evaluate side-chains 213 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 178 optimal weight: 6.9990 chunk 130 optimal weight: 8.9990 chunk 164 optimal weight: 7.9990 chunk 60 optimal weight: 9.9990 chunk 26 optimal weight: 0.0570 chunk 154 optimal weight: 6.9990 chunk 139 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 101 optimal weight: 0.2980 chunk 75 optimal weight: 5.9990 chunk 140 optimal weight: 8.9990 overall best weight: 2.0702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1607 ASN ** A1611 ASN ** 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 = 0.4020 r_free = 0.4020 target = 0.159932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 101)---------------| | r_work = 0.3624 r_free = 0.3624 target = 0.127340 restraints weight = 24128.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.126652 restraints weight = 24411.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.127408 restraints weight = 21360.725| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.4568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 13015 Z= 0.188 Angle : 0.800 12.739 17837 Z= 0.396 Chirality : 0.049 0.409 2180 Planarity : 0.006 0.135 2322 Dihedral : 6.668 54.646 2211 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.97 % Favored : 89.03 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.20), residues: 1869 helix: 0.91 (0.17), residues: 1000 sheet: -4.37 (0.43), residues: 100 loop : -3.63 (0.20), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.083 0.003 TRP A 533 HIS 0.005 0.001 HIS A1812 PHE 0.032 0.002 PHE A1329 TYR 0.035 0.002 TYR A 385 ARG 0.004 0.000 ARG A1680 Details of bonding type rmsd link_NAG-ASN : bond 0.00741 ( 7) link_NAG-ASN : angle 4.37635 ( 21) link_BETA1-4 : bond 0.00418 ( 3) link_BETA1-4 : angle 2.18812 ( 9) hydrogen bonds : bond 0.04131 ( 675) hydrogen bonds : angle 4.91693 ( 1989) link_BETA1-6 : bond 0.01315 ( 1) link_BETA1-6 : angle 2.01562 ( 3) SS BOND : bond 0.00348 ( 4) SS BOND : angle 1.81642 ( 8) link_BETA1-3 : bond 0.00460 ( 1) link_BETA1-3 : angle 2.32188 ( 3) covalent geometry : bond 0.00422 (12999) covalent geometry : angle 0.78292 (17793) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4507.62 seconds wall clock time: 80 minutes 2.03 seconds (4802.03 seconds total)