Starting phenix.real_space_refine on Thu Oct 29 17:04:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9tua_56254/10_2026/9tua_56254.cif Found real_map, /net/cci-nas-00/data/ceres_data/9tua_56254/10_2026/9tua_56254.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9tua_56254/10_2026/9tua_56254.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9tua_56254/10_2026/9tua_56254.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9tua_56254/10_2026/9tua_56254.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9tua_56254/10_2026/9tua_56254.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 10 6.06 5 P 59 5.49 5 S 141 5.16 5 C 19904 2.51 5 N 5706 2.21 5 O 6038 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31858 Number of models: 1 Model: "" Number of chains: 8 Chain: "I" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 121 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "Y" Number of atoms: 16243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2046, 16243 Classifications: {'peptide': 2046} Link IDs: {'PTRANS': 98, 'TRANS': 1947} Chain breaks: 4 Chain: "y" Number of atoms: 14456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1823, 14456 Classifications: {'peptide': 1823} Link IDs: {'PTRANS': 92, 'TRANS': 1730} Chain breaks: 6 Chain: "i" Number of atoms: 511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 511 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "g" Number of atoms: 334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 334 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "G" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 121 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "Y" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 36 Unusual residues: {' ZN': 5, 'AGS': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "y" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 36 Unusual residues: {' ZN': 5, 'AGS': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3589 SG CYS Y 437 30.476 54.507 109.299 1.00161.78 S ATOM 3627 SG CYS Y 442 30.713 51.456 111.245 1.00178.04 S ATOM 3848 SG CYS Y 467 30.118 51.103 107.518 1.00181.56 S ATOM 3862 SG CYS Y 469 27.313 52.306 109.747 1.00189.08 S ATOM 3937 SG CYS Y 479 46.989 69.072 112.778 1.00181.04 S ATOM 3953 SG CYS Y 482 46.983 66.248 115.343 1.00169.88 S ATOM 4547 SG CYS Y 586 45.057 69.413 116.036 1.00202.00 S ATOM 4566 SG CYS Y 589 48.991 69.285 115.942 1.00214.74 S ATOM 11113 SG CYS Y1423 19.945 68.052 65.137 1.00193.34 S ATOM 11139 SG CYS Y1426 21.219 64.581 64.239 1.00202.46 S ATOM 11223 SG CYS Y1439 21.302 67.198 61.618 1.00221.00 S ATOM 11245 SG CYS Y1442 17.913 66.032 62.762 1.00219.96 S ATOM 11918 SG CYS Y1526 41.253 93.832 71.843 1.00209.44 S ATOM 11938 SG CYS Y1529 44.270 92.638 73.852 1.00204.99 S ATOM 12236 SG CYS Y1571 44.442 96.018 71.972 1.00218.17 S ATOM 13099 SG CYS Y1681 36.303 47.123 93.559 1.00171.43 S ATOM 13111 SG CYS Y1683 34.040 50.078 94.298 1.00181.85 S ATOM 13145 SG CYS Y1687 37.823 50.554 93.798 1.00171.38 S ATOM 13171 SG CYS Y1690 35.536 49.689 90.852 1.00161.47 S ATOM 19832 SG CYS y 437 148.266 54.441 95.926 1.00195.43 S ATOM 19870 SG CYS y 442 150.427 55.984 98.683 1.00194.13 S ATOM 20091 SG CYS y 467 149.497 57.219 94.692 1.00205.86 S ATOM 20105 SG CYS y 469 152.340 55.081 95.850 1.00201.92 S ATOM 20196 SG CYS y 482 126.774 49.344 105.867 1.00167.27 S ATOM 20756 SG CYS y 586 127.702 47.897 101.879 1.00187.67 S ATOM 20769 SG CYS y 588 129.403 48.484 104.393 1.00190.44 S ATOM 20775 SG CYS y 589 125.312 48.977 103.407 1.00184.80 S ATOM 27201 SG CYS y1423 115.730 71.545 50.666 1.00204.06 S ATOM 27227 SG CYS y1426 118.068 73.951 49.615 1.00209.66 S ATOM 27311 SG CYS y1439 114.458 74.887 49.698 1.00246.55 S ATOM 28006 SG CYS y1526 92.830 74.912 75.559 1.00209.60 S ATOM 28026 SG CYS y1529 91.839 76.794 78.673 1.00188.46 S ATOM 28304 SG CYS y1571 89.084 75.402 76.397 1.00204.27 S ATOM 29167 SG CYS y1681 146.348 76.890 75.839 1.00255.22 S ATOM 29179 SG CYS y1683 144.848 74.652 78.452 1.00228.61 S ATOM 29213 SG CYS y1687 144.776 78.448 79.053 1.00202.43 S ATOM 29239 SG CYS y1690 142.574 77.036 76.522 1.00243.38 S Time building chain proxies: 7.26, per 1000 atoms: 0.23 Number of scatterers: 31858 At special positions: 0 Unit cell: (173.056, 146.432, 169.728, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 10 29.99 S 141 16.00 P 59 15.00 O 6038 8.00 N 5706 7.00 C 19904 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.60 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN Y2201 " pdb="ZN ZN Y2201 " - pdb=" SG CYS Y 442 " pdb="ZN ZN Y2201 " - pdb=" SG CYS Y 467 " pdb="ZN ZN Y2201 " - pdb=" SG CYS Y 437 " pdb="ZN ZN Y2201 " - pdb=" SG CYS Y 469 " pdb=" ZN Y2202 " pdb="ZN ZN Y2202 " - pdb=" SG CYS Y 482 " pdb="ZN ZN Y2202 " - pdb=" SG CYS Y 589 " pdb="ZN ZN Y2202 " - pdb=" SG CYS Y 479 " pdb="ZN ZN Y2202 " - pdb=" SG CYS Y 586 " pdb=" ZN Y2203 " pdb="ZN ZN Y2203 " - pdb=" SG CYS Y1439 " pdb="ZN ZN Y2203 " - pdb=" SG CYS Y1442 " pdb="ZN ZN Y2203 " - pdb=" SG CYS Y1423 " pdb="ZN ZN Y2203 " - pdb=" SG CYS Y1426 " pdb=" ZN Y2204 " pdb="ZN ZN Y2204 " - pdb=" NE2 HIS Y1554 " pdb="ZN ZN Y2204 " - pdb=" SG CYS Y1526 " pdb="ZN ZN Y2204 " - pdb=" SG CYS Y1529 " pdb="ZN ZN Y2204 " - pdb=" SG CYS Y1571 " pdb=" ZN Y2205 " pdb="ZN ZN Y2205 " - pdb=" SG CYS Y1690 " pdb="ZN ZN Y2205 " - pdb=" SG CYS Y1683 " pdb="ZN ZN Y2205 " - pdb=" SG CYS Y1681 " pdb="ZN ZN Y2205 " - pdb=" SG CYS Y1687 " pdb=" ZN y2202 " pdb="ZN ZN y2202 " - pdb=" SG CYS y 437 " pdb="ZN ZN y2202 " - pdb=" SG CYS y 469 " pdb="ZN ZN y2202 " - pdb=" SG CYS y 467 " pdb="ZN ZN y2202 " - pdb=" SG CYS y 442 " pdb=" ZN y2203 " pdb="ZN ZN y2203 " - pdb=" SG CYS y 589 " pdb="ZN ZN y2203 " - pdb=" SG CYS y 588 " pdb="ZN ZN y2203 " - pdb=" SG CYS y 482 " pdb="ZN ZN y2203 " - pdb=" SG CYS y 586 " pdb=" ZN y2204 " pdb="ZN ZN y2204 " - pdb=" SG CYS y1423 " pdb="ZN ZN y2204 " - pdb=" SG CYS y1426 " pdb="ZN ZN y2204 " - pdb=" SG CYS y1439 " pdb=" ZN y2205 " pdb="ZN ZN y2205 " - pdb=" NE2 HIS y1554 " pdb="ZN ZN y2205 " - pdb=" SG CYS y1529 " pdb="ZN ZN y2205 " - pdb=" SG CYS y1526 " pdb="ZN ZN y2205 " - pdb=" SG CYS y1571 " pdb=" ZN y2206 " pdb="ZN ZN y2206 " - pdb=" SG CYS y1690 " pdb="ZN ZN y2206 " - pdb=" SG CYS y1687 " pdb="ZN ZN y2206 " - pdb=" SG CYS y1683 " pdb="ZN ZN y2206 " - pdb=" SG CYS y1681 " Number of angles added : 48 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7254 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 36 sheets defined 42.7% alpha, 13.6% beta 9 base pairs and 31 stacking pairs defined. Time for finding SS restraints: 4.37 Creating SS restraints... Processing helix chain 'Y' and resid 7 through 28 Processing helix chain 'Y' and resid 31 through 43 Processing helix chain 'Y' and resid 70 through 75 Processing helix chain 'Y' and resid 80 through 87 Processing helix chain 'Y' and resid 94 through 107 Processing helix chain 'Y' and resid 120 through 141 Proline residue: Y 128 - end of helix Processing helix chain 'Y' and resid 155 through 171 removed outlier: 3.692A pdb=" N ILE Y 159 " --> pdb=" O LEU Y 155 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLU Y 164 " --> pdb=" O ASN Y 160 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG Y 165 " --> pdb=" O SER Y 161 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N TRP Y 169 " --> pdb=" O ARG Y 165 " (cutoff:3.500A) Processing helix chain 'Y' and resid 193 through 198 removed outlier: 3.669A pdb=" N LEU Y 198 " --> pdb=" O GLN Y 194 " (cutoff:3.500A) Processing helix chain 'Y' and resid 208 through 213 Processing helix chain 'Y' and resid 221 through 231 removed outlier: 3.605A pdb=" N LEU Y 229 " --> pdb=" O LEU Y 225 " (cutoff:3.500A) Processing helix chain 'Y' and resid 234 through 240 removed outlier: 4.205A pdb=" N ILE Y 238 " --> pdb=" O ASP Y 234 " (cutoff:3.500A) Processing helix chain 'Y' and resid 253 through 256 Processing helix chain 'Y' and resid 259 through 276 Processing helix chain 'Y' and resid 298 through 314 Processing helix chain 'Y' and resid 333 through 337 Processing helix chain 'Y' and resid 344 through 350 removed outlier: 3.873A pdb=" N LEU Y 348 " --> pdb=" O SER Y 344 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER Y 350 " --> pdb=" O THR Y 346 " (cutoff:3.500A) Processing helix chain 'Y' and resid 352 through 361 removed outlier: 3.646A pdb=" N TYR Y 357 " --> pdb=" O PRO Y 353 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN Y 358 " --> pdb=" O GLN Y 354 " (cutoff:3.500A) Processing helix chain 'Y' and resid 363 through 375 Processing helix chain 'Y' and resid 383 through 394 Processing helix chain 'Y' and resid 398 through 412 Processing helix chain 'Y' and resid 446 through 450 Processing helix chain 'Y' and resid 606 through 621 Proline residue: Y 616 - end of helix removed outlier: 3.979A pdb=" N PHE Y 621 " --> pdb=" O THR Y 617 " (cutoff:3.500A) Processing helix chain 'Y' and resid 628 through 633 removed outlier: 3.576A pdb=" N LEU Y 632 " --> pdb=" O GLU Y 629 " (cutoff:3.500A) Processing helix chain 'Y' and resid 647 through 673 removed outlier: 3.866A pdb=" N ALA Y 651 " --> pdb=" O ARG Y 647 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU Y 673 " --> pdb=" O LEU Y 669 " (cutoff:3.500A) Processing helix chain 'Y' and resid 685 through 701 removed outlier: 4.611A pdb=" N VAL Y 701 " --> pdb=" O SER Y 697 " (cutoff:3.500A) Processing helix chain 'Y' and resid 704 through 717 Processing helix chain 'Y' and resid 722 through 740 Proline residue: Y 734 - end of helix Processing helix chain 'Y' and resid 740 through 756 removed outlier: 3.828A pdb=" N ASN Y 756 " --> pdb=" O ALA Y 752 " (cutoff:3.500A) Processing helix chain 'Y' and resid 764 through 772 Processing helix chain 'Y' and resid 774 through 790 removed outlier: 4.832A pdb=" N MET Y 781 " --> pdb=" O LEU Y 777 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ARG Y 782 " --> pdb=" O ALA Y 778 " (cutoff:3.500A) Processing helix chain 'Y' and resid 794 through 808 Processing helix chain 'Y' and resid 827 through 832 Processing helix chain 'Y' and resid 837 through 844 Processing helix chain 'Y' and resid 849 through 869 Processing helix chain 'Y' and resid 878 through 882 Processing helix chain 'Y' and resid 910 through 914 removed outlier: 3.508A pdb=" N ARG Y 914 " --> pdb=" O ILE Y 911 " (cutoff:3.500A) Processing helix chain 'Y' and resid 917 through 927 Processing helix chain 'Y' and resid 934 through 953 Processing helix chain 'Y' and resid 954 through 956 No H-bonds generated for 'chain 'Y' and resid 954 through 956' Processing helix chain 'Y' and resid 968 through 970 No H-bonds generated for 'chain 'Y' and resid 968 through 970' Processing helix chain 'Y' and resid 1033 through 1044 removed outlier: 4.177A pdb=" N ARG Y1037 " --> pdb=" O ALA Y1033 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1044 through 1053 Processing helix chain 'Y' and resid 1057 through 1065 Processing helix chain 'Y' and resid 1080 through 1093 Processing helix chain 'Y' and resid 1103 through 1108 removed outlier: 3.844A pdb=" N MET Y1107 " --> pdb=" O THR Y1103 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1125 through 1134 Processing helix chain 'Y' and resid 1135 through 1137 No H-bonds generated for 'chain 'Y' and resid 1135 through 1137' Processing helix chain 'Y' and resid 1153 through 1161 removed outlier: 3.598A pdb=" N MET Y1157 " --> pdb=" O THR Y1153 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLU Y1158 " --> pdb=" O ALA Y1154 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N VAL Y1159 " --> pdb=" O HIS Y1155 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1164 through 1169 Processing helix chain 'Y' and resid 1182 through 1200 Processing helix chain 'Y' and resid 1208 through 1213 Processing helix chain 'Y' and resid 1218 through 1230 Processing helix chain 'Y' and resid 1232 through 1242 removed outlier: 4.350A pdb=" N ASP Y1236 " --> pdb=" O ASP Y1232 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS Y1237 " --> pdb=" O GLN Y1233 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1251 through 1288 Processing helix chain 'Y' and resid 1294 through 1310 Processing helix chain 'Y' and resid 1311 through 1319 removed outlier: 3.785A pdb=" N SER Y1318 " --> pdb=" O SER Y1314 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1338 through 1349 Processing helix chain 'Y' and resid 1373 through 1381 Processing helix chain 'Y' and resid 1445 through 1447 No H-bonds generated for 'chain 'Y' and resid 1445 through 1447' Processing helix chain 'Y' and resid 1604 through 1624 Processing helix chain 'Y' and resid 1626 through 1628 No H-bonds generated for 'chain 'Y' and resid 1626 through 1628' Processing helix chain 'Y' and resid 1659 through 1667 removed outlier: 3.516A pdb=" N GLN Y1663 " --> pdb=" O GLY Y1659 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE Y1665 " --> pdb=" O ALA Y1661 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ASP Y1666 " --> pdb=" O VAL Y1662 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N HIS Y1667 " --> pdb=" O GLN Y1663 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1668 through 1680 Processing helix chain 'Y' and resid 1698 through 1702 removed outlier: 4.082A pdb=" N ASN Y1701 " --> pdb=" O HIS Y1698 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1704 through 1710 Processing helix chain 'Y' and resid 1713 through 1721 removed outlier: 3.769A pdb=" N ASN Y1721 " --> pdb=" O LEU Y1717 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1739 through 1750 Processing helix chain 'Y' and resid 1773 through 1785 removed outlier: 4.246A pdb=" N GLU Y1777 " --> pdb=" O PRO Y1773 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1800 through 1812 Processing helix chain 'Y' and resid 1888 through 1892 removed outlier: 3.555A pdb=" N LEU Y1891 " --> pdb=" O ALA Y1888 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1911 through 1927 removed outlier: 3.579A pdb=" N PHE Y1915 " --> pdb=" O PRO Y1911 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLY Y1916 " --> pdb=" O LEU Y1912 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N SER Y1917 " --> pdb=" O GLU Y1913 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1927 through 1937 Processing helix chain 'Y' and resid 1952 through 1970 Processing helix chain 'Y' and resid 2000 through 2013 removed outlier: 3.799A pdb=" N LEU Y2012 " --> pdb=" O VAL Y2008 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU Y2013 " --> pdb=" O THR Y2009 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2076 through 2086 Processing helix chain 'y' and resid 8 through 28 removed outlier: 4.003A pdb=" N ALA y 28 " --> pdb=" O VAL y 24 " (cutoff:3.500A) Processing helix chain 'y' and resid 32 through 43 Processing helix chain 'y' and resid 71 through 75 removed outlier: 3.766A pdb=" N ARG y 75 " --> pdb=" O GLU y 72 " (cutoff:3.500A) Processing helix chain 'y' and resid 94 through 106 Processing helix chain 'y' and resid 120 through 141 Proline residue: y 128 - end of helix Processing helix chain 'y' and resid 157 through 171 removed outlier: 4.317A pdb=" N SER y 161 " --> pdb=" O ALA y 157 " (cutoff:3.500A) Processing helix chain 'y' and resid 193 through 198 removed outlier: 3.880A pdb=" N LEU y 198 " --> pdb=" O GLN y 194 " (cutoff:3.500A) Processing helix chain 'y' and resid 206 through 213 removed outlier: 3.625A pdb=" N ILE y 210 " --> pdb=" O SER y 206 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR y 211 " --> pdb=" O ARG y 207 " (cutoff:3.500A) Processing helix chain 'y' and resid 221 through 231 Processing helix chain 'y' and resid 235 through 240 Processing helix chain 'y' and resid 252 through 256 Processing helix chain 'y' and resid 258 through 276 Processing helix chain 'y' and resid 298 through 314 Processing helix chain 'y' and resid 344 through 350 removed outlier: 3.706A pdb=" N SER y 350 " --> pdb=" O THR y 346 " (cutoff:3.500A) Processing helix chain 'y' and resid 352 through 362 Processing helix chain 'y' and resid 363 through 374 removed outlier: 3.626A pdb=" N GLN y 367 " --> pdb=" O TYR