Starting phenix.real_space_refine on Thu Oct 29 20:42:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9tuc_56256/10_2026/9tuc_56256.cif Found real_map, /net/cci-nas-00/data/ceres_data/9tuc_56256/10_2026/9tuc_56256.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9tuc_56256/10_2026/9tuc_56256.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9tuc_56256/10_2026/9tuc_56256.map" model { file = "/net/cci-nas-00/data/ceres_data/9tuc_56256/10_2026/9tuc_56256.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9tuc_56256/10_2026/9tuc_56256.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.013 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 78 5.49 5 S 140 5.16 5 C 20175 2.51 5 N 5813 2.21 5 O 6186 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.03s 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: 32402 Number of models: 1 Model: "" Number of chains: 8 Chain: "Y" Number of atoms: 16281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2049, 16281 Classifications: {'peptide': 2049} Link IDs: {'PTRANS': 97, 'TRANS': 1951} Chain breaks: 3 Chain: "y" Number of atoms: 14541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1833, 14541 Classifications: {'peptide': 1833} Link IDs: {'PTRANS': 89, 'TRANS': 1743} Chain breaks: 2 Chain: "i" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 530 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "g" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 269 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "G" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 269 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "I" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 471 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} 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: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' ZN': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3468 SG CYS Y 437 30.070 53.045 110.436 1.00183.99 S ATOM 3506 SG CYS Y 442 30.351 51.286 112.638 1.00188.99 S ATOM 3727 SG CYS Y 467 29.374 50.590 108.696 1.00188.00 S ATOM 3741 SG CYS Y 469 29.268 48.912 111.413 1.00190.91 S ATOM 3832 SG CYS Y 482 46.841 67.137 114.720 1.00188.67 S ATOM 4419 SG CYS Y 586 43.551 69.126 114.727 1.00221.97 S ATOM 4432 SG CYS Y 588 45.350 68.007 117.918 1.00227.93 S ATOM 4438 SG CYS Y 589 46.658 70.885 115.564 1.00235.33 S ATOM 10998 SG CYS Y1423 19.003 61.489 64.281 1.00215.22 S ATOM 11024 SG CYS Y1426 20.726 58.200 63.870 1.00227.97 S ATOM 11108 SG CYS Y1439 20.574 60.904 60.871 1.00245.31 S ATOM 11130 SG CYS Y1442 18.202 58.119 62.134 1.00256.06 S ATOM 11803 SG CYS Y1526 38.252 89.731 69.520 1.00284.83 S ATOM 11823 SG CYS Y1529 41.366 88.803 71.532 1.00288.19 S ATOM 12157 SG CYS Y1571 41.080 92.375 69.932 1.00308.99 S ATOM 13020 SG CYS Y1681 34.823 44.768 93.042 1.00171.00 S ATOM 13032 SG CYS Y1683 33.299 47.648 94.938 1.00173.25 S ATOM 13066 SG CYS Y1687 37.107 47.630 94.330 1.00156.98 S ATOM 13092 SG CYS Y1690 34.909 48.255 91.519 1.00178.82 S ATOM 19749 SG CYS y 437 110.309 141.194 113.249 1.00221.65 S ATOM 19787 SG CYS y 442 110.086 141.149 116.184 1.00244.89 S ATOM 20008 SG CYS y 467 108.430 143.576 113.209 1.00249.94 S ATOM 20022 SG CYS y 469 108.503 143.521 116.363 1.00274.66 S ATOM 20097 SG CYS y 479 113.125 120.511 106.278 1.00214.62 S ATOM 20113 SG CYS y 482 111.816 119.069 109.454 1.00204.05 S ATOM 20713 SG CYS y 588 114.958 120.543 109.854 1.00259.70 S ATOM 20719 SG CYS y 589 114.660 117.355 107.550 1.00229.02 S ATOM 27207 SG CYS y1423 104.214 141.072 61.704 1.00222.13 S ATOM 27233 SG CYS y1426 101.821 143.893 62.499 1.00229.40 S ATOM 27317 SG CYS y1439 101.402 141.916 59.246 1.00239.03 S ATOM 27339 SG CYS y1442 104.425 144.232 59.747 1.00227.53 S ATOM 28012 SG CYS y1526 97.096 108.058 63.426 1.00225.57 S ATOM 28032 SG CYS y1529 94.932 107.189 66.496 1.00233.06 S ATOM 28366 SG CYS y1571 94.931 104.873 63.335 1.00250.99 S ATOM 29229 SG CYS y1681 88.607 152.284 94.105 1.00277.28 S ATOM 29241 SG CYS y1683 91.008 149.930 95.834 1.00266.84 S ATOM 29275 SG CYS y1687 87.284 148.975 95.353 1.00251.05 S ATOM 29301 SG CYS y1690 89.677 148.892 92.495 1.00269.60 S Time building chain proxies: 6.78, per 1000 atoms: 0.21 Number of scatterers: 32402 At special positions: 0 Unit cell: (158.635, 186.368, 168.619, 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 140 16.00 P 78 15.00 O 6186 8.00 N 5813 7.00 C 20175 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: 3.14 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN Y2202 " pdb="ZN ZN Y2202 " - pdb=" SG CYS Y 442 " pdb="ZN ZN Y2202 " - pdb=" SG CYS Y 469 " pdb="ZN ZN Y2202 " - pdb=" SG CYS Y 437 " pdb="ZN ZN Y2202 " - pdb=" SG CYS Y 467 " pdb=" ZN Y2203 " pdb="ZN ZN Y2203 " - pdb=" SG CYS Y 482 " pdb="ZN ZN Y2203 " - pdb=" SG CYS Y 586 " pdb="ZN ZN Y2203 " - pdb=" SG CYS Y 588 " pdb="ZN ZN Y2203 " - pdb=" SG CYS Y 589 " pdb=" ZN Y2204 " pdb="ZN ZN Y2204 " - pdb=" SG CYS Y1426 " pdb="ZN ZN Y2204 " - pdb=" SG CYS Y1442 " pdb="ZN ZN Y2204 " - pdb=" SG CYS Y1423 " 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 Y1526 " pdb="ZN ZN Y2205 " - pdb=" SG CYS Y1529 " 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 " pdb=" ZN y2201 " pdb="ZN ZN y2201 " - pdb=" SG CYS y 442 " pdb="ZN ZN y2201 " - pdb=" SG CYS y 437 " pdb="ZN ZN y2201 " - pdb=" SG CYS y 467 " 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 588 " pdb=" ZN y2203 " pdb="ZN ZN y2203 " - pdb=" SG CYS y1423 " pdb="ZN ZN y2203 " - pdb=" SG CYS y1442 " pdb="ZN ZN y2203 " - pdb=" SG CYS y1426 " pdb="ZN ZN y2203 " - pdb=" SG CYS y1439 " 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 y1571 " pdb="ZN ZN y2204 " - pdb=" SG CYS y1529 " pdb=" ZN y2205 " pdb="ZN ZN y2205 " - pdb=" SG CYS y1690 " pdb="ZN ZN y2205 " - pdb=" SG CYS y1687 " pdb="ZN ZN y2205 " - pdb=" SG CYS y1683 " pdb="ZN ZN y2205 " - pdb=" SG CYS y1681 " Number of angles added : 54 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7270 Finding SS restraints... Secondary structure from input PDB file: 148 helices and 26 sheets defined 43.9% alpha, 9.4% beta 20 base pairs and 41 stacking pairs defined. Time for finding SS restraints: 3.95 Creating SS restraints... Processing helix chain 'Y' and resid 7 through 28 removed outlier: 3.665A pdb=" N ALA Y 28 " --> pdb=" O VAL Y 24 " (cutoff:3.500A) Processing helix chain 'Y' and resid 31 through 43 Processing helix chain 'Y' and resid 71 through 75 Processing helix chain 'Y' and resid 80 through 87 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 155 through 168 removed outlier: 4.414A pdb=" N GLU Y 168 " --> pdb=" O GLU Y 164 " (cutoff:3.500A) Processing helix chain 'Y' and resid 170 through 174 removed outlier: 4.009A pdb=" N LYS Y 174 " --> pdb=" O ARG Y 171 " (cutoff:3.500A) Processing helix chain 'Y' and resid 194 through 200 Processing helix chain 'Y' and resid 206 through 213 Processing helix chain 'Y' and resid 221 through 231 Processing helix chain 'Y' and resid 234 through 241 removed outlier: 3.974A pdb=" N ILE Y 238 " --> pdb=" O ASP Y 234 " (cutoff:3.500A) Processing helix chain 'Y' and resid 258 through 276 removed outlier: 4.079A pdb=" N ALA Y 262 " --> pdb=" O GLY Y 258 " (cutoff:3.500A) Processing helix chain 'Y' and resid 298 through 314 Processing helix chain 'Y' and resid 333 through 337 removed outlier: 3.723A pdb=" N LEU Y 336 " --> pdb=" O SER Y 333 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE Y 337 " --> pdb=" O GLU Y 334 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 333 through 337' Processing helix chain 'Y' and resid 344 through 351 Processing helix chain 'Y' and resid 352 through 361 Processing helix chain 'Y' and resid 363 through 374 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 removed outlier: 3.753A pdb=" N ASN Y 450 " --> pdb=" O HIS Y 447 " (cutoff:3.500A) Processing helix chain 'Y' and resid 606 through 620 Proline residue: Y 616 - end of helix Processing helix chain 'Y' and resid 629 through 633 Processing helix chain 'Y' and resid 647 through 674 removed outlier: 3.856A pdb=" N ALA Y 651 " --> pdb=" O ARG Y 647 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU Y 674 " --> pdb=" O CYS Y 670 " (cutoff:3.500A) Processing helix chain 'Y' and resid 685 through 700 Processing helix chain 'Y' and resid 704 through 717 Processing helix chain 'Y' and resid 722 through 732 Processing helix chain 'Y' and resid 732 through 740 removed outlier: 3.677A pdb=" N SER Y 740 " --> pdb=" O VAL Y 736 " (cutoff:3.500A) Processing helix chain 'Y' and resid 740 through 755 Processing helix chain 'Y' and resid 764 through 774 removed outlier: 3.795A pdb=" N SER Y 774 " --> pdb=" O GLN Y 770 " (cutoff:3.500A) Processing helix chain 'Y' and resid 774 through 790 removed outlier: 5.309A pdb=" N MET Y 781 " --> pdb=" O LEU Y 777 " (cutoff:3.500A) removed outlier: 4.862A 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 828 through 833 Processing helix chain 'Y' and resid 837 through 844 Processing helix chain 'Y' and resid 849 through 870 Processing helix chain 'Y' and resid 878 through 882 Processing helix chain 'Y' and resid 918 through 927 Processing helix chain 'Y' and resid 934 through 953 Processing helix chain 'Y' and resid 967 through 971 removed outlier: 3.519A pdb=" N ALA Y 971 " --> pdb=" O ILE Y 967 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 967 through 971' Processing helix chain 'Y' and resid 1021 through 1025 removed outlier: 3.677A pdb=" N TRP Y1024 " --> pdb=" O VAL Y1021 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1033 through 1044 removed outlier: 3.875A pdb=" N ARG Y1037 " --> pdb=" O ALA Y1033 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1045 through 1053 Processing helix chain 'Y' and resid 1057 through 1065 removed outlier: 3.504A pdb=" N LEU Y1065 " --> pdb=" O ASP Y1061 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1080 through 1094 Processing helix chain 'Y' and resid 1125 through 1135 removed outlier: 3.928A pdb=" N ARG Y1135 " --> pdb=" O GLN Y1131 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1153 through 1162 removed outlier: 3.694A pdb=" N MET Y1157 " --> pdb=" O THR Y1153 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLU Y1158 " --> pdb=" O ALA Y1154 " (cutoff:3.500A) removed outlier: 5.046A 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 1180 through 1201 removed outlier: 4.403A pdb=" N VAL Y1184 " --> pdb=" O SER Y1180 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1218 through 1230 Processing helix chain 'Y' and resid 1231 through 1242 Processing helix chain 'Y' and resid 1251 through 1288 removed outlier: 3.881A pdb=" N LEU Y1255 " --> pdb=" O THR Y1251 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1294 through 1310 Processing helix chain 'Y' and resid 1311 through 1319 removed outlier: 3.512A pdb=" N GLU Y1319 " --> pdb=" O LYS Y1315 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1338 through 1348 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 1542 through 1547 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 1660 through 1666 Processing helix chain 'Y' and resid 1668 through 1680 Processing helix chain 'Y' and resid 1695 through 1703 removed outlier: 4.010A pdb=" N VAL Y1700 " --> pdb=" O GLN Y1697 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ASN Y1701 " --> pdb=" O HIS Y1698 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1704 through 1712 removed outlier: 3.679A pdb=" N ALA Y1708 " --> pdb=" O ASP Y1704 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1713 through 1721 removed outlier: 3.701A pdb=" N ASN Y1721 " --> pdb=" O LEU Y1717 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1723 through 1727 Processing helix chain 'Y' and resid 1739 through 1750 Processing helix chain 'Y' and resid 1768 through 1772 Processing helix chain 'Y' and resid 1773 through 1784 removed outlier: 4.418A 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 1914 through 1927 Processing helix chain 'Y' and resid 1927 through 1936 Processing helix chain 'Y' and resid 1952 through 1970 Processing helix chain 'Y' and resid 2000 through 2014 removed outlier: 3.673A pdb=" N ARG Y2004 " --> pdb=" O ASN Y2000 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2075 through 2083 Processing helix chain 'Y' and resid 2084 through 2086 No H-bonds generated for 'chain 'Y' and resid 2084 through 2086' Processing helix chain 'y' and resid 7 through 28 removed outlier: 3.883A pdb=" N ALA y 28 " --> pdb=" O VAL y 24 " (cutoff:3.500A) Processing helix chain 'y' and resid 31 through 43 Processing helix chain 'y' and resid 71 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 116 through 119 removed outlier: 3.606A pdb=" N SER y 119 " --> pdb=" O GLY y 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 116 through 119' Processing helix chain 'y' and resid 120 through 141 Proline residue: y 128 - end of helix Processing helix chain 'y' and resid 155 through 170 removed outlier: 3.715A pdb=" N ILE y 159 " --> pdb=" O LEU y 155 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN y 163 " --> pdb=" O ILE y 159 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N GLU y 164 " --> pdb=" O ASN y 160 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ARG y 165 " --> pdb=" O SER y 161 " (cutoff:3.500A) Processing helix chain 'y' and resid 193 through 200 Processing helix chain 'y' and resid 206 through 213 Processing helix chain 'y' and resid 221 