y 363 " (cutoff:3.500A) Processing helix chain 'y' and resid 383 through 394 Processing helix chain 'y' and resid 398 through 411 Processing helix chain 'y' and resid 446 through 450 Processing helix chain 'y' and resid 606 through 620 removed outlier: 3.865A pdb=" N PHE y 610 " --> pdb=" O GLY y 606 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU y 613 " --> pdb=" O PHE y 609 " (cutoff:3.500A) Proline residue: y 616 - end of helix Processing helix chain 'y' and resid 628 through 633 removed outlier: 3.852A pdb=" N LEU y 632 " --> pdb=" O GLU y 629 " (cutoff:3.500A) Processing helix chain 'y' and resid 646 through 674 removed outlier: 4.222A pdb=" N ALA y 651 " --> pdb=" O ARG y 647 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS y 663 " --> pdb=" O GLN y 659 " (cutoff:3.500A) Processing helix chain 'y' and resid 685 through 700 removed outlier: 3.545A pdb=" N CYS y 689 " --> pdb=" O SER y 685 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU y 691 " --> pdb=" O ALA y 687 " (cutoff:3.500A) Processing helix chain 'y' and resid 705 through 716 Processing helix chain 'y' and resid 726 through 732 Processing helix chain 'y' and resid 732 through 740 removed outlier: 4.032A pdb=" N VAL y 736 " --> pdb=" O ILE y 732 " (cutoff:3.500A) Processing helix chain 'y' and resid 740 through 753 Processing helix chain 'y' and resid 764 through 774 Processing helix chain 'y' and resid 774 through 789 removed outlier: 4.248A pdb=" N MET y 781 " --> pdb=" O LEU y 777 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ARG y 782 " --> pdb=" O ALA y 778 " (cutoff:3.500A) Processing helix chain 'y' and resid 794 through 807 Processing helix chain 'y' and resid 827 through 833 removed outlier: 4.325A pdb=" N ASP y 831 " --> pdb=" O TYR y 827 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS y 832 " --> pdb=" O PRO y 828 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL y 833 " --> pdb=" O PHE y 829 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 827 through 833' Processing helix chain 'y' and resid 837 through 844 Processing helix chain 'y' and resid 849 through 868 Processing helix chain 'y' and resid 878 through 883 Processing helix chain 'y' and resid 917 through 927 Processing helix chain 'y' and resid 934 through 953 Processing helix chain 'y' and resid 1021 through 1025 removed outlier: 3.726A pdb=" N TRP y1024 " --> pdb=" O VAL y1021 " (cutoff:3.500A) Processing helix chain 'y' and resid 1033 through 1044 removed outlier: 3.780A pdb=" N ARG y1037 " --> pdb=" O ALA y1033 " (cutoff:3.500A) Processing helix chain 'y' and resid 1044 through 1053 Processing helix chain 'y' and resid 1057 through 1065 Processing helix chain 'y' and resid 1080 through 1093 Processing helix chain 'y' and resid 1125 through 1134 removed outlier: 3.597A pdb=" N TYR y1129 " --> pdb=" O ALA y1125 " (cutoff:3.500A) Processing helix chain 'y' and resid 1135 through 1137 No H-bonds generated for 'chain 'y' and resid 1135 through 1137' Processing helix chain 'y' and resid 1153 through 1162 removed outlier: 3.742A pdb=" N ASP y1162 " --> pdb=" O GLU y1158 " (cutoff:3.500A) Processing helix chain 'y' and resid 1164 through 1169 Processing helix chain 'y' and resid 1180 through 1201 removed outlier: 3.980A pdb=" N VAL y1184 " --> pdb=" O SER y1180 " (cutoff:3.500A) Processing helix chain 'y' and resid 1202 through 1209 removed outlier: 3.903A pdb=" N LYS y1206 " --> pdb=" O PRO y1202 " (cutoff:3.500A) Processing helix chain 'y' and resid 1219 through 1230 Processing helix chain 'y' and resid 1230 through 1242 removed outlier: 4.410A pdb=" N ASP y1236 " --> pdb=" O ASP y1232 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N LYS y1237 " --> pdb=" O GLN y1233 " (cutoff:3.500A) Processing helix chain 'y' and resid 1251 through 1288 removed outlier: 3.606A pdb=" N LEU y1255 " --> pdb=" O THR y1251 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASN y1280 " --> pdb=" O ILE y1276 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ILE y1281 " --> pdb=" O LEU y1277 " (cutoff:3.500A) Processing helix chain 'y' and resid 1294 through 1309 Processing helix chain 'y' and resid 1311 through 1318 Processing helix chain 'y' and resid 1338 through 1354 removed outlier: 4.221A pdb=" N LEU y1342 " --> pdb=" O THR y1338 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLU y1343 " --> pdb=" O ALA y1339 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N LYS y1344 " --> pdb=" O ASP y1340 " (cutoff:3.500A) Processing helix chain 'y' and resid 1373 through 1381 removed outlier: 4.287A pdb=" N ARG y1379 " --> pdb=" O PRO y1375 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU y1380 " --> pdb=" O THR y1376 " (cutoff:3.500A) Processing helix chain 'y' and resid 1445 through 1447 No H-bonds generated for 'chain 'y' and resid 1445 through 1447' Processing helix chain 'y' and resid 1604 through 1624 removed outlier: 3.542A pdb=" N ALA y1608 " --> pdb=" O ASP y1604 " (cutoff:3.500A) Processing helix chain 'y' and resid 1626 through 1628 No H-bonds generated for 'chain 'y' and resid 1626 through 1628' Processing helix chain 'y' and resid 1657 through 1667 removed outlier: 3.998A pdb=" N GLN y1663 " --> pdb=" O GLY y1659 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N LEU y1664 " --> pdb=" O TYR y1660 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N ILE y1665 " --> pdb=" O ALA y1661 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ASP y1666 " --> pdb=" O VAL y1662 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N HIS y1667 " --> pdb=" O GLN y1663 " (cutoff:3.500A) Processing helix chain 'y' and resid 1668 through 1680 Processing helix chain 'y' and resid 1693 through 1699 removed outlier: 4.086A pdb=" N HIS y1698 " --> pdb=" O TYR y1694 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TYR y1699 " --> pdb=" O ASP y1695 " (cutoff:3.500A) Processing helix chain 'y' and resid 1704 through 1713 removed outlier: 3.935A pdb=" N ALA y1708 " --> pdb=" O ASP y1704 " (cutoff:3.500A) Processing helix chain 'y' and resid 1714 through 1719 removed outlier: 4.009A pdb=" N GLN y1718 " --> pdb=" O ASN y1714 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG y1719 " --> pdb=" O VAL y1715 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 1714 through 1719' Processing helix chain 'y' and resid 1739 through 1751 removed outlier: 3.610A pdb=" N GLU y1751 " --> pdb=" O CYS y1747 " (cutoff:3.500A) Processing helix chain 'y' and resid 1773 through 1785 removed outlier: 4.081A pdb=" N GLU y1777 " --> pdb=" O PRO y1773 " (cutoff:3.500A) Processing helix chain 'y' and resid 1800 through 1812 Processing sheet with id=AA1, first strand: chain 'Y' and resid 380 through 382 removed outlier: 6.962A pdb=" N LEU Y 422 " --> pdb=" O SER Y1144 " (cutoff:3.500A) removed outlier: 8.725A pdb=" N ALA Y1146 " --> pdb=" O LEU Y 422 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N MET Y 424 " --> pdb=" O ALA Y1146 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N THR Y1148 " --> pdb=" O MET Y 424 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLY Y 426 " --> pdb=" O THR Y1148 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N CYS Y1150 " --> pdb=" O GLY Y 426 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE Y 428 " --> pdb=" O CYS Y1150 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N VAL Y1117 " --> pdb=" O ILE Y1147 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N LEU Y1149 " --> pdb=" O VAL Y1117 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N MET Y1119 " --> pdb=" O LEU Y1149 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU Y 641 " --> pdb=" O ALA Y1118 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'Y' and resid 217 through 220 removed outlier: 6.439A pdb=" N ALA Y 149 " --> pdb=" O MET Y 218 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N THR Y 220 " --> pdb=" O ALA Y 149 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N PHE Y 151 " --> pdb=" O THR Y 220 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILE Y 150 " --> pdb=" O VAL Y 249 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ASP Y 251 " --> pdb=" O ILE Y 150 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU Y 152 " --> pdb=" O ASP Y 251 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'Y' and resid 413 through 414 Processing sheet with id=AA4, first strand: chain 'Y' and resid 499 through 503 removed outlier: 4.166A pdb=" N ASN Y 569 " --> pdb=" O ALA Y 540 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'Y' and resid 499 through 503 removed outlier: 4.143A pdb=" N GLU Y 475 " --> pdb=" O SER Y 488 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'Y' and resid 762 through 763 Processing sheet with id=AA7, first strand: chain 'Y' and resid 872 through 873 Processing sheet with id=AA8, first strand: chain 'Y' and resid 988 through 989 removed outlier: 3.676A pdb=" N VAL Y1012 " --> pdb=" O ARG Y 981 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'Y' and resid 1371 through 1372 removed outlier: 6.036A pdb=" N ASN Y1333 " --> pdb=" O PHE Y1460 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N THR Y1462 " --> pdb=" O ASN Y1333 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ASN Y1335 " --> pdb=" O THR Y1462 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'Y' and resid 1429 through 1432 Processing sheet with id=AB2, first strand: chain 'Y' and resid 1484 through 1486 Processing sheet with id=AB3, first strand: chain 'Y' and resid 1484 through 1486 removed outlier: 3.737A pdb=" N SER Y1508 " --> pdb=" O THR Y1587 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N THR Y1587 " --> pdb=" O SER Y1508 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N GLU Y1510 " --> pdb=" O SER Y1585 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N SER Y1585 " --> pdb=" O GLU Y1510 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N PHE Y1512 " --> pdb=" O TYR Y1583 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N TYR Y1583 " --> pdb=" O PHE Y1512 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N PHE Y1514 " --> pdb=" O LEU Y1581 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU Y1581 " --> pdb=" O PHE Y1514 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ASP Y1588 " --> pdb=" O ASP Y1652 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP Y1652 " --> pdb=" O ASP Y1588 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N LEU Y1594 " --> pdb=" O TYR Y1646 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N TYR Y1646 " --> pdb=" O LEU Y1594 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N TYR Y1643 " --> pdb=" O ASP Y1639 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ASP Y1639 " --> pdb=" O TYR Y1643 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Y' and resid 1532 through 1534 Processing sheet with id=AB5, first strand: chain 'Y' and resid 1554 through 1555 removed outlier: 3.927A pdb=" N HIS Y1554 " --> pdb=" O CYS Y1571 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'Y' and resid 1734 through 1735 removed outlier: 3.855A pdb=" N ALA Y1837 " --> pdb=" O TRP Y1848 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ALA Y1850 " --> pdb=" O TRP Y1835 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N TRP Y1835 " --> pdb=" O ALA Y1850 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'Y' and resid 1734 through 1735 removed outlier: 3.855A pdb=" N ALA Y1837 " --> pdb=" O TRP Y1848 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ALA Y1850 " --> pdb=" O TRP Y1835 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N TRP Y1835 " --> pdb=" O ALA Y1850 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LEU Y1836 " --> pdb=" O VAL Y1759 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N VAL Y1788 " --> pdb=" O GLN Y1819 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N LYS Y1821 " --> pdb=" O VAL Y1788 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N LEU Y1790 " --> pdb=" O LYS Y1821 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N VAL Y1820 " --> pdb=" O LEU Y1886 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'Y' and resid 1902 through 1903 Processing sheet with id=AB9, first strand: chain 'Y' and resid 2025 through 2028 removed outlier: 7.040A pdb=" N THR Y1941 " --> pdb=" O SER Y1976 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N THR Y1978 " --> pdb=" O THR Y1941 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL Y1943 " --> pdb=" O THR Y1978 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N CYS Y1980 " --> pdb=" O VAL Y1943 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N TYR Y1945 " --> pdb=" O CYS Y1980 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N HIS Y1942 " --> pdb=" O THR Y2044 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N THR Y2044 " --> pdb=" O HIS Y1942 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL Y2043 " --> pdb=" O HIS Y2051 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'Y' and resid 2063 through 2064 Processing sheet with id=AC2, first strand: chain 'y' and resid 381 through 382 removed outlier: 6.484A pdb=" N LEU y 422 " --> pdb=" O SER y1144 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N ALA y1146 " --> pdb=" O LEU y 422 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N MET y 424 " --> pdb=" O ALA y1146 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N THR y1148 " --> pdb=" O MET y 424 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N GLY y 426 " --> pdb=" O THR y1148 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N VAL y1117 " --> pdb=" O ILE y1147 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N LEU y1149 " --> pdb=" O VAL y1117 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N MET y1119 " --> pdb=" O LEU y1149 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU y 641 " --> pdb=" O LEU y1116 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA y1118 " --> pdb=" O LEU y 641 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N GLU y1073 " --> pdb=" O ASN y1100 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'y' and resid 179 through 181 removed outlier: 6.356A pdb=" N ILE y 150 " --> pdb=" O VAL y 249 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU y 111 " --> pdb=" O ILE y 287 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N SER y 110 " --> pdb=" O LYS y 321 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N VAL y 323 " --> pdb=" O SER y 110 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU y 112 " --> pdb=" O VAL y 323 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'y' and resid 459 through 460 removed outlier: 5.189A pdb=" N GLU y 475 " --> pdb=" O SER y 488 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N SER y 488 " --> pdb=" O GLU y 475 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'y' and resid 499 through 503 removed outlier: 4.278A pdb=" N SER y 488 " --> pdb=" O GLU y 475 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N GLU y 475 " --> pdb=" O SER y 488 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'y' and resid 546 through 549 Processing sheet with id=AC7, first strand: chain 'y' and resid 762 through 763 Processing sheet with id=AC8, first strand: chain 'y' and resid 957 through 958 Processing sheet with id=AC9, first strand: chain 'y' and resid 988 through 989 Processing sheet with id=AD1, first strand: chain 'y' and resid 1371 through 1372 removed outlier: 3.601A pdb=" N ARG y1372 " --> pdb=" O VAL y1332 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'y' and resid 1387 through 1389 Processing sheet with id=AD3, first strand: chain 'y' and resid 1429 through 1432 Processing sheet with id=AD4, first strand: chain 'y' and resid 1484 through 1486 Processing sheet with id=AD5, first strand: chain 'y' and resid 1484 through 1486 removed outlier: 4.153A pdb=" N SER y1508 " --> pdb=" O THR y1587 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N THR y1587 " --> pdb=" O SER y1508 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLU y1510 " --> pdb=" O SER y1585 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N SER y1585 " --> pdb=" O GLU y1510 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N PHE y1512 " --> pdb=" O TYR y1583 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N TYR y1583 " --> pdb=" O PHE y1512 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ASP y1588 " --> pdb=" O ASP y1652 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP y1652 " --> pdb=" O ASP y1588 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'y' and resid 1523 through 1525 Processing sheet with id=AD7, first strand: chain 'y' and resid 1554 through 1555 removed outlier: 3.884A pdb=" N HIS y1554 " --> pdb=" O CYS y1571 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'y' and resid 1734 through 1735 removed outlier: 3.940A pdb=" N ALA y1837 " --> pdb=" O TRP y1848 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ALA y1850 " --> pdb=" O TRP y1835 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N TRP y1835 " --> pdb=" O ALA y1850 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'y' and resid 1734 through 1735 removed outlier: 3.940A pdb=" N ALA y1837 " --> pdb=" O TRP y1848 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ALA y1850 " --> pdb=" O TRP y1835 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N TRP y1835 " --> pdb=" O ALA y1850 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU y1836 " --> pdb=" O VAL y1759 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N CYS y1756 " --> pdb=" O GLU y1789 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N LEU y1791 " --> pdb=" O CYS y1756 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU y1758 " --> pdb=" O LEU y1791 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N VAL y1788 " --> pdb=" O GLN y1819 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N LYS y1821 " --> pdb=" O VAL y1788 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N LEU y1790 " --> pdb=" O LYS y1821 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N VAL y1820 " --> pdb=" O LEU y1886 " (cutoff:3.500A) 1308 hydrogen bonds defined for protein. 