through 231 Processing helix chain 'y' and resid 234 through 240 removed outlier: 4.228A pdb=" N ILE y 238 " --> pdb=" O ASP y 234 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS y 240 " --> pdb=" O PRO y 236 " (cutoff:3.500A) Processing helix chain 'y' and resid 241 through 245 removed outlier: 4.244A pdb=" N MET y 244 " --> pdb=" O SER y 241 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LEU y 245 " --> pdb=" O GLN y 242 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 241 through 245' Processing helix chain 'y' and resid 253 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 316 through 318 No H-bonds generated for 'chain 'y' and resid 316 through 318' Processing helix chain 'y' and resid 333 through 337 Processing helix chain 'y' and resid 345 through 351 Processing helix chain 'y' and resid 352 through 362 removed outlier: 3.530A pdb=" N GLN y 358 " --> pdb=" O GLN y 354 " (cutoff:3.500A) Processing helix chain 'y' and resid 363 through 374 Processing helix chain 'y' and resid 383 through 394 removed outlier: 4.334A pdb=" N THR y 393 " --> pdb=" O VAL y 389 " (cutoff:3.500A) Processing helix chain 'y' and resid 398 through 412 Processing helix chain 'y' and resid 446 through 450 removed outlier: 3.809A pdb=" N ASN y 450 " --> pdb=" O HIS y 447 " (cutoff:3.500A) Processing helix chain 'y' and resid 606 through 622 removed outlier: 4.197A 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 627 through 632 Processing helix chain 'y' and resid 633 through 638 Processing helix chain 'y' and resid 646 through 674 Processing helix chain 'y' and resid 685 through 699 removed outlier: 3.548A pdb=" N LEU y 691 " --> pdb=" O ALA y 687 " (cutoff:3.500A) Processing helix chain 'y' and resid 704 through 716 removed outlier: 4.458A pdb=" N ILE y 708 " --> pdb=" O LEU y 704 " (cutoff:3.500A) 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: 3.824A pdb=" N ASN y 756 " --> pdb=" O ALA y 752 " (cutoff:3.500A) Processing helix chain 'y' and resid 764 through 774 removed outlier: 3.608A pdb=" N SER y 774 " --> pdb=" O GLN y 770 " (cutoff:3.500A) Processing helix chain 'y' and resid 774 through 790 removed outlier: 4.246A pdb=" N MET y 781 " --> pdb=" O LEU y 777 " (cutoff:3.500A) removed outlier: 4.638A 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 816 through 821 Processing helix chain 'y' and resid 827 through 832 removed outlier: 3.793A pdb=" N ASP y 831 " --> pdb=" O TYR y 827 " (cutoff:3.500A) Processing helix chain 'y' and resid 837 through 844 Processing helix chain 'y' and resid 846 through 870 removed outlier: 4.375A pdb=" N LEU y 851 " --> pdb=" O PRO y 847 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ALA y 852 " --> pdb=" O ASP y 848 " (cutoff:3.500A) Processing helix chain 'y' and resid 878 through 882 Processing helix chain 'y' and resid 910 through 914 Processing helix chain 'y' and resid 917 through 927 Processing helix chain 'y' and resid 934 through 953 Processing helix chain 'y' and resid 966 through 970 Processing helix chain 'y' and resid 1021 through 1025 removed outlier: 3.528A pdb=" N TRP y1024 " --> pdb=" O VAL y1021 " (cutoff:3.500A) Processing helix chain 'y' and resid 1033 through 1044 removed outlier: 3.558A pdb=" N ARG y1037 " --> pdb=" O ALA y1033 " (cutoff:3.500A) Processing helix chain 'y' and resid 1044 through 1054 Processing helix chain 'y' and resid 1057 through 1065 removed outlier: 3.594A pdb=" N ARG y1062 " --> pdb=" O THR y1058 " (cutoff:3.500A) Processing helix chain 'y' and resid 1080 through 1093 Processing helix chain 'y' and resid 1125 through 1134 Processing helix chain 'y' and resid 1153 through 1162 Processing helix chain 'y' and resid 1163 through 1166 removed outlier: 3.774A pdb=" N ALA y1166 " --> pdb=" O PRO y1163 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 1163 through 1166' Processing helix chain 'y' and resid 1180 through 1200 removed outlier: 3.522A pdb=" N VAL y1184 " --> pdb=" O SER y1180 " (cutoff:3.500A) Processing helix chain 'y' and resid 1208 through 1213 Processing helix chain 'y' and resid 1218 through 1230 removed outlier: 3.860A pdb=" N ASN y1228 " --> pdb=" O LEU y1224 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N HIS y1229 " --> pdb=" O HIS y1225 " (cutoff:3.500A) Processing helix chain 'y' and resid 1234 through 1242 Processing helix chain 'y' and resid 1251 through 1288 removed outlier: 3.796A pdb=" N ASP y1287 " --> pdb=" O ALA y1283 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN y1288 " --> pdb=" O LEU y1284 " (cutoff:3.500A) Processing helix chain 'y' and resid 1294 through 1310 Processing helix chain 'y' and resid 1311 through 1319 Processing helix chain 'y' and resid 1338 through 1345 removed outlier: 3.622A pdb=" N LEU y1342 " --> pdb=" O THR y1338 " (cutoff:3.500A) Processing helix chain 'y' and resid 1373 through 1381 removed outlier: 4.395A pdb=" N ARG y1379 " --> pdb=" O PRO y1375 " (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 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 1661 through 1665 Processing helix chain 'y' and resid 1668 through 1680 Processing helix chain 'y' and resid 1695 through 1703 removed outlier: 3.720A pdb=" N HIS y1698 " --> pdb=" O ASP y1695 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ASN y1701 " --> pdb=" O HIS y1698 " (cutoff:3.500A) Processing helix chain 'y' and resid 1704 through 1711 removed outlier: 3.687A pdb=" N ALA y1708 " --> pdb=" O ASP y1704 " (cutoff:3.500A) Processing helix chain 'y' and resid 1713 through 1721 Processing helix chain 'y' and resid 1739 through 1750 Processing helix chain 'y' and resid 1773 through 1785 removed outlier: 4.077A 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 1825 through 1827 No H-bonds generated for 'chain 'y' and resid 1825 through 1827' Processing sheet with id=AA1, first strand: chain 'Y' and resid 380 through 382 removed outlier: 3.715A pdb=" N SER Y1144 " --> pdb=" O LEU Y 422 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N VAL Y1117 " --> pdb=" O ILE Y1147 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N LEU Y1149 " --> pdb=" O VAL Y1117 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N MET Y1119 " --> pdb=" O LEU Y1149 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LEU Y 641 " --> pdb=" O LEU Y1116 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA Y1118 " --> pdb=" O LEU Y 641 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N GLU Y1073 " --> pdb=" O ASN Y1100 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N SER Y1102 " --> pdb=" O GLU Y1073 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N HIS Y1075 " --> pdb=" O SER Y1102 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'Y' and resid 217 through 219 removed outlier: 6.361A pdb=" N ALA Y 149 " --> pdb=" O MET Y 218 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ILE Y 150 " --> pdb=" O VAL Y 249 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'Y' and resid 435 through 436 removed outlier: 3.707A pdb=" N TRP Y 435 " --> pdb=" O TRP Y 460 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 459 through 460 current: chain 'Y' and resid 485 through 493 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 499 through 503 current: chain 'Y' and resid 565 through 571 Processing sheet with id=AA4, first strand: chain 'Y' and resid 585 through 586 Processing sheet with id=AA5, first strand: chain 'Y' and resid 762 through 763 Processing sheet with id=AA6, first strand: chain 'Y' and resid 872 through 873 Processing sheet with id=AA7, first strand: chain 'Y' and resid 988 through 989 removed outlier: 3.565A pdb=" N VAL Y1012 " --> pdb=" O ARG Y 981 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'Y' and resid 1371 through 1372 removed outlier: 3.889A pdb=" N GLY Y1459 " --> pdb=" O MET Y1400 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'Y' and resid 1385 through 1389 removed outlier: 3.786A pdb=" N ALA Y1385 " --> pdb=" O SER Y1396 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'Y' and resid 1419 through 1423 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 1429 through 1432 current: chain 'Y' and resid 1501 through 1515 removed outlier: 4.093A pdb=" N SER Y1508 " --> pdb=" O THR Y1587 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N THR Y1587 " --> pdb=" O SER Y1508 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLU Y1510 " --> pdb=" O SER Y1585 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N SER Y1585 " --> pdb=" O GLU Y1510 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N PHE Y1512 " --> pdb=" O TYR Y1583 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N TYR Y1583 " --> pdb=" O PHE Y1512 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N PHE Y1514 " --> pdb=" O LEU Y1581 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N LEU Y1581 " --> pdb=" O PHE Y1514 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 1580 through 1594 current: chain 'Y' and resid 1644 through 1652 Processing sheet with id=AB2, first strand: chain 'Y' and resid 1532 through 1534 Processing sheet with id=AB3, first strand: chain 'Y' and resid 1554 through 1555 removed outlier: 4.079A pdb=" N HIS Y1554 " --> pdb=" O CYS Y1571 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Y' and resid 1734 through 1735 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 1734 through 1735 current: chain 'Y' and resid 1790 through 1792 removed outlier: 6.258A pdb=" N LEU Y1790 " --> pdb=" O LYS Y1821 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 1820 through 1822 current: chain 'Y' and resid 1833 through 1840 removed outlier: 7.161A pdb=" N TRP Y1848 " --> pdb=" O LEU Y1836 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N GLN Y1838 " --> pdb=" O GLN Y1846 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLN Y1846 " --> pdb=" O GLN Y1838 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'Y' and resid 1901 through 1904 removed outlier: 3.902A pdb=" N SER Y2099 " --> pdb=" O LEU Y1904 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE Y2102 " --> pdb=" O LEU Y2054 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU Y2054 " --> pdb=" O ILE Y2102 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR Y1945 " --> pdb=" O THR Y1978 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP Y1947 " --> pdb=" O CYS Y1980 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'y' and resid 380 through 382 removed outlier: 6.699A pdb=" N LEU y 422 " --> pdb=" O SER y1144 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N ALA y1146 " --> pdb=" O LEU y 422 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N MET y 424 " --> pdb=" O ALA y1146 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N THR y1148 " --> pdb=" O MET y 424 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N GLY y 426 " --> pdb=" O THR y1148 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N CYS y1150 " --> pdb=" O GLY y 426 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ILE y 428 " --> pdb=" O CYS y1150 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU y 641 " --> pdb=" O ALA y1118 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N THR y 642 " --> pdb=" O CYS y1101 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N GLU y1073 " --> pdb=" O ASN y1100 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'y' and resid 203 through 204 removed outlier: 7.172A pdb=" N PHE y 179 " --> pdb=" O ALA y 204 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ALA y 149 " --> pdb=" O MET y 218 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N THR y 220 " --> pdb=" O ALA y 149 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N PHE y 151 " --> pdb=" O THR y 220 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ASP y 251 " --> pdb=" O LEU y 152 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE y 248 " --> pdb=" O ILE y 288 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N THR y 290 " --> pdb=" O ILE y 248 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LEU y 250 " --> pdb=" O THR y 290 " (cutoff:3.500A) removed outlier: 9.033A pdb=" N ALA y 292 " --> pdb=" O LEU y 250 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER y 115 " --> pdb=" O SER y 291 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N SER y 110 " --> pdb=" O LYS y 321 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N VAL y 323 " --> pdb=" O SER y 110 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU y 112 " --> pdb=" O VAL y 323 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'y' and resid 435 through 437 WARNING: can't find start of bonding for strands! previous: chain 'y' and resid 459 through 460 current: chain 'y' and resid 485 through 493 Processing sheet with id=AB9, first strand: chain 'y' and resid 547 through 549 Processing sheet with id=AC1, first strand: chain 'y' and resid 762 through 763 Processing sheet with id=AC2, first strand: chain 'y' and resid 891 through 892 removed outlier: 6.164A pdb=" N MET y 891 " --> pdb=" O GLN y 906 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'y' and resid 957 through 958 Processing sheet with id=AC4, first strand: chain 'y' and resid 988 through 989 removed outlier: 3.672A pdb=" N VAL y1012 " --> pdb=" O ARG y 981 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'y' and resid 1371 through 1372 Processing sheet with id=AC6, first strand: chain 'y' and resid 1419 through 1423 WARNING: can't find start of