3672 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 20 hydrogen bonds 36 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 31 stacking parallelities Total time for adding SS restraints: 10.55 Time building geometry restraints manager: 3.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 10761 1.36 - 1.51: 9069 1.51 - 1.66: 12629 1.66 - 1.80: 122 1.80 - 1.95: 87 Bond restraints: 32668 Sorted by residual: bond pdb=" O3B AGS Y2206 " pdb=" PB AGS Y2206 " ideal model delta sigma weight residual 1.673 1.581 0.092 2.00e-02 2.50e+03 2.14e+01 bond pdb=" O3B AGS y2201 " pdb=" PB AGS y2201 " ideal model delta sigma weight residual 1.673 1.585 0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" O3A AGS Y2206 " pdb=" PA AGS Y2206 " ideal model delta sigma weight residual 1.664 1.583 0.081 2.00e-02 2.50e+03 1.65e+01 bond pdb=" O3A AGS y2201 " pdb=" PA AGS y2201 " ideal model delta sigma weight residual 1.664 1.590 0.074 2.00e-02 2.50e+03 1.38e+01 bond pdb=" C3' DA i 14 " pdb=" C2' DA i 14 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.13e+01 ... (remaining 32663 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.90: 44095 2.90 - 5.80: 320 5.80 - 8.70: 64 8.70 - 11.61: 20 11.61 - 14.51: 9 Bond angle restraints: 44508 Sorted by residual: angle pdb=" CB MET Y 747 " pdb=" CG MET Y 747 " pdb=" SD MET Y 747 " ideal model delta sigma weight residual 112.70 127.21 -14.51 3.00e+00 1.11e-01 2.34e+01 angle pdb=" CA GLU y 720 " pdb=" CB GLU y 720 " pdb=" CG GLU y 720 " ideal model delta sigma weight residual 114.10 123.20 -9.10 2.00e+00 2.50e-01 2.07e+01 angle pdb=" N3 DT i 9 " pdb=" C4 DT i 9 " pdb=" O4 DT i 9 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.95e+01 angle pdb=" CB MET Y 65 " pdb=" CG MET Y 65 " pdb=" SD MET Y 65 " ideal model delta sigma weight residual 112.70 125.58 -12.88 3.00e+00 1.11e-01 1.84e+01 angle pdb=" O4' DA G 3 " pdb=" C4' DA G 3 " pdb=" C3' DA G 3 " ideal model delta sigma weight residual 106.00 103.43 2.57 6.00e-01 2.78e+00 1.83e+01 ... (remaining 44503 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.06: 18829 35.06 - 70.12: 743 70.12 - 105.19: 47 105.19 - 140.25: 4 140.25 - 175.31: 2 Dihedral angle restraints: 19625 sinusoidal: 8400 harmonic: 11225 Sorted by residual: dihedral pdb=" O2B AGS y2201 " pdb=" O3B AGS y2201 " pdb=" PB AGS y2201 " pdb=" PG AGS y2201 " ideal model delta sinusoidal sigma weight residual 7.37 -167.94 175.31 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O2B AGS Y2206 " pdb=" O3B AGS Y2206 " pdb=" PB AGS Y2206 " pdb=" PG AGS Y2206 " ideal model delta sinusoidal sigma weight residual 7.37 -154.42 161.79 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" CA GLU Y1860 " pdb=" C GLU Y1860 " pdb=" N LEU Y1861 " pdb=" CA LEU Y1861 " ideal model delta harmonic sigma weight residual 180.00 157.38 22.62 0 5.00e+00 4.00e-02 2.05e+01 ... (remaining 19622 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 4297 0.064 - 0.128: 531 0.128 - 0.192: 28 0.192 - 0.255: 5 0.255 - 0.319: 3 Chirality restraints: 4864 Sorted by residual: chirality pdb=" CG LEU y1274 " pdb=" CB LEU y1274 " pdb=" CD1 LEU y1274 " pdb=" CD2 LEU y1274 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" CB ILE y 150 " pdb=" CA ILE y 150 " pdb=" CG1 ILE y 150 " pdb=" CG2 ILE y 150 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CB VAL y1472 " pdb=" CA VAL y1472 " pdb=" CG1 VAL y1472 " pdb=" CG2 VAL y1472 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.94e+00 ... (remaining 4861 not shown) Planarity restraints: 5605 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU y 720 " 0.010 2.00e-02 2.50e+03 2.09e-02 4.37e+00 pdb=" C GLU y 720 " -0.036 2.00e-02 2.50e+03 pdb=" O GLU y 720 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU y 721 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET y 409 " 0.009 2.00e-02 2.50e+03 1.71e-02 2.93e+00 pdb=" C MET y 409 " -0.030 2.00e-02 2.50e+03 pdb=" O MET y 409 " 0.011 2.00e-02 2.50e+03 pdb=" N ALA y 410 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY Y1970 " 0.008 2.00e-02 2.50e+03 1.66e-02 2.75e+00 pdb=" C GLY Y1970 " -0.029 2.00e-02 2.50e+03 pdb=" O GLY Y1970 " 0.011 2.00e-02 2.50e+03 pdb=" N MET Y1971 " 0.010 2.00e-02 2.50e+03 ... (remaining 5602 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 252 2.48 - 3.09: 22696 3.09 - 3.69: 53830 3.69 - 4.30: 72537 4.30 - 4.90: 115970 Nonbonded interactions: 265285 Sorted by model distance: nonbonded pdb=" N CYS y 589 " pdb="ZN ZN y2203 " model vdw 1.876 2.310 nonbonded pdb=" O2 DC i 3 " pdb=" N2 DG g 28 " model vdw 2.117 2.496 nonbonded pdb=" OG1 THR y 642 " pdb=" OD1 ASN y1100 " model vdw 2.122 3.040 nonbonded pdb=" OG1 THR Y1553 " pdb=" O CYS Y1571 " model vdw 2.163 3.040 nonbonded pdb=" C CYS y 588 " pdb="ZN ZN y2203 " model vdw 2.170 2.460 ... (remaining 265280 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 Found NCS groups: ncs_group { reference = (chain 'Y' and (resid 4 through 575 or resid 581 through 1209 or resid 1215 thro \ ugh 1349 or resid 1369 through 1402 or resid 1414 through 1559 or resid 1568 thr \ ough 1896 or resid 2202 through 2205)) selection = (chain 'y' and (resid 4 through 505 or resid 534 through 1349 or resid 1369 thro \ ugh 1896 or resid 2202 through 2205)) } 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: 2.140 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: 0.030 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 40.510 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 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 : 0.003 0.092 32707 Z= 0.195 Angle : 0.785 32.793 44556 Z= 0.365 Chirality : 0.042 0.319 4864 Planarity : 0.003 0.036 5605 Dihedral : 17.405 175.310 12371 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.53 % Favored : 95.42 % Rotamer: Outliers : 1.94 % Allowed : 20.28 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.14), residues: 3845 helix: 0.99 (0.14), residues: 1469 sheet: -0.43 (0.22), residues: 577 loop : -1.27 (0.14), residues: 1799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG y1603 TYR 0.011 0.001 TYR y1699 PHE 0.021 0.001 PHE Y1686 TRP 0.018 0.001 TRP Y1998 HIS 0.007 0.001 HIS Y1689 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.20 (32668) covalent geometry : angle 0.69453 / 0.36 (44508) hydrogen bonds : bond 0.14658 / 11.14 ( 1292) hydrogen bonds : angle 5.92996 / 4.38 ( 3708) metal coordination : bond 0.00628 / 0.63 ( 39) metal coordination : angle 11.16715 / 8.03 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 3299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 133 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 124 CYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8664 (p) REVERT: Y 218 MET cc_start: 0.8470 (ttm) cc_final: 0.8214 (ttp) REVERT: Y 612 ASN cc_start: 0.9049 (t0) cc_final: 0.8848 (m110) REVERT: Y 1105 MET cc_start: 0.8308 (tpp) cc_final: 0.7787 (tpp) REVERT: Y 1248 MET cc_start: 0.8875 (OUTLIER) cc_final: 0.7786 (tmm) REVERT: Y 1250 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8733 (tt) REVERT: Y 1474 MET cc_start: 0.8865 (tmm) cc_final: 0.8443 (tmm) REVERT: y 224 MET cc_start: 0.8327 (mpp) cc_final: 0.8010 (mpt) REVERT: y 228 MET cc_start: 0.8883 (pp-130) cc_final: 0.8603 (ppp) REVERT: y 747 MET cc_start: 0.8652 (tmm) cc_final: 0.8015 (ptp) REVERT: y 883 MET cc_start: 0.8583 (mmm) cc_final: 0.7808 (mmm) REVERT: y 952 ILE cc_start: 0.9201 (OUTLIER) cc_final: 0.8936 (tp) REVERT: y 1012 VAL cc_start: 0.9282 (OUTLIER) cc_final: 0.9001 (p) REVERT: y 1225 HIS cc_start: 0.8505 (m-70) cc_final: 0.8244 (m-70) REVERT: y 1381 TYR cc_start: 0.8926 (m-80) cc_final: 0.8643 (m-80) REVERT: y 1395 ARG cc_start: 0.7510 (mmm160) cc_final: 0.6927 (tpt170) REVERT: y 1463 ASP cc_start: 0.7399 (t70) cc_final: 0.6939 (t70) REVERT: y 1515 SER cc_start: 0.8797 (t) cc_final: 0.8402 (p) REVERT: y 1540 ARG cc_start: 0.7569 (tmm-80) cc_final: 0.6641 (tmm-80) REVERT: y 1578 ASP cc_start: 0.8540 (m-30) cc_final: 0.8312 (m-30) REVERT: y 1699 TYR cc_start: 0.8005 (OUTLIER) cc_final: 0.7625 (m-80) REVERT: y 1749 ASN cc_start: 0.6925 (m110) cc_final: 0.6576 (p0) outliers start: 64 outliers final: 45 residues processed: 185 average time/residue: 0.1867 time to fit residues: 59.0139 Evaluate side-chains 176 residues out of total 3299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 125 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 112 LEU Chi-restraints excluded: chain Y residue 124 CYS Chi-restraints excluded: chain Y residue 130 LEU Chi-restraints excluded: chain Y residue 200 VAL Chi-restraints excluded: chain Y residue 206 SER Chi-restraints excluded: chain Y residue 217 ILE Chi-restraints excluded: chain Y residue 228 MET Chi-restraints excluded: chain Y residue 320 VAL Chi-restraints excluded: chain Y residue 430 THR Chi-restraints excluded: chain Y residue 767 LEU Chi-restraints excluded: chain Y residue 848 ASP Chi-restraints excluded: chain Y residue 889 VAL Chi-restraints excluded: chain Y residue 944 LEU Chi-restraints excluded: chain Y residue 990 ASP Chi-restraints excluded: chain Y residue 1122 VAL Chi-restraints excluded: chain Y residue 1201 VAL Chi-restraints excluded: chain Y residue 1205 THR Chi-restraints excluded: chain Y residue 1214 GLU Chi-restraints excluded: chain Y residue 1248 MET Chi-restraints excluded: chain Y residue 1250 LEU Chi-restraints excluded: chain Y residue 1262 MET Chi-restraints excluded: chain Y residue 1396 SER Chi-restraints excluded: chain Y residue 1556 LEU Chi-restraints excluded: chain Y residue 1641 ASN Chi-restraints excluded: chain y residue 27 LEU Chi-restraints excluded: chain y residue 52 LEU Chi-restraints excluded: chain y residue 85 ASP Chi-restraints excluded: chain y residue 181 LEU Chi-restraints excluded: chain y residue 248 ILE Chi-restraints excluded: chain y residue 291 SER Chi-restraints excluded: chain y residue 442 CYS Chi-restraints excluded: chain y residue 459 VAL Chi-restraints excluded: chain y residue 476 VAL Chi-restraints excluded: chain y residue 553 THR Chi-restraints excluded: chain y residue 586 CYS Chi-restraints excluded: chain y residue 676 ASN Chi-restraints excluded: chain y residue 678 THR Chi-restraints excluded: chain y residue 952 ILE Chi-restraints excluded: chain y residue 1012 VAL Chi-restraints excluded: chain y residue 1120 ASN Chi-restraints excluded: chain y residue 1155 HIS Chi-restraints excluded: chain y residue 1176 VAL Chi-restraints excluded: chain y residue 1277 LEU Chi-restraints excluded: chain y residue 1329 VAL Chi-restraints excluded: chain y residue 1340 ASP Chi-restraints excluded: chain y residue 1415 HIS Chi-restraints excluded: chain y residue 1433 THR Chi-restraints excluded: chain y residue 1434 THR Chi-restraints excluded: chain y residue 1487 VAL Chi-restraints excluded: chain y residue 1557 LEU Chi-restraints excluded: chain y residue 1699 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: [197, 388, 215, 20, 132, 261, 248, 207, 155, 244, 183] chunk 197 optimal weight: 9.9990 chunk 388 optimal weight: 40.0000 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 10.0000 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Y 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 893 GLN ** Y1513 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 286 GLN y 534 GLN y 582 ASN y 659 GLN y 765 GLN y 796 GLN ** y1120 ASN ** 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 = 0.3863 r_free = 0.3863 target = 0.086856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.061273 restraints weight = 175148.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.062818 restraints weight = 79313.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.064106 restraints weight = 50883.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.064925 restraints weight = 37593.