bonding for strands! previous: chain 'y' and resid 1429 through 1432 current: chain 'y' and resid 1501 through 1515 WARNING: can't find start of bonding for strands! previous: chain 'y' and resid 1501 through 1515 current: chain 'y' and resid 1532 through 1534 WARNING: can't find start of bonding for strands! previous: chain 'y' and resid 1532 through 1534 current: chain 'y' and resid 1644 through 1652 Processing sheet with id=AC7, first strand: chain 'y' and resid 1554 through 1555 removed outlier: 3.724A pdb=" N HIS y1554 " --> pdb=" O CYS y1571 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'y' and resid 1755 through 1760 removed outlier: 6.176A pdb=" N CYS y1756 " --> pdb=" O GLU y1789 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N LEU y1791 " --> pdb=" O CYS y1756 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LEU y1758 " --> pdb=" O LEU y1791 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N VAL y1788 " --> pdb=" O GLN y1819 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N LYS y1821 " --> pdb=" O VAL y1788 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N LEU y1790 " --> pdb=" O LYS y1821 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'y' and resid 1818 through 1822 current: chain 'y' and resid 1833 through 1840 removed outlier: 5.397A pdb=" N TRP y1835 " --> pdb=" O ALA y1850 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ALA y1850 " --> pdb=" O TRP y1835 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ALA y1837 " --> pdb=" O TRP y1848 " (cutoff:3.500A) 1223 hydrogen bonds defined for protein. 3462 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 46 hydrogen bonds 84 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 41 stacking parallelities Total time for adding SS restraints: 10.36 Time building geometry restraints manager: 4.03 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: 10937 1.36 - 1.51: 9388 1.51 - 1.66: 12736 1.66 - 1.80: 137 1.80 - 1.95: 71 Bond restraints: 33269 Sorted by residual: bond pdb=" C1' DT i 13 " pdb=" N1 DT i 13 " ideal model delta sigma weight residual 1.468 1.552 -0.084 1.40e-02 5.10e+03 3.56e+01 bond pdb=" O3B AGS Y2201 " pdb=" PB AGS Y2201 " ideal model delta sigma weight residual 1.673 1.581 0.092 2.00e-02 2.50e+03 2.13e+01 bond pdb=" O3A AGS Y2201 " pdb=" PA AGS Y2201 " ideal model delta sigma weight residual 1.664 1.584 0.080 2.00e-02 2.50e+03 1.61e+01 bond pdb=" N1 DT i 13 " pdb=" C2 DT i 13 " ideal model delta sigma weight residual 1.376 1.403 -0.027 8.00e-03 1.56e+04 1.13e+01 bond pdb=" C3' DT i 13 " pdb=" C2' DT i 13 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.14e+00 ... (remaining 33264 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.99: 45098 2.99 - 5.98: 255 5.98 - 8.97: 43 8.97 - 11.96: 10 11.96 - 14.95: 1 Bond angle restraints: 45407 Sorted by residual: angle pdb=" N3 DT G 26 " pdb=" C4 DT G 26 " pdb=" O4 DT G 26 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.92e+01 angle pdb=" N3 DT g 26 " pdb=" C4 DT g 26 " pdb=" O4 DT g 26 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.91e+01 angle pdb=" N3 DT I 11 " pdb=" C4 DT I 11 " pdb=" O4 DT I 11 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+01 angle pdb=" CA LEU Y1828 " pdb=" CB LEU Y1828 " pdb=" CG LEU Y1828 " ideal model delta sigma weight residual 116.30 131.25 -14.95 3.50e+00 8.16e-02 1.83e+01 angle pdb=" N3 DT G 30 " pdb=" C4 DT G 30 " pdb=" O4 DT G 30 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.76e+01 ... (remaining 45402 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.10: 18628 29.10 - 58.19: 1154 58.19 - 87.29: 100 87.29 - 116.38: 4 116.38 - 145.48: 2 Dihedral angle restraints: 19888 sinusoidal: 8629 harmonic: 11259 Sorted by residual: dihedral pdb=" CA ALA Y1975 " pdb=" C ALA Y1975 " pdb=" N SER Y1976 " pdb=" CA SER Y1976 " ideal model delta harmonic sigma weight residual -180.00 -155.66 -24.34 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA ASP Y 779 " pdb=" C ASP Y 779 " pdb=" N ARG Y 780 " pdb=" CA ARG Y 780 " ideal model delta harmonic sigma weight residual 180.00 -158.05 -21.95 0 5.00e+00 4.00e-02 1.93e+01 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 -131.05 138.42 1 3.00e+01 1.11e-03 1.86e+01 ... (remaining 19885 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 4113 0.052 - 0.103: 736 0.103 - 0.155: 98 0.155 - 0.207: 5 0.207 - 0.259: 2 Chirality restraints: 4954 Sorted by residual: chirality pdb=" C3' AGS Y2201 " pdb=" C2' AGS Y2201 " pdb=" C4' AGS Y2201 " pdb=" O3' AGS Y2201 " both_signs ideal model delta sigma weight residual False -2.37 -2.63 0.26 2.00e-01 2.50e+01 1.67e+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 -2.39 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CG LEU Y1828 " pdb=" CB LEU Y1828 " pdb=" CD1 LEU Y1828 " pdb=" CD2 LEU Y1828 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.05e+00 ... (remaining 4951 not shown) Planarity restraints: 5654 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET Y1474 " 0.040 5.00e-02 4.00e+02 6.17e-02 6.09e+00 pdb=" N PRO Y1475 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO Y1475 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO Y1475 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY Y1910 " 0.038 5.00e-02 4.00e+02 5.79e-02 5.37e+00 pdb=" N PRO Y1911 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO Y1911 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO Y1911 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP Y2047 " -0.009 2.00e-02 2.50e+03 1.91e-02 3.66e+00 pdb=" CG ASP Y2047 " 0.033 2.00e-02 2.50e+03 pdb=" OD1 ASP Y2047 " -0.012 2.00e-02 2.50e+03 pdb=" OD2 ASP Y2047 " -0.012 2.00e-02 2.50e+03 ... (remaining 5651 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 532 2.60 - 3.17: 29140 3.17 - 3.75: 57380 3.75 - 4.32: 74111 4.32 - 4.90: 115634 Nonbonded interactions: 276797 Sorted by model distance: nonbonded pdb=" N2 DG G 21 " pdb=" O2 DC I 10 " model vdw 2.023 2.496 nonbonded pdb=" O2 DC i 10 " pdb=" N2 DG g 21 " model vdw 2.045 2.496 nonbonded pdb=" OD1 ASN Y 221 " pdb=" OG1 THR Y 223 " model vdw 2.145 3.040 nonbonded pdb=" OE2 GLU Y 551 " pdb=" OG1 THR Y 554 " model vdw 2.151 3.040 nonbonded pdb=" OE2 GLU Y 578 " pdb=" ND2 ASN Y 581 " model vdw 2.223 3.120 ... (remaining 276792 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 'G' selection = chain 'g' } ncs_group { reference = chain 'I' selection = (chain 'i' and resid 1 through 23) } ncs_group { reference = (chain 'Y' and (resid 4 through 1345 or resid 1369 through 1888 or resid 2202 th \ rough 2206)) selection = chain 'y' } 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: 2.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 40.600 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 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 33309 Z= 0.202 Angle : 0.797 34.471 45461 Z= 0.364 Chirality : 0.040 0.259 4954 Planarity : 0.003 0.062 5654 Dihedral : 17.228 145.477 12618 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 18.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.37 % Favored : 95.60 % Rotamer: Outliers : 1.66 % Allowed : 18.30 % Favored : 80.04 % 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: -0.20 (0.14), residues: 3868 helix: 1.14 (0.14), residues: 1480 sheet: -0.57 (0.22), residues: 534 loop : -1.03 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG y1132 TYR 0.008 0.001 TYR y1454 PHE 0.012 0.001 PHE y 456 TRP 0.029 0.001 TRP Y1291 HIS 0.003 0.001 HIS Y 743 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.20 (33269) covalent geometry : angle 0.63727 / 0.35 (45407) hydrogen bonds : bond 0.14127 / 9.30 ( 1269) hydrogen bonds : angle 5.59703 / 3.99 ( 3546) metal coordination : bond 0.00873 / 0.60 ( 40) metal coordination : angle 13.91573 / 10.32 ( 54) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 3311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 152 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 268 LEU cc_start: 0.9630 (mt) cc_final: 0.9332 (tt) REVERT: Y 660 ASP cc_start: 0.9378 (m-30) cc_final: 0.9112 (m-30) REVERT: Y 822 LEU cc_start: 0.9648 (OUTLIER) cc_final: 0.9307 (mm) REVERT: Y 891 MET cc_start: 0.8469 (tpp) cc_final: 0.8042 (tpp) REVERT: Y 1213 PHE cc_start: 0.9052 (OUTLIER) cc_final: 0.8767 (t80) REVERT: Y 1813 MET cc_start: 0.9033 (mmm) cc_final: 0.8557 (mmm) REVERT: Y 1903 ASN cc_start: 0.9472 (OUTLIER) cc_final: 0.8816 (p0) REVERT: Y 1971 MET cc_start: 0.6756 (mmp) cc_final: 0.6501 (mmp) REVERT: Y 1977 LEU cc_start: 0.9493 (mt) cc_final: 0.9218 (tt) REVERT: Y 2045 PHE cc_start: 0.8942 (m-80) cc_final: 0.8513 (m-80) REVERT: y 65 MET cc_start: 0.8319 (tmm) cc_final: 0.7995 (ptm) REVERT: y 244 MET cc_start: 0.8336 (ppp) cc_final: 0.8068 (ppp) REVERT: y 827 TYR cc_start: 0.8648 (m-80) cc_final: 0.8238 (m-10) REVERT: y 1089 LYS cc_start: 0.9665 (pptt) cc_final: 0.9408 (pptt) REVERT: y 1114 MET cc_start: 0.5349 (tpp) cc_final: 0.4646 (ptp) REVERT: y 1120 ASN cc_start: 0.9128 (OUTLIER) cc_final: 0.8899 (p0) REVERT: y 1400 MET cc_start: 0.7121 (pmm) cc_final: 0.6787 (pmm) REVERT: y 1523 TYR cc_start: 0.8344 (m-80) cc_final: 0.7730 (m-80) REVERT: y 1581 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8524 (mm) outliers start: 55 outliers final: 46 residues processed: 194 average time/residue: 0.1664 time to fit residues: 56.7474 Evaluate side-chains 198 residues out of total 3311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 147 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: [197, 388, 215, 20, 132, 261, 248, 207, 155, 244, 183] chunk 197 optimal weight: 0.5980 chunk 388 optimal weight: 50.0000 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 0.0010 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 8.9990 overall best weight: 2.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Y 4 GLN Y 194 GLN Y 404 GLN ** Y 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 569 ASN ** Y 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 748 GLN ** Y 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 893 GLN ** Y1083 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y1467 GLN ** Y1521 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y1621 HIS ** Y1689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y1738 ASN Y1749 ASN ** Y2006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y2085 ASN y 221 ASN ** y 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 751 GLN y 797 GLN ** y 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y1075 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y1121 ASN ** y1635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y1727 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.061630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.043563 restraints weight = 301382.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.044894 restraints weight = 171179.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.045737 restraints weight = 117829.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.046307 restraints weight = 92194.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.046643 restraints weight = 78564.608| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 33309 Z= 0.158 Angle : 0.793 37.897 45461 Z= 0.336 Chirality : 0.042 0.204 4954 Planarity : 0.005 0.092 5654 Dihedral : 14.722 156.467 5113 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.71 % Favored : 95.27 % Rotamer: Outliers : 0.12 % Allowed : 3.23 % Favored : 96.65 % 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 (0.13), residues: 3868 helix: 0.83 (0.13), residues: 1524 sheet: -0.60 (0.22), residues: 544 loop : -1.08 (0.15), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG Y1804 TYR 0.029 0.001 TYR y 182 PHE 0.035 0.002 PHE Y1213 TRP 0.049 0.002 TRP y 101 HIS 0.011 0.001 HIS Y1689 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.16 (33269) covalent geometry : angle 0.63142 / 0.32 (45407) hydrogen bonds : bond 0.04568 / 2.94 ( 1269) hydrogen bonds : angle 5.10999 / 3.64 ( 3546) metal coordination : bond 0.01365 / 0.93 ( 40) metal coordination : angle 13.92223 / 10.46 ( 54) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 3311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 191 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: symmetry clash REVERT: Y 4 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7892 (pp30) REVERT: Y 268 LEU cc_start: 0.9596 (mt) cc_final: 0.9344 (tt) REVERT: Y 660 ASP cc_start: 0.9313 (m-30) cc_final: 0.9075 (m-30) REVERT: Y 891 MET cc_start: 0.8424 (tpp) cc_final: 0.8062 (tpp) REVERT: Y 1105 MET cc_start: 0.8960 (ppp) cc_final: 0.8720 (tmm) REVERT: Y 1467 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.7827 (pp30) REVERT: Y 1619 LEU cc_start: 0.9624 (tp) cc_final: 0.9411 (tp) REVERT: Y 1971 MET cc_start: 0.6638 (mmp) cc_final: 0.6414 (mmp) REVERT: Y 2045 PHE cc_start: 0.8913 (m-80) cc_final: 0.8443 (m-80) REVERT: y 38 LEU cc_start: 0.9499 (mt) cc_final: 0.9154 (pp) REVERT: y 244 MET cc_start: 0.8583 (ppp) cc_final: 0.8362 (ppp) REVERT: y 406 LEU cc_start: 0.9281 (mt) cc_final: 0.8812 (tt) REVERT: y 409 MET cc_start: 0.8319 (mpp) cc_final: 0.7828 (mpp) REVERT: y 662 ASP cc_start: 0.9336 (t70) cc_final: 0.9040 (t0) REVERT: y 827 TYR cc_start: 0.8987 (m-80) cc_final: 0.8492 (m-10) REVERT: y 1400 MET cc_start: 0.7724 (pmm) cc_final: 0.7410 (pmm) REVERT: y 1523 TYR cc_start: 0.8687 (m-80) cc_final: 0.8243 (m-80) outliers start: 4 outliers final: 1 residues processed: 195 average time/residue: 0.1822 time to fit residues: 60.1599 Evaluate side-chains 145 residues out of total 3311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 142 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: [341, 71, 101, 28, 84, 97, 332, 72, 23, 102, 316] chunk 341 optimal weight: 8.9990 chunk 71 optimal weight: 10.0000 chunk 101 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 84 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 chunk 332 optimal weight: 5.9990 chunk 72 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 chunk 316 optimal weight: 5.