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.065365 restraints weight = 31380.489| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.0637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 32707 Z= 0.176 Angle : 0.734 34.829 44556 Z= 0.326 Chirality : 0.041 0.271 4864 Planarity : 0.004 0.046 5605 Dihedral : 14.424 170.472 4979 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.79 % Favored : 95.19 % Rotamer: Outliers : 3.00 % Allowed : 18.79 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.14), residues: 3845 helix: 0.96 (0.14), residues: 1499 sheet: -0.53 (0.22), residues: 580 loop : -1.27 (0.14), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG y1603 TYR 0.011 0.001 TYR y1307 PHE 0.014 0.001 PHE Y 125 TRP 0.016 0.001 TRP y 101 HIS 0.006 0.001 HIS y 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.18 (32668) covalent geometry : angle 0.63109 / 0.32 (44508) hydrogen bonds : bond 0.04446 / 3.26 ( 1292) hydrogen bonds : angle 5.08206 / 3.76 ( 3708) metal coordination : bond 0.01181 / 1.05 ( 39) metal coordination : angle 11.41385 / 9.65 ( 48) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 144 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 43 PHE cc_start: 0.8985 (OUTLIER) cc_final: 0.7960 (m-80) REVERT: Y 124 CYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8601 (p) REVERT: Y 1052 GLU cc_start: 0.9181 (OUTLIER) cc_final: 0.8887 (pt0) REVERT: Y 1105 MET cc_start: 0.7814 (tpp) cc_final: 0.7408 (tpp) REVERT: Y 1248 MET cc_start: 0.8925 (OUTLIER) cc_final: 0.8348 (tmm) REVERT: Y 1474 MET cc_start: 0.8980 (tmm) cc_final: 0.8611 (tmm) REVERT: Y 1740 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8917 (tm) REVERT: Y 1778 LEU cc_start: 0.9750 (OUTLIER) cc_final: 0.9454 (mm) REVERT: y 224 MET cc_start: 0.7717 (mpp) cc_final: 0.7275 (mpp) REVERT: y 228 MET cc_start: 0.8918 (pp-130) cc_final: 0.8690 (ppp) REVERT: y 883 MET cc_start: 0.8896 (mmm) cc_final: 0.8463 (tpp) REVERT: y 1078 GLN cc_start: 0.9210 (mm110) cc_final: 0.8729 (mm110) REVERT: y 1157 MET cc_start: 0.8788 (mmt) cc_final: 0.8571 (mmt) REVERT: y 1381 TYR cc_start: 0.9143 (m-80) cc_final: 0.8799 (m-80) REVERT: y 1395 ARG cc_start: 0.7974 (mmm160) cc_final: 0.7165 (tpt170) REVERT: y 1463 ASP cc_start: 0.7763 (t70) cc_final: 0.7280 (t70) REVERT: y 1515 SER cc_start: 0.8159 (t) cc_final: 0.7932 (p) REVERT: y 1540 ARG cc_start: 0.7608 (tmm-80) cc_final: 0.6885 (tmm-80) REVERT: y 1749 ASN cc_start: 0.6306 (m110) cc_final: 0.5709 (p0) outliers start: 99 outliers final: 48 residues processed: 232 average time/residue: 0.1882 time to fit residues: 74.0290 Evaluate side-chains 185 residues out of total 3299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 131 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 43 PHE Chi-restraints excluded: chain Y residue 74 LEU Chi-restraints excluded: chain Y residue 83 LEU Chi-restraints excluded: chain Y residue 124 CYS Chi-restraints excluded: chain Y residue 130 LEU Chi-restraints excluded: chain Y residue 181 LEU Chi-restraints excluded: chain Y residue 200 VAL Chi-restraints excluded: chain Y residue 217 ILE Chi-restraints excluded: chain Y residue 290 THR Chi-restraints excluded: chain Y residue 320 VAL Chi-restraints excluded: chain Y residue 332 VAL Chi-restraints excluded: chain Y residue 409 MET Chi-restraints excluded: chain Y residue 431 LEU Chi-restraints excluded: chain Y residue 678 THR Chi-restraints excluded: chain Y residue 736 VAL Chi-restraints excluded: chain Y residue 767 LEU Chi-restraints excluded: chain Y residue 843 LEU Chi-restraints excluded: chain Y residue 848 ASP Chi-restraints excluded: chain Y residue 889 VAL Chi-restraints excluded: chain Y residue 902 GLN Chi-restraints excluded: chain Y residue 944 LEU Chi-restraints excluded: chain Y residue 1052 GLU Chi-restraints excluded: chain Y residue 1101 CYS Chi-restraints excluded: chain Y residue 1122 VAL Chi-restraints excluded: chain Y residue 1201 VAL Chi-restraints excluded: chain Y residue 1205 THR Chi-restraints excluded: chain Y residue 1248 MET Chi-restraints excluded: chain Y residue 1294 THR Chi-restraints excluded: chain Y residue 1374 LEU Chi-restraints excluded: chain Y residue 1396 SER Chi-restraints excluded: chain Y residue 1556 LEU Chi-restraints excluded: chain Y residue 1740 LEU Chi-restraints excluded: chain Y residue 1778 LEU Chi-restraints excluded: chain y residue 27 LEU Chi-restraints excluded: chain y residue 52 LEU Chi-restraints excluded: chain y residue 181 LEU Chi-restraints excluded: chain y residue 248 ILE Chi-restraints excluded: chain y residue 381 VAL Chi-restraints excluded: chain y residue 424 MET Chi-restraints excluded: chain y residue 442 CYS Chi-restraints excluded: chain y residue 476 VAL Chi-restraints excluded: chain y residue 553 THR Chi-restraints excluded: chain y residue 678 THR Chi-restraints excluded: chain y residue 762 MET Chi-restraints excluded: chain y residue 1120 ASN Chi-restraints excluded: chain y residue 1155 HIS Chi-restraints excluded: chain y residue 1176 VAL Chi-restraints excluded: chain y residue 1248 MET Chi-restraints excluded: chain y residue 1262 MET Chi-restraints excluded: chain y residue 1329 VAL Chi-restraints excluded: chain y residue 1415 HIS Chi-restraints excluded: chain y residue 1433 THR Chi-restraints excluded: chain y residue 1487 VAL Chi-restraints excluded: chain y residue 1664 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: [176, 331, 85, 319, 313, 261, 36, 291, 150, 324, 166] chunk 176 optimal weight: 10.0000 chunk 331 optimal weight: 20.0000 chunk 85 optimal weight: 6.9990 chunk 319 optimal weight: 20.0000 chunk 313 optimal weight: 8.9990 chunk 261 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 291 optimal weight: 10.0000 chunk 150 optimal weight: 5.9990 chunk 324 optimal weight: 20.0000 chunk 166 optimal weight: 2.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Y 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 188 HIS ** Y 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y1228 ASN ** Y1513 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 441 GLN y 565 HIS ** y 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y1539 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.085668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.059908 restraints weight = 170611.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.061419 restraints weight = 77932.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.062608 restraints weight = 50046.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.063272 restraints weight = 37160.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.063793 restraints weight = 31510.904| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 32707 Z= 0.218 Angle : 0.738 34.192 44556 Z= 0.328 Chirality : 0.042 0.257 4864 Planarity : 0.004 0.056 5605 Dihedral : 13.939 162.001 4941 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.81 % Favored : 95.16 % Rotamer: Outliers : 3.55 % Allowed : 18.67 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.14), residues: 3845 helix: 0.88 (0.14), residues: 1516 sheet: -0.71 (0.21), residues: 597 loop : -1.28 (0.15), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG y 400 TYR 0.013 0.001 TYR y1307 PHE 0.017 0.001 PHE Y 173 TRP 0.016 0.001 TRP y 101 HIS 0.014 0.001 HIS y1325 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.22 (32668) covalent geometry : angle 0.63288 / 0.32 (44508) hydrogen bonds : bond 0.04130 / 3.05 ( 1292) hydrogen bonds : angle 4.97399 / 3.71 ( 3708) metal coordination : bond 0.02017 / 2.28 ( 39) metal coordination : angle 11.56835 / 10.12 ( 48) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 3299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 140 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 43 PHE cc_start: 0.8990 (OUTLIER) cc_final: 0.7908 (m-80) REVERT: Y 124 CYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8644 (p) REVERT: Y 218 MET cc_start: 0.8652 (ttm) cc_final: 0.8368 (ttp) REVERT: Y 705 LYS cc_start: 0.4935 (OUTLIER) cc_final: 0.4723 (tppt) REVERT: Y 1052 GLU cc_start: 0.9138 (OUTLIER) cc_final: 0.8835 (pt0) REVERT: Y 1105 MET cc_start: 0.7706 (tpp) cc_final: 0.7393 (tpp) REVERT: Y 1248 MET cc_start: 0.8952 (OUTLIER) cc_final: 0.8460 (tmm) REVERT: Y 1319 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8299 (mp0) REVERT: Y 1474 MET cc_start: 0.8983 (tmm) cc_final: 0.8601 (tmm) REVERT: Y 1740 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.9041 (tm) REVERT: Y 1778 LEU cc_start: 0.9751 (OUTLIER) cc_final: 0.9439 (mm) REVERT: y 183 ASN cc_start: 0.8954 (OUTLIER) cc_final: 0.7946 (m-40) REVERT: y 224 MET cc_start: 0.7648 (mpp) cc_final: 0.6999 (mpp) REVERT: y 249 VAL cc_start: 0.8260 (OUTLIER) cc_final: 0.7933 (p) REVERT: y 264 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8789 (mm) REVERT: y 268 LEU cc_start: 0.9363 (tm) cc_final: 0.9163 (pp) REVERT: y 272 MET cc_start: 0.4957 (tmt) cc_final: 0.4748 (tmt) REVERT: y 441 GLN cc_start: 0.9124 (OUTLIER) cc_final: 0.8801 (mp10) REVERT: y 493 MET cc_start: 0.7961 (tpp) cc_final: 0.7626 (tpp) REVERT: y 762 MET cc_start: 0.9157 (OUTLIER) cc_final: 0.8948 (tpp) REVERT: y 883 MET cc_start: 0.8810 (mmm) cc_final: 0.8203 (tpp) REVERT: y 1078 GLN cc_start: 0.9200 (mm110) cc_final: 0.8760 (mm110) REVERT: y 1083 GLN cc_start: 0.9508 (tt0) cc_final: 0.9192 (pt0) REVERT: y 1157 MET cc_start: 0.8864 (mmt) cc_final: 0.8619 (mmt) REVERT: y 1381 TYR cc_start: 0.9135 (m-80) cc_final: 0.8834 (m-80) REVERT: y 1388 VAL cc_start: 0.9663 (t) cc_final: 0.9425 (p) REVERT: y 1395 ARG cc_start: 0.8018 (mmm160) cc_final: 0.7314 (tpt90) REVERT: y 1463 ASP cc_start: 0.8081 (t70) cc_final: 0.7609 (t70) REVERT: y 1540 ARG cc_start: 0.7714 (tmm-80) cc_final: 0.7006 (tmm-80) REVERT: y 1749 ASN cc_start: 0.6276 (m110) cc_final: 0.5649 (p0) outliers start: 117 outliers final: 63 residues processed: 247 average time/residue: 0.1814 time to fit residues: 75.6191 Evaluate side-chains 206 residues out of total 3299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 130 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 23 VAL Chi-restraints excluded: chain Y residue 43 PHE Chi-restraints excluded: chain Y residue 74 LEU Chi-restraints excluded: chain Y residue 83 LEU Chi-restraints excluded: chain Y residue 124 CYS Chi-restraints excluded: chain Y residue 130 LEU Chi-restraints excluded: chain Y residue 181 LEU Chi-restraints excluded: chain Y residue 200 VAL Chi-restraints excluded: chain Y residue 217 ILE Chi-restraints excluded: chain Y residue 228 MET Chi-restraints excluded: chain Y residue 239 GLU Chi-restraints excluded: chain Y residue 290 THR Chi-restraints excluded: chain Y residue 320 VAL Chi-restraints excluded: chain Y residue 332 VAL Chi-restraints excluded: chain Y residue 430 THR Chi-restraints excluded: chain Y residue 431 LEU Chi-restraints excluded: chain Y residue 674 LEU Chi-restraints excluded: chain Y residue 678 THR Chi-restraints excluded: chain Y residue 705 LYS Chi-restraints excluded: chain Y residue 736 VAL Chi-restraints excluded: chain Y residue 760 LYS Chi-restraints excluded: chain Y residue 767 LEU Chi-restraints excluded: chain Y residue 843 LEU Chi-restraints excluded: chain Y residue 848 ASP Chi-restraints excluded: chain Y residue 889 VAL Chi-restraints excluded: chain Y residue 902 GLN Chi-restraints excluded: chain Y residue 944 LEU Chi-restraints excluded: chain Y residue 1052 GLU Chi-restraints excluded: chain Y residue 1101 CYS Chi-restraints excluded: chain Y residue 1122 VAL Chi-restraints excluded: chain Y residue 1201 VAL Chi-restraints excluded: chain Y residue 1205 THR Chi-restraints excluded: chain Y residue 1214 GLU Chi-restraints excluded: chain Y residue 1248 MET Chi-restraints excluded: chain Y residue 1294 THR Chi-restraints excluded: chain Y residue 1319 GLU Chi-restraints excluded: chain Y residue 1331 VAL Chi-restraints excluded: chain Y residue 1374 LEU Chi-restraints excluded: chain Y residue 1396 SER Chi-restraints excluded: chain Y residue 1556 LEU Chi-restraints excluded: chain Y residue 1641 ASN Chi-restraints excluded: chain Y residue 1740 LEU Chi-restraints excluded: chain Y residue 1778 LEU Chi-restraints excluded: chain Y residue 1885 THR Chi-restraints excluded: chain Y residue 2102 ILE Chi-restraints excluded: chain y residue 27 LEU Chi-restraints excluded: chain y residue 52 LEU Chi-restraints excluded: chain y residue 112 LEU Chi-restraints excluded: chain y residue 183 ASN Chi-restraints excluded: chain y residue 248 ILE Chi-restraints excluded: chain y residue 249 VAL Chi-restraints excluded: chain y residue 264 LEU Chi-restraints excluded: chain y residue 322 VAL Chi-restraints excluded: chain y residue 323 VAL Chi-restraints excluded: chain y residue 381 VAL Chi-restraints excluded: chain y residue 424 MET Chi-restraints excluded: chain y residue 441 GLN Chi-restraints excluded: chain y residue 476 VAL Chi-restraints excluded: chain y residue 553 THR Chi-restraints excluded: chain y residue 678 THR Chi-restraints excluded: chain y residue 762 MET Chi-restraints excluded: chain y residue 775 VAL Chi-restraints excluded: chain y residue 791 LEU Chi-restraints excluded: chain y residue 1012 VAL Chi-restraints excluded: chain y residue 1120 ASN Chi-restraints excluded: chain y residue 1128 ASN Chi-restraints excluded: chain y residue 1155 HIS Chi-restraints excluded: chain y residue 1176 VAL Chi-restraints excluded: chain y residue 1234 LEU Chi-restraints excluded: chain y residue 1248 MET Chi-restraints excluded: chain y residue 1262 MET Chi-restraints excluded: chain y residue 1277 LEU Chi-restraints excluded: chain y residue 1279 GLU Chi-restraints excluded: chain y residue 1329 VAL Chi-restraints excluded: chain y residue 1487 VAL Chi-restraints excluded: chain y residue 1664 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: [352, 223, 245, 234, 163, 336, 165, 312, 61, 140, 81] chunk 352 optimal weight: 0.2980 chunk 223 optimal weight: 20.0000 chunk 245 optimal weight: 6.9990 chunk 234 optimal weight: 5.9990 chunk 163 optimal weight: 1.9990 chunk 336 optimal weight: 8.9990 chunk 165 optimal weight: 0.6980 chunk 312 optimal weight: 30.0000 chunk 61 optimal weight: 5.9990 chunk 140 optimal weight: 6.9990 chunk 81 optimal weight: 7.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Y 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 770 GLN ** Y1513 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1805 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 582 ASN ** y1264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.085868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.060120 restraints weight = 169364.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.061646 restraints weight = 77368.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.062547 restraints weight = 49581.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.062547 restraints weight = 37829.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.062547 restraints weight = 37829.243| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 32707 Z= 0.179 Angle : 0.715 34.268 44556 Z= 0.315 Chirality : 0.041 0.219 4864 Planarity : 0.004 0.053 5605 Dihedral : 13.695 161.374 4935 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.86 % Favored : 95.11 % Rotamer: Outliers : 3.76 % Allowed : 18.55 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.14), residues: 3845 helix: 0.92 (0.14), residues: 1512 sheet: -0.67 (0.22), residues: 586 loop : -1.28 (0.15), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG y1424 TYR 0.011 0.001 TYR y1307 PHE 0.015 0.001 PHE Y 125 TRP 0.016 0.001 TRP y 101 HIS 0.006 0.001 HIS y1698 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.18 (32668) covalent geometry : angle 0.60906 / 0.31 (44508) hydrogen bonds : bond 0.03881 / 2.84 ( 1292) hydrogen bonds : angle 4.85242 / 3.63 ( 3708) metal coordination : bond 0.01281 / 1.30 ( 39) metal coordination : angle 11.42691 / 9.32 ( 48) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 3299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 140 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 43 PHE cc_start: 0.9022 (OUTLIER) cc_final: 0.7972 (m-80) REVERT: Y 124 CYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8669 (p) REVERT: Y 218 MET cc_start: 0.8582 (ttm) cc_final: 0.8288 (ttp) REVERT: Y 593 GLN cc_start: 0.9330 (OUTLIER) cc_final: 0.8952 (tm-30) REVERT: Y 705 LYS cc_start: 0.4991 (OUTLIER) cc_final: 0.4754 (tppt) REVERT: Y 742 GLU cc_start: 0.6878 (OUTLIER) cc_final: 0.6390 (mm-30) REVERT: Y 891 MET cc_start: 0.7970 (tpt) cc_final: 0.7442 (tpt) REVERT: Y 999 TYR cc_start: 0.9174 (m-10) cc_final: 0.8912 (m-10) REVERT: Y 1052 GLU cc_start: 0.9183 (OUTLIER) cc_final: 0.8881 (pt0) REVERT: Y 1105 MET cc_start: 0.7749 (tpp) cc_final: 0.7466 (tpp) REVERT: Y 1114 MET cc_start: 0.8497 (pmm) cc_final: 0.7450 (pmm) REVERT: Y 1248 MET cc_start: 0.9004 (OUTLIER) cc_final: 0.8474 (tmm) REVERT: Y 1319 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8301 (mp0) REVERT: Y 1474 MET cc_start: 0.9022 (tmm) cc_final: 0.8645 (tmm) REVERT: Y 1778 LEU cc_start: 0.9751 (OUTLIER) cc_final: 0.9436 (mm) REVERT: y 224 MET cc_start: 0.7706 (mpp) cc_final: 0.7126 (mpp) REVERT: y 228 MET cc_start: 0.9140 (ppp) cc_final: 0.8930 (ppp) REVERT: y 493 MET cc_start: 0.8073 (tpp) cc_final: 0.7836 (tpp) REVERT: y 762 MET cc_start: 0.9126 (OUTLIER) cc_final: 0.8925 (tpp) REVERT: y 883 MET cc_start: 0.8805 (mmm) cc_final: 0.8194 (tpp) REVERT: y 1074 GLU cc_start: 0.8911 (pm20) cc_final: 0.8357 (pm20) REVERT: y 1078 GLN cc_start: 0.9208 (mm110) cc_final: 0.8763 (mm110) REVERT: y 1083 GLN cc_start: 0.9500 (tt0) cc_final: 0.9179 (pt0) REVERT: y 1381 TYR cc_start: 0.9124 (m-80) cc_final: 0.8823 (m-80) REVERT: y 1388 VAL cc_start: 0.9673 (t) cc_final: 0.9434 (p) REVERT: y 1395 ARG cc_start: 0.8005 (mmm160) cc_final: 0.7315 (tpt90) REVERT: y 1463 ASP cc_start: 0.8035 (t70) cc_final: 0.7566 (t70) REVERT: y 1540 ARG cc_start: 0.7704 (tmm-80) cc_final: 0.6962 (tmm-80) REVERT: y 1546 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.8144 (pptt) REVERT: y 1749 ASN cc_start: 0.6285 (m110) cc_final: 0.5705 (p0) outliers start: 124 outliers final: 74 residues processed: 249 average time/residue: 0.1825 time to fit residues: 