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Y 4 GLN Y 465 GLN Y 698 GLN ** Y 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1083 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1521 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y1535 GLN ** Y1689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 751 GLN ** y 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y1075 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y1087 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y1131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y1539 GLN y1727 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.064922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.048075 restraints weight = 325609.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.049317 restraints weight = 174735.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.050266 restraints weight = 116965.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.050845 restraints weight = 90669.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.051052 restraints weight = 77660.950| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 33309 Z= 0.139 Angle : 0.758 37.607 45461 Z= 0.315 Chirality : 0.041 0.213 4954 Planarity : 0.004 0.065 5654 Dihedral : 14.530 157.530 5113 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.42 % Favored : 95.55 % Rotamer: Outliers : 0.12 % Allowed : 3.29 % Favored : 96.59 % 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: -0.37 (0.14), residues: 3868 helix: 0.81 (0.13), residues: 1526 sheet: -0.55 (0.21), residues: 546 loop : -1.03 (0.15), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG y1132 TYR 0.020 0.001 TYR y 182 PHE 0.017 0.001 PHE y 125 TRP 0.039 0.001 TRP Y 764 HIS 0.007 0.001 HIS Y1689 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 (33269) covalent geometry : angle 0.59022 / 0.30 (45407) hydrogen bonds : bond 0.04097 / 2.65 ( 1269) hydrogen bonds : angle 4.91818 / 3.52 ( 3546) metal coordination : bond 0.01284 / 0.97 ( 40) metal coordination : angle 13.82677 / 10.37 ( 54) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 3311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 181 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 4 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7921 (pp30) REVERT: Y 224 MET cc_start: 0.9182 (mtt) cc_final: 0.8963 (mtt) REVERT: Y 268 LEU cc_start: 0.9599 (mt) cc_final: 0.9353 (tt) REVERT: Y 424 MET cc_start: 0.8527 (tmm) cc_final: 0.8198 (tmm) REVERT: Y 660 ASP cc_start: 0.9320 (m-30) cc_final: 0.9077 (m-30) REVERT: Y 891 MET cc_start: 0.8474 (tpp) cc_final: 0.8133 (tpp) REVERT: Y 1589 MET cc_start: 0.8826 (ppp) cc_final: 0.8075 (ppp) REVERT: Y 2045 PHE cc_start: 0.8727 (m-80) cc_final: 0.8303 (m-80) REVERT: y 38 LEU cc_start: 0.9461 (mt) cc_final: 0.9103 (pp) REVERT: y 244 MET cc_start: 0.8833 (ppp) cc_final: 0.8631 (ppp) REVERT: y 406 LEU cc_start: 0.9289 (mt) cc_final: 0.8973 (tt) REVERT: y 806 GLU cc_start: 0.8586 (tp30) cc_final: 0.8294 (tp30) REVERT: y 1119 MET cc_start: 0.8763 (mmt) cc_final: 0.8413 (mmm) REVERT: y 1281 ILE cc_start: 0.7845 (mm) cc_final: 0.7620 (mm) REVERT: y 1400 MET cc_start: 0.8036 (pmm) cc_final: 0.7806 (pmm) REVERT: y 1523 TYR cc_start: 0.8704 (m-80) cc_final: 0.8070 (m-80) outliers start: 4 outliers final: 0 residues processed: 184 average time/residue: 0.1742 time to fit residues: 54.9487 Evaluate side-chains 143 residues out of total 3311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 142 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: [370, 115, 165, 214, 212, 381, 178, 33, 304, 330, 236] chunk 370 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 165 optimal weight: 5.9990 chunk 214 optimal weight: 2.9990 chunk 212 optimal weight: 30.0000 chunk 381 optimal weight: 20.0000 chunk 178 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 304 optimal weight: 0.4980 chunk 330 optimal weight: 3.9990 chunk 236 optimal weight: 30.0000 overall best weight: 3.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Y 4 GLN Y 404 GLN Y 698 GLN ** Y 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1083 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y1128 ASN ** Y1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1521 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y1819 GLN ** y 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 751 GLN ** y 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y1075 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y1131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y1727 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.060661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.042675 restraints weight = 303596.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.043982 restraints weight = 172813.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.044810 restraints weight = 118897.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.045354 restraints weight = 93373.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.045688 restraints weight = 79966.442| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 33309 Z= 0.180 Angle : 0.765 37.714 45461 Z= 0.322 Chirality : 0.040 0.196 4954 Planarity : 0.004 0.057 5654 Dihedral : 14.403 161.446 5113 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.02 % Favored : 94.96 % Rotamer: Outliers : 0.06 % Allowed : 3.20 % Favored : 96.74 % 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 (0.13), residues: 3868 helix: 0.80 (0.13), residues: 1519 sheet: -0.69 (0.22), residues: 516 loop : -1.06 (0.15), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG y1138 TYR 0.011 0.001 TYR y 671 PHE 0.022 0.001 PHE y 125 TRP 0.059 0.002 TRP y 101 HIS 0.006 0.001 HIS y 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.18 (33269) covalent geometry : angle 0.60030 / 0.31 (45407) hydrogen bonds : bond 0.03961 / 2.57 ( 1269) hydrogen bonds : angle 4.91066 / 3.53 ( 3546) metal coordination : bond 0.01274 / 0.97 ( 40) metal coordination : angle 13.75431 / 10.38 ( 54) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 