77.1286 Evaluate side-chains 217 residues out of total 3299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 132 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 23 VAL Chi-restraints excluded: chain Y residue 43 PHE Chi-restraints excluded: chain Y residue 83 LEU Chi-restraints excluded: chain Y residue 104 ILE Chi-restraints excluded: chain Y residue 114 SER Chi-restraints excluded: chain Y residue 124 CYS Chi-restraints excluded: chain Y residue 130 LEU Chi-restraints excluded: chain Y residue 181 LEU Chi-restraints excluded: chain Y residue 200 VAL Chi-restraints excluded: chain Y residue 217 ILE Chi-restraints excluded: chain Y residue 228 MET Chi-restraints excluded: chain Y residue 239 GLU Chi-restraints excluded: chain Y residue 290 THR Chi-restraints excluded: chain Y residue 320 VAL Chi-restraints excluded: chain Y residue 332 VAL Chi-restraints excluded: chain Y residue 397 ILE Chi-restraints excluded: chain Y residue 431 LEU Chi-restraints excluded: chain Y residue 593 GLN Chi-restraints excluded: chain Y residue 674 LEU Chi-restraints excluded: chain Y residue 678 THR Chi-restraints excluded: chain Y residue 705 LYS Chi-restraints excluded: chain Y residue 736 VAL Chi-restraints excluded: chain Y residue 742 GLU Chi-restraints excluded: chain Y residue 767 LEU Chi-restraints excluded: chain Y residue 843 LEU Chi-restraints excluded: chain Y residue 848 ASP Chi-restraints excluded: chain Y residue 889 VAL Chi-restraints excluded: chain Y residue 902 GLN Chi-restraints excluded: chain Y residue 944 LEU Chi-restraints excluded: chain Y residue 1005 GLU Chi-restraints excluded: chain Y residue 1052 GLU Chi-restraints excluded: chain Y residue 1072 LEU Chi-restraints excluded: chain Y residue 1101 CYS Chi-restraints excluded: chain Y residue 1122 VAL Chi-restraints excluded: chain Y residue 1201 VAL Chi-restraints excluded: chain Y residue 1205 THR Chi-restraints excluded: chain Y residue 1214 GLU Chi-restraints excluded: chain Y residue 1248 MET Chi-restraints excluded: chain Y residue 1262 MET Chi-restraints excluded: chain Y residue 1294 THR Chi-restraints excluded: chain Y residue 1319 GLU Chi-restraints excluded: chain Y residue 1331 VAL Chi-restraints excluded: chain Y residue 1374 LEU Chi-restraints excluded: chain Y residue 1388 VAL Chi-restraints excluded: chain Y residue 1396 SER Chi-restraints excluded: chain Y residue 1556 LEU Chi-restraints excluded: chain Y residue 1632 VAL Chi-restraints excluded: chain Y residue 1641 ASN Chi-restraints excluded: chain Y residue 1678 LEU Chi-restraints excluded: chain Y residue 1740 LEU Chi-restraints excluded: chain Y residue 1778 LEU Chi-restraints excluded: chain Y residue 1885 THR Chi-restraints excluded: chain Y residue 2102 ILE Chi-restraints excluded: chain y residue 27 LEU Chi-restraints excluded: chain y residue 52 LEU Chi-restraints excluded: chain y residue 181 LEU Chi-restraints excluded: chain y residue 248 ILE Chi-restraints excluded: chain y residue 322 VAL Chi-restraints excluded: chain y residue 381 VAL Chi-restraints excluded: chain y residue 424 MET Chi-restraints excluded: chain y residue 442 CYS Chi-restraints excluded: chain y residue 476 VAL Chi-restraints excluded: chain y residue 553 THR Chi-restraints excluded: chain y residue 611 LEU Chi-restraints excluded: chain y residue 678 THR Chi-restraints excluded: chain y residue 762 MET Chi-restraints excluded: chain y residue 775 VAL Chi-restraints excluded: chain y residue 1120 ASN Chi-restraints excluded: chain y residue 1128 ASN Chi-restraints excluded: chain y residue 1176 VAL Chi-restraints excluded: chain y residue 1234 LEU Chi-restraints excluded: chain y residue 1248 MET Chi-restraints excluded: chain y residue 1262 MET Chi-restraints excluded: chain y residue 1274 LEU Chi-restraints excluded: chain y residue 1304 LEU Chi-restraints excluded: chain y residue 1319 GLU Chi-restraints excluded: chain y residue 1329 VAL Chi-restraints excluded: chain y residue 1373 ASP Chi-restraints excluded: chain y residue 1379 ARG Chi-restraints excluded: chain y residue 1433 THR Chi-restraints excluded: chain y residue 1487 VAL Chi-restraints excluded: chain y residue 1546 LYS Chi-restraints excluded: chain y residue 1632 VAL Chi-restraints excluded: chain y residue 1664 LEU Chi-restraints excluded: chain y residue 1794 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: [91, 321, 297, 357, 275, 274, 322, 215, 264, 384, 168] chunk 91 optimal weight: 1.9990 chunk 321 optimal weight: 0.4980 chunk 297 optimal weight: 0.9980 chunk 357 optimal weight: 0.9990 chunk 275 optimal weight: 0.2980 chunk 274 optimal weight: 10.0000 chunk 322 optimal weight: 10.0000 chunk 215 optimal weight: 6.9990 chunk 264 optimal weight: 7.9990 chunk 384 optimal weight: 0.7980 chunk 168 optimal weight: 7.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Y 4 GLN ** Y 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 450 ASN ** Y 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1513 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1805 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y1100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y1120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.087118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.061748 restraints weight = 172466.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.063353 restraints weight = 77470.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.064452 restraints weight = 48193.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.065206 restraints weight = 36150.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.065643 restraints weight = 30395.463| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 32707 Z= 0.110 Angle : 0.689 35.410 44556 Z= 0.302 Chirality : 0.041 0.236 4864 Planarity : 0.004 0.055 5605 Dihedral : 13.477 162.934 4933 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.40 % Favored : 95.58 % Rotamer: Outliers : 3.52 % Allowed : 19.19 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.14), residues: 3845 helix: 0.96 (0.14), residues: 1510 sheet: -0.59 (0.22), residues: 578 loop : -1.28 (0.14), residues: 1757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG y 400 TYR 0.010 0.001 TYR Y1523 PHE 0.015 0.001 PHE Y 125 TRP 0.018 0.001 TRP y 101 HIS 0.005 0.001 HIS y 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 (32668) covalent geometry : angle 0.58846 / 0.29 (44508) hydrogen bonds : bond 0.03649 / 2.66 ( 1292) hydrogen bonds : angle 4.67677 / 3.50 ( 3708) metal coordination : bond 0.00949 / 0.79 ( 39) metal coordination : angle 10.95192 / 7.86 ( 48) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 3299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 163 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 43 PHE cc_start: 0.8998 (OUTLIER) cc_final: 0.8021 (m-80) REVERT: Y 124 CYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8518 (p) REVERT: Y 239 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.8332 (mp0) REVERT: Y 272 MET cc_start: 0.8752 (mtm) cc_final: 0.8409 (mtm) REVERT: Y 742 GLU cc_start: 0.6682 (OUTLIER) cc_final: 0.6239 (mm-30) REVERT: Y 999 TYR cc_start: 0.9122 (m-10) cc_final: 0.8808 (m-10) REVERT: Y 1052 GLU cc_start: 0.9190 (OUTLIER) cc_final: 0.8862 (pt0) REVERT: Y 1105 MET cc_start: 0.7702 (tpp) cc_final: 0.7464 (tpp) REVERT: Y 1114 MET cc_start: 0.8361 (pmm) cc_final: 0.7436 (pmm) REVERT: Y 1248 MET cc_start: 0.8929 (OUTLIER) cc_final: 0.8410 (tmm) REVERT: Y 1366 ILE cc_start: 0.6432 (OUTLIER) cc_final: 0.6167 (tt) REVERT: Y 1474 MET cc_start: 0.9033 (tmm) cc_final: 0.8668 (tmm) REVERT: Y 1478 LEU cc_start: 0.9411 (OUTLIER) cc_final: 0.9041 (mt) REVERT: Y 1589 MET cc_start: 0.9136 (pp-130) cc_final: 0.8123 (pp-130) REVERT: Y 1778 LEU cc_start: 0.9716 (OUTLIER) cc_final: 0.9418 (pp) REVERT: Y 1998 TRP cc_start: 0.7515 (OUTLIER) cc_final: 0.7185 (m-90) REVERT: y 183 ASN cc_start: 0.8969 (OUTLIER) cc_final: 0.7840 (m-40) REVERT: y 224 MET cc_start: 0.7594 (mpp) cc_final: 0.6899 (mpp) REVERT: y 228 MET cc_start: 0.9175 (ppp) cc_final: 0.8959 (ppp) REVERT: y 493 MET cc_start: 0.8003 (tpp) cc_final: 0.7788 (tpp) REVERT: y 648 GLN cc_start: 0.8850 (pm20) cc_final: 0.8611 (pm20) REVERT: y 659 GLN cc_start: 0.9508 (OUTLIER) cc_final: 0.9242 (mm110) REVERT: y 818 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.7867 (tm-30) REVERT: y 868 GLU cc_start: 0.9269 (OUTLIER) cc_final: 0.8906 (pt0) REVERT: y 883 MET cc_start: 0.8793 (mmm) cc_final: 0.8286 (tpp) REVERT: y 893 GLN cc_start: 0.6473 (mp10) cc_final: 0.6243 (mp10) REVERT: y 1078 GLN cc_start: 0.9197 (mm110) cc_final: 0.8784 (mm110) REVERT: y 1079 ARG cc_start: 0.8085 (mtt180) cc_final: 0.7592 (mtm180) REVERT: y 1083 GLN cc_start: 0.9525 (tt0) cc_final: 0.9151 (pt0) REVERT: y 1260 GLN cc_start: 0.8440 (tm-30) cc_final: 0.8100 (tm-30) REVERT: y 1371 SER cc_start: 0.9581 (p) cc_final: 0.9292 (m) REVERT: y 1381 TYR cc_start: 0.9185 (m-80) cc_final: 0.8941 (m-80) REVERT: y 1388 VAL cc_start: 0.9648 (t) cc_final: 0.9399 (p) REVERT: y 1395 ARG cc_start: 0.7976 (mmm160) cc_final: 0.7239 (tpt90) REVERT: y 1463 ASP cc_start: 0.8117 (t70) cc_final: 0.7477 (t70) REVERT: y 1523 TYR cc_start: 0.7572 (m-80) cc_final: 0.7286 (m-80) REVERT: y 1540 ARG cc_start: 0.7854 (tmm-80) cc_final: 0.7234 (tmm-80) REVERT: y 1749 ASN cc_start: 0.6269 (m110) cc_final: 0.5704 (p0) outliers start: 116 outliers final: 68 residues processed: 266 average time/residue: 0.1845 time to fit residues: 83.2714 Evaluate side-chains 224 residues out of total 3299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 142 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 43 PHE Chi-restraints excluded: chain Y residue 83 LEU Chi-restraints excluded: chain Y residue 104 ILE Chi-restraints excluded: chain Y residue 114 SER Chi-restraints excluded: chain Y residue 124 CYS Chi-restraints excluded: chain Y residue 130 LEU Chi-restraints excluded: chain Y residue 181 LEU Chi-restraints excluded: chain Y residue 193 ILE Chi-restraints excluded: chain Y residue 200 VAL Chi-restraints excluded: chain Y residue 217 ILE Chi-restraints excluded: chain Y residue 228 MET Chi-restraints excluded: chain Y residue 239 GLU Chi-restraints excluded: chain Y residue 252 GLU Chi-restraints excluded: chain Y residue 290 THR Chi-restraints excluded: chain Y residue 320 VAL Chi-restraints excluded: chain Y residue 430 THR Chi-restraints excluded: chain Y residue 431 LEU Chi-restraints excluded: chain Y residue 674 LEU Chi-restraints excluded: chain Y residue 742 GLU Chi-restraints excluded: chain Y residue 843 LEU Chi-restraints excluded: chain Y residue 889 VAL Chi-restraints excluded: chain Y residue 902 GLN Chi-restraints excluded: chain Y residue 944 LEU Chi-restraints excluded: chain Y residue 1005 GLU Chi-restraints excluded: chain Y residue 1052 GLU Chi-restraints excluded: chain Y residue 1072 LEU Chi-restraints excluded: chain Y residue 1101 CYS Chi-restraints excluded: chain Y residue 1122 VAL Chi-restraints excluded: chain Y residue 1201 VAL Chi-restraints excluded: chain Y residue 1205 THR Chi-restraints excluded: chain Y residue 1214 GLU Chi-restraints excluded: chain Y residue 1248 MET Chi-restraints excluded: chain Y residue 1262 MET Chi-restraints excluded: chain Y residue 1294 THR Chi-restraints excluded: chain Y residue 1319 GLU Chi-restraints excluded: chain Y residue 1331 VAL Chi-restraints excluded: chain Y residue 1366 ILE Chi-restraints excluded: chain Y residue 1374 LEU Chi-restraints excluded: chain Y residue 1388 VAL Chi-restraints excluded: chain Y residue 1478 LEU Chi-restraints excluded: chain Y residue 1556 LEU Chi-restraints excluded: chain Y residue 1678 LEU Chi-restraints excluded: chain Y residue 1740 LEU Chi-restraints excluded: chain Y residue 1778 LEU Chi-restraints excluded: chain Y residue 1998 TRP Chi-restraints excluded: chain Y residue 2102 ILE Chi-restraints excluded: chain y residue 27 LEU Chi-restraints excluded: chain y residue 52 LEU Chi-restraints excluded: chain y residue 181 LEU Chi-restraints excluded: chain y residue 183 ASN Chi-restraints excluded: chain y residue 248 ILE Chi-restraints excluded: chain y residue 322 VAL Chi-restraints excluded: chain y residue 323 VAL Chi-restraints excluded: chain y residue 381 VAL Chi-restraints excluded: chain y residue 424 MET Chi-restraints excluded: chain y residue 442 CYS Chi-restraints excluded: chain y residue 476 VAL Chi-restraints excluded: chain y residue 553 THR Chi-restraints excluded: chain y residue 659 GLN Chi-restraints excluded: chain y residue 678 THR Chi-restraints excluded: chain y residue 701 VAL Chi-restraints excluded: chain y residue 763 SER Chi-restraints excluded: chain y residue 818 GLU Chi-restraints excluded: chain y residue 868 GLU Chi-restraints excluded: chain y residue 1012 VAL Chi-restraints excluded: chain y residue 1120 ASN Chi-restraints excluded: chain y residue 1155 HIS Chi-restraints excluded: chain y residue 1176 VAL Chi-restraints excluded: chain y residue 1248 MET Chi-restraints excluded: chain y residue 1262 MET Chi-restraints excluded: chain y residue 1277 LEU Chi-restraints excluded: chain y residue 1304 LEU Chi-restraints excluded: chain y residue 1329 VAL Chi-restraints excluded: chain y residue 1373 ASP Chi-restraints excluded: chain y residue 1379 ARG Chi-restraints excluded: chain y residue 1386 ASP Chi-restraints excluded: chain y residue 1415 HIS Chi-restraints excluded: chain y residue 1433 THR Chi-restraints excluded: chain y residue 1487 VAL Chi-restraints excluded: chain y residue 1546 LYS Chi-restraints excluded: chain y residue 1632 VAL Chi-restraints excluded: chain y residue 1664 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: [345, 66, 259, 11, 230, 27, 270, 311, 133, 193, 277] chunk 345 optimal weight: 0.9990 chunk 66 optimal weight: 30.0000 chunk 259 optimal weight: 20.0000 chunk 11 optimal weight: 0.7980 chunk 230 optimal weight: 10.0000 chunk 27 optimal weight: 0.6980 chunk 270 optimal weight: 0.7980 chunk 311 optimal weight: 9.9990 chunk 133 optimal weight: 0.0970 chunk 193 optimal weight: 5.9990 chunk 277 optimal weight: 20.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Y 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1513 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1805 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y1100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y1120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.087239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.061623 restraints weight = 167705.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.063306 restraints weight = 76136.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.064515 restraints weight = 47452.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.065220 restraints weight = 35375.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.065669 restraints weight = 29838.680| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 32707 Z= 0.108 Angle : 0.695 35.414 44556 Z= 0.302 Chirality : 0.041 0.328 4864 Planarity : 0.004 0.053 5605 Dihedral : 13.344 166.267 4928 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.50 % Favored : 95.47 % Rotamer: Outliers : 3.18 % Allowed : 19.79 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.14), residues: 3845 helix: 1.00 (0.14), residues: 1498 sheet: -0.56 (0.22), residues: 577 loop : -1.25 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG y 400 TYR 0.014 0.001 TYR y1694 PHE 0.014 0.001 PHE Y 125 TRP 0.016 0.001 TRP y 101 HIS 0.004 0.001 HIS y 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 (32668) covalent geometry : angle 0.59731 / 0.30 (44508) hydrogen bonds : bond 0.03546 / 2.59 ( 1292) hydrogen bonds : angle 4.61951 / 3.45 ( 3708) metal coordination : bond 0.00734 / 0.67 ( 39) metal coordination : angle 10.82259 / 7.58 ( 48) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 3299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 154 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 43 PHE cc_start: 0.9028 (OUTLIER) cc_final: 0.7939 (m-80) REVERT: Y 124 CYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8577 (p) REVERT: Y 239 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8364 (mp0) REVERT: Y 705 LYS cc_start: 0.5194 (OUTLIER) cc_final: 0.4938 (tppt) REVERT: Y 742 GLU cc_start: 0.6679 (OUTLIER) cc_final: 0.6276 (mm-30) REVERT: Y 891 MET cc_start: 0.7924 (tpt) cc_final: 0.7611 (tpt) REVERT: Y 999 TYR cc_start: 0.9125 (m-10) cc_final: 0.8838 (m-10) REVERT: Y 1052 GLU cc_start: 0.9182 (OUTLIER) cc_final: 0.8847 (pt0) REVERT: Y 1105 MET cc_start: 0.7715 (tpp) cc_final: 0.7458 (tpp) REVERT: Y 1114 MET cc_start: 0.8392 (pmm) cc_final: 0.7510 (pmm) REVERT: Y 1248 MET cc_start: 0.8936 (OUTLIER) cc_final: 0.8431 (tmm) REVERT: Y 1366 ILE cc_start: 0.6412 (OUTLIER) cc_final: 0.6149 (tt) REVERT: Y 1474 MET cc_start: 0.9012 (tmm) cc_final: 0.8664 (tmm) REVERT: Y 1589 MET cc_start: 0.9141 (pp-130) cc_final: 0.8160 (pp-130) REVERT: Y 1778 LEU cc_start: 0.9710 (OUTLIER) cc_final: 0.9424 (pp) REVERT: Y 1998 TRP cc_start: 0.7514 (OUTLIER) cc_final: 0.7157 (m-90) REVERT: y 183 ASN cc_start: 0.9030 (OUTLIER) cc_final: 0.7880 (m-40) REVERT: y 224 MET cc_start: 0.7612 (mpp) cc_final: 0.7010 (mpp) REVERT: y 228 MET cc_start: 0.9257 (ppp) cc_final: 0.8992 (ppp) REVERT: y 361 CYS cc_start: 0.9188 (OUTLIER) cc_final: 0.8786 (p) REVERT: y 648 GLN cc_start: 0.8844 (pm20) cc_final: 0.8606 (pm20) REVERT: y 762 MET cc_start: 0.9033 (OUTLIER) cc_final: 0.8823 (tpp) REVERT: y 822 LEU cc_start: 0.9564 (mp) cc_final: 0.9338 (mm) REVERT: y 883 MET cc_start: 0.8758 (mmm) cc_final: 0.8282 (tpp) REVERT: y 952 ILE cc_start: 0.9425 (tp) cc_final: 0.9170 (tp) REVERT: y 1012 VAL cc_start: 0.9620 (OUTLIER) cc_final: 0.9285 (p) REVERT: y 1078 GLN cc_start: 0.9171 (mm110) cc_final: 0.8789 (mm110) REVERT: y 1083 GLN cc_start: 0.9523 (tt0) cc_final: 0.9197 (pt0) REVERT: y 1157 MET cc_start: 0.8707 (mmt) cc_final: 0.8386 (mmt) REVERT: y 1260 GLN cc_start: 0.8411 (tm-30) cc_final: 0.8147 (tp-100) REVERT: y 1263 MET cc_start: 0.7679 (ppp) cc_final: 0.7333 (ppp) REVERT: y 1269 ARG cc_start: 0.8251 (ptt90) cc_final: 0.7844 (ptt-90) REVERT: y 1336 TYR cc_start: 0.8457 (p90) cc_final: 0.8223 (p90) REVERT: y 1371 SER cc_start: 0.9559 (p) cc_final: 0.9246 (m) REVERT: y 1381 TYR cc_start: 0.9175 (m-80) cc_final: 0.8923 (m-80) REVERT: y 1388 VAL cc_start: 0.9643 (t) cc_final: 0.9391 (p) REVERT: y 1395 ARG cc_start: 0.7965 (mmm160) cc_final: 0.7227 (tpt90) REVERT: y 1463 ASP cc_start: 0.7935 (t70) cc_final: 0.7508 (t0) REVERT: y 1523 TYR cc_start: 0.7657 (m-80) cc_final: 0.7349 (m-80) REVERT: y 1540 ARG cc_start: 0.7838 (tmm-80) cc_final: 0.7248 (tmm-80) REVERT: y 1749 ASN cc_start: 0.6218 (m110) cc_final: 0.5684 (p0) outliers start: 105 outliers final: 72 residues processed: 245 average time/residue: 0.1822 time to fit residues: 75.2837 Evaluate side-chains 229 residues out of total 3299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 143 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 43 PHE Chi-restraints excluded: chain Y residue 83 LEU Chi-restraints excluded: chain Y residue 104 ILE Chi-restraints excluded: chain Y residue 114 SER Chi-restraints excluded: chain Y residue 124 CYS Chi-restraints excluded: chain Y residue 130 LEU Chi-restraints excluded: chain Y residue 181 LEU Chi-restraints excluded: chain Y residue 193 ILE Chi-restraints excluded: chain Y residue 200 VAL Chi-restraints excluded: chain Y residue 217 ILE Chi-restraints excluded: chain Y residue 228 MET Chi-restraints excluded: chain Y residue 239 GLU Chi-restraints excluded: chain Y residue 252 GLU Chi-restraints excluded: chain Y residue 320 VAL Chi-restraints excluded: chain Y residue 397 ILE Chi-restraints excluded: chain Y residue 430 THR Chi-restraints excluded: chain Y residue 431 LEU Chi-restraints excluded: chain Y residue 618 LEU Chi-restraints excluded: chain Y residue 674 LEU Chi-restraints excluded: chain Y residue 705 LYS Chi-restraints excluded: chain Y residue 742 GLU Chi-restraints excluded: chain Y residue 843 LEU Chi-restraints excluded: chain Y residue 889 VAL Chi-restraints excluded: chain Y residue 902 GLN Chi-restraints excluded: chain Y residue 907 LEU Chi-restraints excluded: chain Y residue 944 LEU Chi-restraints excluded: chain Y residue 1005 GLU Chi-restraints excluded: chain Y residue 1052 GLU Chi-restraints excluded: chain Y residue 1072 LEU Chi-restraints excluded: chain Y residue 1101 CYS Chi-restraints excluded: chain Y residue 1122 VAL Chi-restraints excluded: chain Y residue 1201 VAL Chi-restraints excluded: chain Y residue 1205 THR Chi-restraints excluded: chain Y residue 1214 GLU Chi-restraints excluded: chain Y residue 1248 MET Chi-restraints excluded: chain Y residue 1262 MET Chi-restraints excluded: chain Y residue 1294 THR Chi-restraints excluded: chain Y residue 1319 GLU Chi-restraints excluded: chain Y residue 1331 VAL Chi-restraints excluded: chain Y residue 1336 TYR Chi-restraints excluded: chain Y residue 1366 ILE Chi-restraints excluded: chain Y residue 1374 LEU Chi-restraints excluded: chain Y residue 1388 VAL Chi-restraints excluded: chain Y residue 1556 LEU Chi-restraints excluded: chain Y residue 1678 LEU Chi-restraints excluded: chain Y residue 1740 LEU Chi-restraints excluded: chain Y residue 1757 SER Chi-restraints excluded: chain Y residue 1778 LEU Chi-restraints excluded: chain Y residue 1931 LYS Chi-restraints excluded: chain Y residue 1998 TRP Chi-restraints excluded: chain Y residue 2102 ILE Chi-restraints excluded: chain y residue 27 LEU Chi-restraints excluded: chain y residue 52 LEU Chi-restraints excluded: chain y residue 181 LEU Chi-restraints excluded: chain y residue 183 ASN Chi-restraints excluded: chain y residue 248 ILE Chi-restraints excluded: chain y residue 322 VAL Chi-restraints excluded: chain y residue 323 VAL Chi-restraints excluded: chain y residue 361 CYS Chi-restraints excluded: chain y residue 381 VAL Chi-restraints excluded: chain y residue 424 MET Chi-restraints excluded: chain y residue 442 CYS Chi-restraints excluded: chain y residue 476 VAL Chi-restraints excluded: chain y residue 553 THR Chi-restraints excluded: chain y residue 620 GLU Chi-restraints excluded: chain y residue 678 THR Chi-restraints excluded: chain y residue 762 MET Chi-restraints excluded: chain y residue 763 SER Chi-restraints excluded: chain y residue 791 LEU Chi-restraints excluded: chain y residue 1012 VAL Chi-restraints excluded: chain y residue 1120 ASN Chi-restraints excluded: chain y residue 1234 LEU Chi-restraints excluded: chain y residue 1248 MET Chi-restraints excluded: chain y residue 1262 MET Chi-restraints excluded: chain y residue 1277 LEU Chi-restraints excluded: chain y residue 1329 VAL Chi-restraints excluded: chain y residue 1373 ASP Chi-restraints excluded: chain y residue 1379 ARG Chi-restraints excluded: chain y residue 1386 ASP Chi-restraints excluded: chain y residue 1415 HIS Chi-restraints excluded: chain y residue 1433 THR Chi-restraints excluded: chain y residue 1487 VAL Chi-restraints excluded: chain y residue 1546 LYS Chi-restraints excluded: chain y residue 1632 VAL Chi-restraints excluded: chain y residue 1664 LEU Chi-restraints excluded: chain y residue 1794 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: [138, 198, 350, 271, 382, 142, 254, 69, 215, 2, 315] chunk 138 optimal weight: 2.9990 chunk 198 optimal weight: 40.0000 chunk 350 optimal weight: 20.0000 chunk 271 optimal weight: 0.8980 chunk 382 optimal weight: 40.0000 chunk 142 optimal weight: 6.9990 chunk 254 optimal weight: 0.4980 chunk 69 optimal weight: 9.9990 chunk 215 optimal weight: 10.0000 chunk 2 optimal weight: 2.9990 chunk 315 optimal weight: 7.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Y 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1513 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1805 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 582 ASN ** y1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y1100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y1265 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.086222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.060455 restraints weight = 170149.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.062146 restraints weight = 77875.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.063314 restraints weight = 48600.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.064009 restraints weight = 36411.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.064443 restraints weight = 30802.123| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 32707 Z= 0.174 Angle : 0.713 34.500 44556 Z= 0.313 Chirality : 0.041 0.248 4864 Planarity : 0.004 0.056 5605 Dihedral : 13.285 170.013 4927 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.76 % Favored : 95.19 % Rotamer: Outliers : 3.21 % Allowed : 20.28 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.14), residues: 3845 helix: 1.09 (0.14), residues: 1507 sheet: -0.60 (0.22), residues: 578 loop : -1.21 (0.15), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG y 400 TYR 0.011 0.001 TYR y1643 PHE 0.014 0.001 PHE Y 173 TRP 0.014 0.001 TRP y 101 HIS 0.006 0.001 HIS y1698 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 (32668) covalent geometry : angle 0.61664 / 0.31 (44508) hydrogen bonds : bond 0.03584 / 2.63 ( 1292) hydrogen bonds : angle 4.63667 / 3.47 ( 3708) metal coordination : bond 0.01160 / 1.09 ( 39) metal coordination : angle 10.90992 / 8.00 ( 48) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 3299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 146 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 43 PHE cc_start: 0.9055 (OUTLIER) cc_final: 0.8024 (m-80) REVERT: Y 124 CYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8689 (p) REVERT: Y 239 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8383 (mp0) REVERT: Y 705 LYS cc_start: 0.5189 (OUTLIER) cc_final: 0.4944 (tppt) REVERT: Y 742 GLU cc_start: 0.6741 (OUTLIER) cc_final: 0.6318 (mm-30) REVERT: Y 1052 GLU cc_start: 0.9174 (OUTLIER) cc_final: 0.8868 (pt0) REVERT: Y 1105 MET cc_start: 0.7711 (tpp) cc_final: 0.7484 (tpp) REVERT: Y 1114 MET cc_start: 0.8490 (pmm) cc_final: 0.7507 (pmm) REVERT: Y 1248 MET cc_start: 0.9013 (OUTLIER) cc_final: 0.8464 (tmm) REVERT: Y 1366 ILE cc_start: 0.6335 (OUTLIER) cc_final: 0.6110 (tt) REVERT: Y 1474 MET cc_start: 0.9007 (tmm) cc_final: 0.8674 (tmm) REVERT: Y 1589 MET cc_start: 0.9155 (pp-130) cc_final: 0.8096 (pp-130) REVERT: Y 1740 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8902 (tm) REVERT: Y 1778 LEU cc_start: 0.9731 (OUTLIER) cc_final: 0.9432 (mm) REVERT: Y 1998 TRP cc_start: 0.7495 (OUTLIER) cc_final: 0.7134 (m-90) REVERT: y 224 MET cc_start: 0.7635 (mpp) cc_final: 0.7193 (mpp) REVERT: y 361 CYS cc_start: 0.9172 (OUTLIER) cc_final: 0.8880 (p) REVERT: y 648 GLN cc_start: 0.8879 (pm20) cc_final: 0.8650 (pm20) REVERT: y 818 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.7869 (pp20) REVERT: y 883 MET cc_start: 0.8776 (mmm) cc_final: 0.8224 (tpp) REVERT: y 952 ILE cc_start: 0.9462 (tp) cc_final: 0.9190 (tp) REVERT: y 1012 VAL cc_start: 0.9630 (OUTLIER) cc_final: 0.9296 (p) REVERT: y 1083 GLN cc_start: 0.9538 (tt0) cc_final: 0.9205 (pt0) REVERT: y 1105 MET cc_start: 0.8726 (tpt) cc_final: 0.8427 (tpt) REVERT: y 1157 MET cc_start: 0.8742 (mmt) cc_final: 0.8488 (mmt) REVERT: y 1371 SER cc_start: 0.9559 (p) cc_final: 0.9241 (m) REVERT: y 1381 TYR cc_start: 0.9168 (m-80) cc_final: 0.8882 (m-80) REVERT: y 1388 VAL cc_start: 0.9660 (t) cc_final: 0.9403 (p) REVERT: y 1395 ARG cc_start: 0.7974 (mmm160) cc_final: 0.7277 (tpt90) REVERT: y 1463 ASP cc_start: 0.8028 (t70) cc_final: 0.7544 (t70) REVERT: y 1540 ARG cc_start: 0.7903 (tmm-80) cc_final: 0.7316 (tmm-80) REVERT: y 1749 ASN cc_start: 0.6109 (m110) cc_final: 0.5643 (p0) outliers start: 106 outliers final: 78 residues processed: 242 average time/residue: 0.1875 time to fit residues: 76.1052 Evaluate side-chains 228 residues out of total 3299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 136 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 43 PHE Chi-restraints excluded: chain Y residue 83 LEU Chi-restraints excluded: chain Y residue 104 ILE Chi-restraints excluded: chain Y residue 114 SER Chi-restraints excluded: chain Y residue 124 CYS Chi-restraints excluded: chain Y residue 130 LEU Chi-restraints excluded: chain Y residue 181 LEU Chi-restraints excluded: chain Y residue 193 ILE Chi-restraints excluded: chain Y residue 200 VAL Chi-restraints excluded: chain Y residue 217 ILE Chi-restraints excluded: chain Y residue 228 MET Chi-restraints excluded: chain Y residue 239 GLU Chi-restraints excluded: chain Y residue 252 GLU Chi-restraints excluded: chain Y residue 320 VAL Chi-restraints excluded: chain Y residue 332 VAL Chi-restraints excluded: chain Y residue 397 ILE Chi-restraints excluded: chain Y residue 430 THR Chi-restraints excluded: chain Y residue 431 LEU Chi-restraints excluded: chain Y residue 674 LEU Chi-restraints excluded: chain Y residue 705 LYS Chi-restraints excluded: chain Y residue 736 VAL Chi-restraints excluded: chain Y residue 742 GLU Chi-restraints excluded: chain Y residue 760 LYS Chi-restraints excluded: chain Y residue 767 LEU Chi-restraints excluded: chain Y residue 843 LEU Chi-restraints excluded: chain Y residue 889 VAL Chi-restraints excluded: chain Y residue 902 GLN Chi-restraints excluded: chain Y residue 907 LEU Chi-restraints excluded: chain Y residue 944 LEU Chi-restraints excluded: chain Y residue 1005 GLU Chi-restraints excluded: chain Y residue 1052 GLU Chi-restraints excluded: chain Y residue 1072 LEU Chi-restraints excluded: chain Y residue 1101 CYS Chi-restraints excluded: chain Y residue 1122 VAL Chi-restraints excluded: chain Y residue 1205 THR Chi-restraints excluded: chain Y residue 1214 GLU Chi-restraints excluded: chain Y residue 1248 MET Chi-restraints excluded: chain Y residue 1262 MET Chi-restraints excluded: chain Y residue 1294 THR Chi-restraints excluded: chain Y residue 1319 GLU Chi-restraints excluded: chain Y residue 1331 VAL Chi-restraints excluded: chain Y residue 1336 TYR Chi-restraints excluded: chain Y residue 1366 ILE Chi-restraints excluded: chain Y residue 1374 LEU Chi-restraints excluded: chain Y residue 1388 VAL Chi-restraints excluded: chain Y residue 1556 LEU Chi-restraints excluded: chain Y residue 1678 LEU Chi-restraints excluded: chain Y residue 1740 LEU Chi-restraints excluded: chain Y residue 1757 SER Chi-restraints excluded: chain Y residue 1778 LEU Chi-restraints excluded: chain Y residue 1931 LYS Chi-restraints excluded: chain Y residue 1998 TRP Chi-restraints excluded: chain Y residue 2102 ILE Chi-restraints excluded: chain y residue 27 LEU Chi-restraints excluded: chain y residue 52 LEU Chi-restraints excluded: chain y residue 181 LEU Chi-restraints excluded: chain y residue 248 ILE Chi-restraints excluded: chain y residue 322 VAL Chi-restraints excluded: chain y residue 323 VAL Chi-restraints excluded: chain y residue 361 CYS Chi-restraints excluded: chain y residue 381 VAL Chi-restraints excluded: chain y residue 424 MET Chi-restraints excluded: chain y residue 442 CYS Chi-restraints excluded: chain y residue 476 VAL Chi-restraints excluded: chain y residue 553 THR Chi-restraints excluded: chain y residue 620 GLU Chi-restraints excluded: chain y residue 678 THR Chi-restraints excluded: chain y residue 701 VAL Chi-restraints excluded: chain y residue 763 SER Chi-restraints excluded: chain y residue 775 VAL Chi-restraints excluded: chain y residue 791 LEU Chi-restraints excluded: chain y residue 794 THR Chi-restraints excluded: chain y residue 818 GLU Chi-restraints excluded: chain y residue 1012 VAL Chi-restraints excluded: chain y residue 1120 ASN Chi-restraints excluded: chain y residue 1155 HIS Chi-restraints excluded: chain y residue 1176 VAL Chi-restraints excluded: chain y residue 1234 LEU Chi-restraints excluded: chain y residue 1248 MET Chi-restraints excluded: chain y residue 1262 MET Chi-restraints excluded: chain y residue 1277 LEU Chi-restraints excluded: chain y residue 1329 VAL Chi-restraints excluded: chain y residue 1373 ASP Chi-restraints excluded: chain y residue 1379 ARG Chi-restraints excluded: chain y residue 1386 ASP Chi-restraints excluded: chain y residue 1415 HIS Chi-restraints excluded: chain y residue 1433 THR Chi-restraints excluded: chain y residue 1487 VAL Chi-restraints excluded: chain y residue 1546 LYS Chi-restraints excluded: chain y residue 1632 VAL Chi-restraints excluded: chain y residue 1664 LEU Chi-restraints excluded: chain y residue 1794 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: [279, 54, 56, 333, 18, 17, 214, 117, 354, 11, 118] chunk 279 optimal weight: 7.9990 chunk 54 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 chunk 333 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 214 optimal weight: 7.9990 chunk 117 optimal weight: 0.9980 chunk 354 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 118 optimal weight: 9.9990 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Y 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1513 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1805 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y1100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y1264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.086611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.060906 restraints weight = 168678.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.062596 restraints weight = 76608.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.063795 restraints weight = 47567.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.064532 restraints weight = 35345.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.064875 restraints weight = 29676.137| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 32707 Z= 0.125 Angle : 0.708 34.726 44556 Z= 0.310 Chirality : 0.041 0.364 4864 Planarity : 0.003 0.054 5605 Dihedral : 13.247 172.947 4926 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.68 % Favored : 95.27 % Rotamer: Outliers : 3.09 % Allowed : 20.40 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.14), residues: 3845 helix: 1.08 (0.14), residues: 1502 sheet: -0.55 (0.22), residues: 577 loop : -1.22 (0.15), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG y 400 TYR 0.009 0.001 TYR y1643 PHE 0.014 0.001 PHE Y 125 TRP 0.015 0.001 TRP y 101 HIS 0.005 0.001 HIS Y1689 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (32668) covalent geometry : angle 0.61403 / 0.30 (44508) hydrogen bonds : bond 0.03519 / 2.56 ( 1292) hydrogen bonds : angle 4.59595 / 3.43 ( 3708) metal coordination : bond 0.00854 / 0.81 ( 39) metal coordination : angle 10.78226 / 7.47 ( 48) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 3299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 150 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 43 PHE cc_start: 0.9029 (OUTLIER) cc_final: 0.8084 (m-80) REVERT: Y 124 CYS cc_start: 0.8976 (OUTLIER) cc_final: 0.8684 (p) REVERT: Y 239 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8361 (mp0) REVERT: Y 705 LYS cc_start: 0.5259 (OUTLIER) cc_final: 0.4935 (tppt) REVERT: Y 742 GLU cc_start: 0.6736 (OUTLIER) cc_final: 0.6323 (mm-30) REVERT: Y 891 MET cc_start: 0.7945 (tpt) cc_final: 0.7647 (tpt) REVERT: Y 999 TYR cc_start: 0.9152 (m-10) cc_final: 0.8878 (m-10) REVERT: Y 1052 GLU cc_start: 0.9173 (OUTLIER) cc_final: 0.8851 (pt0) REVERT: Y 1105 MET cc_start: 0.7683 (tpp) cc_final: 0.7452 (tpp) REVERT: Y 1114 MET cc_start: 0.8372 (pmm) cc_final: 0.7457 (pmm) REVERT: Y 1248 MET cc_start: 0.8972 (OUTLIER) cc_final: 0.8422 (tmm) REVERT: Y 1366 ILE cc_start: 0.6335 (OUTLIER) cc_final: 0.6106 (tt) REVERT: Y 1474 MET cc_start: 0.8981 (tmm) cc_final: 0.8695 (tmm) REVERT: Y 1589 MET cc_start: 0.9154 (pp-130) cc_final: 0.8112 (pp-130) REVERT: Y 1778 LEU cc_start: 0.9724 (OUTLIER) cc_final: 0.9440 (mm) REVERT: Y 1998 TRP cc_start: 0.7582 (OUTLIER) cc_final: 0.7210 (m-90) REVERT: y 183 ASN cc_start: 0.9086 (OUTLIER) cc_final: 0.7947 (m-40) REVERT: y 224 MET cc_start: 0.7568 (mpp) cc_final: 0.7068 (mpp) REVERT: y 228 MET cc_start: 0.9144 (ppp) cc_final: 0.8859 (ppp) REVERT: y 361 CYS cc_start: 0.9167 (OUTLIER) cc_final: 0.8773 (p) REVERT: y 648 GLN cc_start: 0.8900 (pm20) cc_final: 0.8606 (pm20) REVERT: y 762 MET cc_start: 0.9055 (tpp) cc_final: 0.8683 (tpp) REVERT: y 818 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.7835 (tm-30) REVERT: y 868 GLU cc_start: 0.9283 (OUTLIER) cc_final: 0.8856 (pt0) REVERT: y 883 MET cc_start: 0.8771 (mmm) cc_final: 0.8250 (tpp) REVERT: y 952 ILE cc_start: 0.9470 (tp) cc_final: 0.9198 (tp) REVERT: y 1012 VAL cc_start: 0.9624 (OUTLIER) cc_final: 0.9292 (p) REVERT: y 1078 GLN cc_start: 0.9092 (mm-40) cc_final: 0.8820 (mm110) REVERT: y 1079 ARG cc_start: 0.7896 (mtt180) cc_final: 0.7447 (mtm180) REVERT: y 1083 GLN cc_start: 0.9521 (tt0) cc_final: 0.9128 (pt0) REVERT: y 1157 MET cc_start: 0.8749 (mmt) cc_final: 0.8510 (mmt) REVERT: y 1336 TYR cc_start: 0.8490 (p90) cc_final: 0.8268 (p90) REVERT: y 1371 SER cc_start: 0.9545 (p) cc_final: 0.9222 (m) REVERT: y 1388 VAL cc_start: 0.9632 (t) cc_final: 0.9405 (p) REVERT: y 1395 ARG cc_start: 0.7990 (mmm160) cc_final: 0.7270 (tpt90) REVERT: y 1463 ASP cc_start: 0.8043 (t70) cc_final: 0.7531 (t70) REVERT: y 1523 TYR cc_start: 0.7712 (m-80) cc_final: 0.7399 (m-80) REVERT: y 1540 ARG cc_start: 0.7932 (tmm-80) cc_final: 0.7354 (tmm-80) REVERT: y 1749 ASN cc_start: 0.6216 (m110) cc_final: 0.5709 (p0) outliers start: 102 outliers final: 71 residues processed: 241 average time/residue: 0.1873 time to fit residues: 75.5619 Evaluate side-chains 228 residues out of total 3299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 142 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 43 PHE Chi-restraints excluded: chain Y residue 83 LEU Chi-restraints excluded: chain Y residue 124 CYS Chi-restraints excluded: chain Y residue 130 LEU Chi-restraints excluded: chain Y residue 181 LEU Chi-restraints excluded: chain Y residue 193 ILE Chi-restraints excluded: chain Y residue 200 VAL Chi-restraints excluded: chain Y residue 217 ILE Chi-restraints excluded: chain Y residue 228 MET Chi-restraints excluded: chain Y residue 239 GLU Chi-restraints excluded: chain Y residue 252 GLU Chi-restraints excluded: chain Y residue 320 VAL Chi-restraints excluded: chain Y residue 397 ILE Chi-restraints excluded: chain Y residue 430 THR Chi-restraints excluded: chain Y residue 431 LEU Chi-restraints excluded: chain Y residue 618 LEU Chi-restraints excluded: chain Y residue 674 LEU Chi-restraints excluded: chain Y residue 705 LYS Chi-restraints excluded: chain Y residue 742 GLU Chi-restraints excluded: chain Y residue 843 LEU Chi-restraints excluded: chain Y residue 889 VAL Chi-restraints excluded: chain Y residue 902 GLN Chi-restraints excluded: chain Y residue 907 LEU Chi-restraints excluded: chain Y residue 944 LEU Chi-restraints excluded: chain Y residue 1005 GLU Chi-restraints excluded: chain Y residue 1052 GLU Chi-restraints excluded: chain Y residue 1072 LEU Chi-restraints excluded: chain Y residue 1101 CYS Chi-restraints excluded: chain Y residue 1122 VAL Chi-restraints excluded: chain Y residue 1205 THR Chi-restraints excluded: chain Y residue 1214 GLU Chi-restraints excluded: chain Y residue 1248 MET Chi-restraints excluded: chain Y residue 1262 MET Chi-restraints excluded: chain Y residue 1294 THR Chi-restraints excluded: chain Y residue 1319 GLU Chi-restraints excluded: chain Y residue 1331 VAL Chi-restraints excluded: chain Y residue 1336 TYR Chi-restraints excluded: chain Y residue 1366 ILE Chi-restraints excluded: chain Y residue 1374 LEU Chi-restraints excluded: chain Y residue 1388 VAL Chi-restraints excluded: chain Y residue 1556 LEU Chi-restraints excluded: chain Y residue 1678 LEU Chi-restraints excluded: chain Y residue 1740 LEU Chi-restraints excluded: chain Y residue 1757 SER Chi-restraints excluded: chain Y residue 1778 LEU Chi-restraints excluded: chain Y residue 1931 LYS Chi-restraints excluded: chain Y residue 1998 TRP Chi-restraints excluded: chain Y residue 2102 ILE Chi-restraints excluded: chain y residue 27 LEU Chi-restraints excluded: chain y residue 52 LEU Chi-restraints excluded: chain y residue 181 LEU Chi-restraints excluded: chain y residue 183 ASN Chi-restraints excluded: chain y residue 248 ILE Chi-restraints excluded: chain y residue 323 VAL Chi-restraints excluded: chain y residue 361 CYS Chi-restraints excluded: chain y residue 381 VAL Chi-restraints excluded: chain y residue 424 MET Chi-restraints excluded: chain y residue 442 CYS Chi-restraints excluded: chain y residue 476 VAL Chi-restraints excluded: chain y residue 553 THR Chi-restraints excluded: chain y residue 620 GLU Chi-restraints excluded: chain y residue 678 THR Chi-restraints excluded: chain y residue 763 SER Chi-restraints excluded: chain y residue 791 LEU Chi-restraints excluded: chain y residue 794 THR Chi-restraints excluded: chain y residue 818 GLU Chi-restraints excluded: chain y residue 868 GLU Chi-restraints excluded: chain y residue 1012 VAL Chi-restraints excluded: chain y residue 1120 ASN Chi-restraints excluded: chain y residue 1155 HIS Chi-restraints excluded: chain y residue 1176 VAL Chi-restraints excluded: chain y residue 1224 LEU Chi-restraints excluded: chain y residue 1234 LEU Chi-restraints excluded: chain y residue 1262 MET Chi-restraints excluded: chain y residue 1277 LEU Chi-restraints excluded: chain y residue 1329 VAL Chi-restraints excluded: chain y residue 1373 ASP Chi-restraints excluded: chain y residue 1379 ARG Chi-restraints excluded: chain y residue 1386 ASP Chi-restraints excluded: chain y residue 1415 HIS Chi-restraints excluded: chain y residue 1433 THR Chi-restraints excluded: chain y residue 1487 VAL Chi-restraints excluded: chain y residue 1546 LYS Chi-restraints excluded: chain y residue 1632 VAL Chi-restraints excluded: chain y residue 1664 LEU Chi-restraints excluded: chain y residue 1794 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: [31, 45, 173, 283, 298, 278, 91, 201, 96, 182, 108] chunk 31 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 173 optimal weight: 0.8980 chunk 283 optimal weight: 9.9990 chunk 298 optimal weight: 5.9990 chunk 278 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 201 optimal weight: 20.0000 chunk 96 optimal weight: 3.9990 chunk 182 optimal weight: 0.0870 chunk 108 optimal weight: 0.4980 overall best weight: 0.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Y 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 751 GLN ** Y1100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1513 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y1805 HIS ** y 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 958 GLN ** y1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y1100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y1120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y1264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.087105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.061436 restraints weight = 168218.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.063160 restraints weight = 76411.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.064358 restraints weight = 47364.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.065083 restraints weight = 35327.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.065222 restraints weight = 29776.928| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 32707 Z= 0.111 Angle : 0.709 35.163 44556 Z= 0.310 Chirality : 0.041 0.326 4864 Planarity : 0.003 0.055 5605 Dihedral : 13.210 177.902 4926 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.40 % Favored : 95.55 % Rotamer: Outliers : 2.94 % Allowed : 20.46 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.14), residues: 3845 helix: 1.09 (0.14), residues: 1501 sheet: -0.53 (0.22), residues: 578 loop : -1.21 (0.15), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG y 400 TYR 0.009 0.001 TYR y1643 PHE 0.014 0.001 PHE Y 125 TRP 0.015 0.001 TRP y 101 HIS 0.004 0.001 HIS Y1689 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (32668) covalent geometry : angle 0.61599 / 0.30 (44508) hydrogen bonds : bond 0.03458 / 2.51 ( 1292) hydrogen bonds : angle 4.54589 / 3.39 ( 3708) metal coordination : bond 0.00689 / 0.65 ( 39) metal coordination : angle 10.72565 / 7.26 ( 48) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 151 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 43 PHE cc_start: 0.9020 (OUTLIER) cc_final: 0.8060 (m-80) REVERT: Y 124 CYS cc_start: 0.8965 (OUTLIER) cc_final: 0.8591 (p) REVERT: Y 239 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8332 (mp0) REVERT: Y 456 PHE cc_start: 0.9331 (OUTLIER) cc_final: 0.8765 (p90) REVERT: Y 702 LEU cc_start: 0.1370 (OUTLIER) cc_final: 0.1161 (mm) REVERT: Y 705 LYS cc_start: 0.5336 (OUTLIER) cc_final: 0.5005 (tppt) REVERT: Y 742 GLU cc_start: 0.6720 (OUTLIER) cc_final: 0.6321 (mm-30) REVERT: Y 891 MET cc_start: 0.7994 (tpt) cc_final: 0.7616 (tpt) REVERT: Y 999 TYR cc_start: 0.9113 (m-10) cc_final: 0.8838 (m-10) REVERT: Y 1052 GLU cc_start: 0.9187 (OUTLIER) cc_final: 0.8863 (pt0) REVERT: Y 1105 MET cc_start: 0.7703 (tpp) cc_final: 0.7437 (tpp) REVERT: Y 1114 MET cc_start: 0.8393 (pmm) cc_final: 0.7490 (pmm) REVERT: Y 1248 MET cc_start: 0.8949 (OUTLIER) cc_final: 0.8405 (tmm) REVERT: Y 1366 ILE cc_start: 0.6426 (OUTLIER) cc_final: 0.6141 (tt) REVERT: Y 1474 MET cc_start: 0.9031 (tmm) cc_final: 0.8730 (tmm) REVERT: Y 1589 MET cc_start: 0.9161 (pp-130) cc_final: 0.8082 (pp-130) REVERT: Y 1778 LEU cc_start: 0.9713 (OUTLIER) cc_final: 0.9438 (mm) REVERT: Y 1971 MET cc_start: 0.7161 (ppp) cc_final: 0.6508 (ppp) REVERT: Y 1998 TRP cc_start: 0.7589 (OUTLIER) cc_final: 0.7220 (m-90) REVERT: y 183 ASN cc_start: 0.9097 (OUTLIER) cc_final: 0.7928 (m-40) REVERT: y 224 MET cc_start: 0.7489 (mpp) cc_final: 0.7040 (mpp) REVERT: y 228 MET cc_start: 0.9135 (ppp) cc_final: 0.8814 (ppp) REVERT: y 361 CYS cc_start: 0.9178 (OUTLIER) cc_final: 0.8785 (p) REVERT: y 648 GLN cc_start: 0.8885 (pm20) cc_final: 0.8595 (pm20) REVERT: y 762 MET cc_start: 0.9102 (tpp) cc_final: 0.8698 (tpp) REVERT: y 818 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.7857 (tm-30) REVERT: y 822 LEU cc_start: 0.9570 (mp) cc_final: 0.9357 (mm) REVERT: y 868 GLU cc_start: 0.9276 (OUTLIER) cc_final: 0.8858 (pt0) REVERT: y 883 MET cc_start: 0.8749 (mmm) cc_final: 0.8249 (tpp) REVERT: y 952 ILE cc_start: 0.9439 (tp) cc_final: 0.9184 (tp) REVERT: y 1012 VAL cc_start: 0.9639 (OUTLIER) cc_final: 0.9324 (p) REVERT: y 1079 ARG cc_start: 0.7960 (mtt180) cc_final: 0.7412 (mtt180) REVERT: y 1083 GLN cc_start: 0.9555 (tt0) cc_final: 0.9279 (pt0) REVERT: y 1105 MET cc_start: 0.8741 (tpt) cc_final: 0.8445 (tpt) REVERT: y 1157 MET cc_start: 0.8747 (mmt) cc_final: 0.8538 (mmt) REVERT: y 1224 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.9073 (mm) REVERT: y 1371 SER cc_start: 0.9537 (p) cc_final: 0.9200 (m) REVERT: y 1388 VAL cc_start: 0.9620 (t) cc_final: 0.9373 (p) REVERT: y 1395 ARG cc_start: 0.7979 (mmm160) cc_final: 0.7249 (tpt90) REVERT: y 1463 ASP cc_start: 0.7998 (t70) cc_final: 0.7553 (t0) REVERT: y 1523 TYR cc_start: 0.7838 (m-80) cc_final: 0.7545 (m-80) REVERT: y 1540 ARG cc_start: 0.7980 (tmm-80) cc_final: 0.7399 (tmm-80) REVERT: y 1749 ASN cc_start: 0.6178 (m110) cc_final: 0.5698 (p0) outliers start: 97 outliers final: 69 residues processed: 236 average time/residue: 0.1939 time to fit residues: 76.1369 Evaluate side-chains 235 residues out of total 3299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 148 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 43 PHE Chi-restraints excluded: chain Y residue 83 LEU Chi-restraints excluded: chain Y residue 124 CYS Chi-restraints excluded: chain Y residue 130 LEU Chi-restraints excluded: chain Y residue 181 LEU Chi-restraints excluded: chain Y residue 193 ILE Chi-restraints excluded: chain Y residue 200 VAL Chi-restraints excluded: chain Y residue 217 ILE Chi-restraints excluded: chain Y residue 228 MET Chi-restraints excluded: chain Y residue 239 GLU Chi-restraints excluded: chain Y residue 252 GLU Chi-restraints excluded: chain Y residue 320 VAL Chi-restraints excluded: chain Y residue 397 ILE Chi-restraints excluded: chain Y residue 430 THR Chi-restraints excluded: chain Y residue 431 LEU Chi-restraints excluded: chain Y residue 456 PHE Chi-restraints excluded: chain Y residue 618 LEU Chi-restraints excluded: chain Y residue 674 LEU Chi-restraints excluded: chain Y residue 702 LEU Chi-restraints excluded: chain Y residue 705 LYS Chi-restraints excluded: chain Y residue 736 VAL Chi-restraints excluded: chain Y residue 742 GLU Chi-restraints excluded: chain Y residue 843 LEU Chi-restraints excluded: chain Y residue 889 VAL Chi-restraints excluded: chain Y residue 944 LEU Chi-restraints excluded: chain Y residue 1005 GLU Chi-restraints excluded: chain Y residue 1052 GLU Chi-restraints excluded: chain Y residue 1072 LEU Chi-restraints excluded: chain Y residue 1101 CYS Chi-restraints excluded: chain Y residue 1122 VAL Chi-restraints excluded: chain Y residue 1205 THR Chi-restraints excluded: chain Y residue 1214 GLU Chi-restraints excluded: chain Y residue 1248 MET Chi-restraints excluded: chain Y residue 1262 MET Chi-restraints excluded: chain Y residue 1294 THR Chi-restraints excluded: chain Y residue 1319 GLU Chi-restraints excluded: chain Y residue 1331 VAL Chi-restraints excluded: chain Y residue 1336 TYR Chi-restraints excluded: chain Y residue 1366 ILE Chi-restraints excluded: chain Y residue 1374 LEU Chi-restraints excluded: chain Y residue 1388 VAL Chi-restraints excluded: chain Y residue 1556 LEU Chi-restraints excluded: chain Y residue 1678 LEU Chi-restraints excluded: chain Y residue 1740 LEU Chi-restraints excluded: chain Y residue 1757 SER Chi-restraints excluded: chain Y residue 1778 LEU Chi-restraints excluded: chain Y residue 1931 LYS Chi-restraints excluded: chain Y residue 1968 GLU Chi-restraints excluded: chain Y residue 1998 TRP Chi-restraints excluded: chain Y residue 2102 ILE Chi-restraints excluded: chain y residue 27 LEU Chi-restraints excluded: chain y residue 52 LEU Chi-restraints excluded: chain y residue 181 LEU Chi-restraints excluded: chain y residue 183 ASN Chi-restraints excluded: chain y residue 361 CYS Chi-restraints excluded: chain y residue 381 VAL Chi-restraints excluded: chain y residue 424 MET Chi-restraints excluded: chain y residue 442 CYS Chi-restraints excluded: chain y residue 476 VAL Chi-restraints excluded: chain y residue 553 THR Chi-restraints excluded: chain y residue 620 GLU Chi-restraints excluded: chain y residue 678 THR Chi-restraints excluded: chain y residue 701 VAL Chi-restraints excluded: chain y residue 763 SER Chi-restraints excluded: chain y residue 791 LEU Chi-restraints excluded: chain y residue 794 THR Chi-restraints excluded: chain y residue 818 GLU Chi-restraints excluded: chain y residue 868 GLU Chi-restraints excluded: chain y residue 1012 VAL Chi-restraints excluded: chain y residue 1120 ASN Chi-restraints excluded: chain y residue 1155 HIS Chi-restraints excluded: chain y residue 1224 LEU Chi-restraints excluded: chain y residue 1234 LEU Chi-restraints excluded: chain y residue 1277 LEU Chi-restraints excluded: chain y residue 1319 GLU Chi-restraints excluded: chain y residue 1329 VAL Chi-restraints excluded: chain y residue 1332 VAL Chi-restraints excluded: chain y residue 1373 ASP Chi-restraints excluded: chain y residue 1379 ARG Chi-restraints excluded: chain y residue 1386 ASP Chi-restraints excluded: chain y residue 1415 HIS Chi-restraints excluded: chain y residue 1433 THR Chi-restraints excluded: chain y residue 1487 VAL Chi-restraints excluded: chain y residue 1546 LYS Chi-restraints excluded: chain y residue 1632 VAL Chi-restraints excluded: chain y residue 1664 LEU Chi-restraints excluded: chain y residue 1794 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: [65, 215, 131, 76, 92, 221, 178, 2, 242, 388, 328] chunk 65 optimal weight: 5.9990 chunk 215 optimal weight: 10.0000 chunk 131 optimal weight: 5.9990 chunk 76 optimal weight: 0.1980 chunk 92 optimal weight: 2.9990 chunk 221 optimal weight: 2.9990 chunk 178 optimal weight: 4.9990 chunk 2 optimal weight: 0.4980 chunk 242 optimal weight: 0.0170 chunk 388 optimal weight: 40.0000 chunk 328 optimal weight: 6.9990 overall best weight: 1.3422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Y 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1513 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y1805 HIS ** y 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 958 GLN ** y1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y1100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y1120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y1265 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.087539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.061624 restraints weight = 168454.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.063331 restraints weight = 76755.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.064477 restraints weight = 47862.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.065227 restraints weight = 35588.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.065581 restraints weight = 29692.162| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 32707 Z= 0.119 Angle : 0.719 35.132 44556 Z= 0.314 Chirality : 0.041 0.334 4864 Planarity : 0.003 0.054 5605 Dihedral : 13.166 176.093 4924 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.42 % Favored : 95.53 % Rotamer: Outliers : 2.64 % Allowed : 20.73 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.14), residues: 3845 helix: 1.08 (0.14), residues: 1500 sheet: -0.52 (0.22), residues: 576 loop : -1.19 (0.15), residues: 1769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Y 904 TYR 0.014 0.001 TYR y1336 PHE 0.013 0.001 PHE Y 125 TRP 0.013 0.001 TRP Y1835 HIS 0.004 0.001 HIS y1698 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (32668) covalent geometry : angle 0.62810 / 0.31 (44508) hydrogen bonds : bond 0.03436 / 2.49 ( 1292) hydrogen bonds : angle 4.54574 / 3.39 ( 3708) metal coordination : bond 0.00744 / 0.70 ( 39) metal coordination : angle 10.71059 / 7.28 ( 48) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 3299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 150 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 43 PHE cc_start: 0.9004 (OUTLIER) cc_final: 0.7967 (m-80) REVERT: Y 124 CYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8668 (p) REVERT: Y 239 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8334 (mp0) REVERT: Y 702 LEU cc_start: 0.1261 (OUTLIER) cc_final: 0.1033 (mm) REVERT: Y 705 LYS cc_start: 0.5329 (OUTLIER) cc_final: 0.5001 (tppt) REVERT: Y 742 GLU cc_start: 0.6690 (OUTLIER) cc_final: 0.6304 (mm-30) REVERT: Y 891 MET cc_start: 0.8048 (tpt) cc_final: 0.7842 (tpt) REVERT: Y 1052 GLU cc_start: 0.9173 (OUTLIER) cc_final: 0.8852 (pt0) REVERT: Y 1105 MET cc_start: 0.7704 (tpp) cc_final: 0.7482 (tpp) REVERT: Y 1114 MET cc_start: 0.8382 (pmm) cc_final: 0.7499 (pmm) REVERT: Y 1248 MET cc_start: 0.8950 (OUTLIER) cc_final: 0.8408 (tmm) REVERT: Y 1474 MET cc_start: 0.9018 (tmm) cc_final: 0.8719 (tmm) REVERT: Y 1589 MET cc_start: 0.9173 (pp-130) cc_final: 0.8098 (pp-130) REVERT: Y 1740 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8855 (tm) REVERT: Y 1778 LEU cc_start: 0.9716 (OUTLIER) cc_final: 0.9443 (mm) REVERT: Y 1971 MET cc_start: 0.7146 (ppp) cc_final: 0.6408 (ppp) REVERT: Y 1998 TRP cc_start: 0.7562 (OUTLIER) cc_final: 0.7187 (m-90) REVERT: y 183 ASN cc_start: 0.9086 (OUTLIER) cc_final: 0.7944 (m-40) REVERT: y 224 MET cc_start: 0.7458 (mpp) cc_final: 0.7008 (mpp) REVERT: y 228 MET cc_start: 0.9154 (ppp) cc_final: 0.8847 (ppp) REVERT: y 361 CYS cc_start: 0.9168 (OUTLIER) cc_final: 0.8774 (p) REVERT: y 648 GLN cc_start: 0.8851 (pm20) cc_final: 0.8524 (pm20) REVERT: y 818 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.7839 (tm-30) REVERT: y 822 LEU cc_start: 0.9556 (mp) cc_final: 0.9352 (mm) REVERT: y 868 GLU cc_start: 0.9267 (OUTLIER) cc_final: 0.8842 (pt0) REVERT: y 883 MET cc_start: 0.8747 (mmm) cc_final: 0.8248 (tpp) REVERT: y 952 ILE cc_start: 0.9444 (tp) cc_final: 0.9189 (tp) REVERT: y 1012 VAL cc_start: 0.9641 (OUTLIER) cc_final: 0.9324 (p) REVERT: y 1016 MET cc_start: 0.8543 (mmp) cc_final: 0.8338 (mmp) REVERT: y 1079 ARG cc_start: 0.7964 (mtt180) cc_final: 0.7458 (mtm180) REVERT: y 1083 GLN cc_start: 0.9547 (tt0) cc_final: 0.9248 (pt0) REVERT: y 1105 MET cc_start: 0.8751 (tpt) cc_final: 0.8458 (tpt) REVERT: y 1224 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.9005 (mm) REVERT: y 1371 SER cc_start: 0.9532 (p) cc_final: 0.9188 (m) REVERT: y 1388 VAL cc_start: 0.9603 (t) cc_final: 0.9277 (p) REVERT: y 1395 ARG cc_start: 0.8011 (mmm160) cc_final: 0.7239 (tpt90) REVERT: y 1463 ASP cc_start: 0.8042 (t70) cc_final: 0.7594 (t0) REVERT: y 1523 TYR cc_start: 0.7838 (m-80) cc_final: 0.7534 (m-80) REVERT: y 1540 ARG cc_start: 0.7968 (tmm-80) cc_final: 0.7404 (tmm-80) REVERT: y 1749 ASN cc_start: 0.6236 (m110) cc_final: 0.5759 (p0) outliers start: 87 outliers final: 67 residues processed: 230 average time/residue: 0.1919 time to fit residues: 73.0453 Evaluate side-chains 228 residues out of total 3299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 144 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 43 PHE Chi-restraints excluded: chain Y residue 83 LEU Chi-restraints excluded: chain Y residue 124 CYS Chi-restraints excluded: chain Y residue 130 LEU Chi-restraints excluded: chain Y residue 181 LEU Chi-restraints excluded: chain Y residue 193 ILE Chi-restraints excluded: chain Y residue 200 VAL Chi-restraints excluded: chain Y residue 217 ILE Chi-restraints excluded: chain Y residue 228 MET Chi-restraints excluded: chain Y residue 239 GLU Chi-restraints excluded: chain Y residue 252 GLU Chi-restraints excluded: chain Y residue 320 VAL Chi-restraints excluded: chain Y residue 397 ILE Chi-restraints excluded: chain Y residue 430 THR Chi-restraints excluded: chain Y residue 431 LEU Chi-restraints excluded: chain Y residue 674 LEU Chi-restraints excluded: chain Y residue 702 LEU Chi-restraints excluded: chain Y residue 705 LYS Chi-restraints excluded: chain Y residue 736 VAL Chi-restraints excluded: chain Y residue 742 GLU Chi-restraints excluded: chain Y residue 843 LEU Chi-restraints excluded: chain Y residue 889 VAL Chi-restraints excluded: chain Y residue 907 LEU Chi-restraints excluded: chain Y residue 944 LEU Chi-restraints excluded: chain Y residue 1005 GLU Chi-restraints excluded: chain Y residue 1052 GLU Chi-restraints excluded: chain Y residue 1072 LEU Chi-restraints excluded: chain Y residue 1101 CYS Chi-restraints excluded: chain Y residue 1122 VAL Chi-restraints excluded: chain Y residue 1205 THR Chi-restraints excluded: chain Y residue 1214 GLU Chi-restraints excluded: chain Y residue 1248 MET Chi-restraints excluded: chain Y residue 1294 THR Chi-restraints excluded: chain Y residue 1319 GLU Chi-restraints excluded: chain Y residue 1331 VAL Chi-restraints excluded: chain Y residue 1336 TYR Chi-restraints excluded: chain Y residue 1374 LEU Chi-restraints excluded: chain Y residue 1388 VAL Chi-restraints excluded: chain Y residue 1556 LEU Chi-restraints excluded: chain Y residue 1678 LEU Chi-restraints excluded: chain Y residue 1740 LEU Chi-restraints excluded: chain Y residue 1757 SER Chi-restraints excluded: chain Y residue 1778 LEU Chi-restraints excluded: chain Y residue 1931 LYS Chi-restraints excluded: chain Y residue 1968 GLU Chi-restraints excluded: chain Y residue 1998 TRP Chi-restraints excluded: chain Y residue 2102 ILE Chi-restraints excluded: chain y residue 27 LEU Chi-restraints excluded: chain y residue 52 LEU Chi-restraints excluded: chain y residue 181 LEU Chi-restraints excluded: chain y residue 183 ASN Chi-restraints excluded: chain y residue 361 CYS Chi-restraints excluded: chain y residue 381 VAL Chi-restraints excluded: chain y residue 424 MET Chi-restraints excluded: chain y residue 442 CYS Chi-restraints excluded: chain y residue 553 THR Chi-restraints excluded: chain y residue 620 GLU Chi-restraints excluded: chain y residue 678 THR Chi-restraints excluded: chain y residue 701 VAL Chi-restraints excluded: chain y residue 763 SER Chi-restraints excluded: chain y residue 791 LEU Chi-restraints excluded: chain y residue 794 THR Chi-restraints excluded: chain y residue 818 GLU Chi-restraints excluded: chain y residue 868 GLU Chi-restraints excluded: chain y residue 1012 VAL Chi-restraints excluded: chain y residue 1120 ASN Chi-restraints excluded: chain y residue 1155 HIS Chi-restraints excluded: chain y residue 1176 VAL Chi-restraints excluded: chain y residue 1224 LEU Chi-restraints excluded: chain y residue 1234 LEU Chi-restraints excluded: chain y residue 1277 LEU Chi-restraints excluded: chain y residue 1319 GLU Chi-restraints excluded: chain y residue 1329 VAL Chi-restraints excluded: chain y residue 1332 VAL Chi-restraints excluded: chain y residue 1373 ASP Chi-restraints excluded: chain y residue 1379 ARG Chi-restraints excluded: chain y residue 1386 ASP Chi-restraints excluded: chain y residue 1415 HIS Chi-restraints excluded: chain y residue 1433 THR Chi-restraints excluded: chain y residue 1487 VAL Chi-restraints excluded: chain y residue 1546 LYS Chi-restraints excluded: chain y residue 1632 VAL Chi-restraints excluded: chain y residue 1664 LEU Chi-restraints excluded: chain y residue 1794 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: [265, 112, 235, 230, 219, 332, 20, 382, 285, 263, 77] chunk 265 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 chunk 235 optimal weight: 20.0000 chunk 230 optimal weight: 3.9990 chunk 219 optimal weight: 40.0000 chunk 332 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 382 optimal weight: 50.0000 chunk 285 optimal weight: 0.0770 chunk 263 optimal weight: 0.5980 chunk 77 optimal weight: 0.9990 overall best weight: 1.5344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Y 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1513 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y1805 HIS ** Y1903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 958 GLN ** y1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y1100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y1120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y1265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y1830 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.087451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.061537 restraints weight = 168832.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.063237 restraints weight = 76915.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.064390 restraints weight = 47898.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.065081 restraints weight = 35740.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.065520 restraints weight = 30167.803| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 32707 Z= 0.124 Angle : 0.722 34.904 44556 Z= 0.316 Chirality : 0.041 0.324 4864 Planarity : 0.004 0.055 5605 Dihedral : 13.084 166.634 4923 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.50 % Favored : 95.45 % Rotamer: Outliers : 2.67 % Allowed : 20.64 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.14), residues: 3845 helix: 1.08 (0.14), residues: 1501 sheet: -0.52 (0.22), residues: 576 loop : -1.16 (0.15), residues: 1768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG Y 904 TYR 0.015 0.001 TYR y1336 PHE 0.014 0.001 PHE Y 125 TRP 0.012 0.001 TRP Y1835 HIS 0.005 0.001 HIS y1698 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (32668) covalent geometry : angle 0.63084 / 0.31 (44508) hydrogen bonds : bond 0.03442 / 2.50 ( 1292) hydrogen bonds : angle 4.54175 / 3.39 ( 3708) metal coordination : bond 0.00802 / 0.75 ( 39) metal coordination : angle 10.69429 / 7.25 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5743.54 seconds wall clock time: 99 minutes 50.43 seconds (5990.43 seconds total)