3311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 174 time to evaluate : 1.215 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Y 4 GLN cc_start: 0.8111 (OUTLIER) cc_final: 0.7878 (pp30) REVERT: Y 224 MET cc_start: 0.9269 (mtt) cc_final: 0.8997 (mtt) REVERT: Y 268 LEU cc_start: 0.9622 (mt) cc_final: 0.9363 (tt) REVERT: Y 424 MET cc_start: 0.8565 (tmm) cc_final: 0.8280 (tmm) REVERT: Y 891 MET cc_start: 0.8526 (tpp) cc_final: 0.8195 (tpp) REVERT: Y 904 ARG cc_start: 0.6454 (mtt180) cc_final: 0.6030 (mtp180) REVERT: Y 1589 MET cc_start: 0.8760 (ppp) cc_final: 0.8096 (ppp) REVERT: y 38 LEU cc_start: 0.9533 (mt) cc_final: 0.9184 (pp) REVERT: y 244 MET cc_start: 0.8155 (ppp) cc_final: 0.7680 (ppp) REVERT: y 409 MET cc_start: 0.8314 (mpp) cc_final: 0.7792 (mpp) REVERT: y 781 MET cc_start: 0.9272 (mmp) cc_final: 0.8927 (mmp) REVERT: y 1400 MET cc_start: 0.7753 (pmm) cc_final: 0.7506 (pmm) REVERT: y 1523 TYR cc_start: 0.8644 (m-80) cc_final: 0.8018 (m-80) outliers start: 2 outliers final: 0 residues processed: 176 average time/residue: 0.1805 time to fit residues: 53.4089 Evaluate side-chains 133 residues out of total 3311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 132 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: [98, 341, 132, 214, 45, 251, 351, 42, 135, 37, 390] chunk 98 optimal weight: 10.0000 chunk 341 optimal weight: 2.9990 chunk 132 optimal weight: 9.9990 chunk 214 optimal weight: 6.9990 chunk 45 optimal weight: 0.0670 chunk 251 optimal weight: 9.9990 chunk 351 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 390 optimal weight: 50.0000 overall best weight: 3.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Y 4 GLN Y 698 GLN ** Y 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1083 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1521 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1996 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y2006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y1075 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y1087 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y1131 GLN y1698 HIS y1727 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.060544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.042560 restraints weight = 301935.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.043869 restraints weight = 171768.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.044679 restraints weight = 118270.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.045226 restraints weight = 92961.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.045557 restraints weight = 79539.215| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 33309 Z= 0.164 Angle : 0.755 37.453 45461 Z= 0.316 Chirality : 0.040 0.223 4954 Planarity : 0.004 0.059 5654 Dihedral : 14.340 164.762 5113 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.96 % Favored : 95.01 % Rotamer: Outliers : 0.06 % Allowed : 2.45 % Favored : 97.49 % 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 (0.13), residues: 3868 helix: 0.82 (0.13), residues: 1513 sheet: -0.76 (0.23), residues: 496 loop : -1.05 (0.15), residues: 1859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG y 413 TYR 0.015 0.001 TYR y1070 PHE 0.031 0.002 PHE y1460 TRP 0.039 0.001 TRP y 101 HIS 0.005 0.001 HIS y 915 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (33269) covalent geometry : angle 0.59097 / 0.30 (45407) hydrogen bonds : bond 0.03876 / 2.53 ( 1269) hydrogen bonds : angle 4.84716 / 3.49 ( 3546) metal coordination : bond 0.01199 / 0.95 ( 40) metal coordination : angle 13.66827 / 10.33 ( 54) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 3311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 174 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 4 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7889 (pp30) REVERT: Y 224 MET cc_start: 0.9330 (mtt) cc_final: 0.9080 (mtt) REVERT: Y 268 LEU cc_start: 0.9623 (mt) cc_final: 0.9356 (tt) REVERT: Y 891 MET cc_start: 0.8517 (tpp) cc_final: 0.8195 (tpp) REVERT: Y 904 ARG cc_start: 0.6587 (mtt180) cc_final: 0.6161 (mtp180) REVERT: Y 1589 MET cc_start: 0.8710 (ppp) cc_final: 0.8069 (ppp) REVERT: y 38 LEU cc_start: 0.9600 (mt) cc_final: 0.9301 (pp) REVERT: y 244 MET cc_start: 0.8051 (ppp) cc_final: 0.7507 (ppp) REVERT: y 272 MET cc_start: 0.8773 (tmm) cc_final: 0.8567 (tmm) REVERT: y 663 LYS cc_start: 0.9678 (mmtt) cc_final: 0.9457 (mmmm) REVERT: y 945 MET cc_start: 0.7696 (ptt) cc_final: 0.7366 (ptm) REVERT: y 1016 MET cc_start: 0.8926 (mmp) cc_final: 0.8422 (mmm) REVERT: y 1114 MET cc_start: 0.6400 (tpt) cc_final: 0.5401 (pmm) REVERT: y 1523 TYR cc_start: 0.8650 (m-80) cc_final: 0.8028 (m-80) outliers start: 2 outliers final: 0 residues processed: 176 average time/residue: 0.1712 time to fit residues: 52.0359 Evaluate side-chains 138 residues out of total 3311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 137 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: [342, 365, 155, 304, 165, 232, 7, 383, 318, 60, 199] chunk 342 optimal weight: 4.9990 chunk 365 optimal weight: 20.0000 chunk 155 optimal weight: 10.0000 chunk 304 optimal weight: 0.9980 chunk 165 optimal weight: 3.9990 chunk 232 optimal weight: 8.9990 chunk 7 optimal weight: 2.9990 chunk 383 optimal weight: 0.9990 chunk 318 optimal weight: 40.0000 chunk 60 optimal weight: 10.0000 chunk 199 optimal weight: 9.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Y 4 GLN Y 698 GLN ** Y 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1083 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1521 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1996 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y1075 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y1087 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y1131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y1264 GLN y1727 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.060632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.042659 restraints weight = 301474.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.043941 restraints weight = 171660.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.044787 restraints weight = 118410.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.045321 restraints weight = 92766.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.045652 restraints weight = 79465.632| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 33309 Z= 0.146 Angle : 0.755 37.257 45461 Z= 0.313 Chirality : 0.040 0.240 4954 Planarity : 0.004 0.056 5654 Dihedral : 14.265 168.859 5113 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.12 % Favored : 94.86 % Rotamer: Outliers : 0.03 % Allowed : 2.17 % Favored : 97.80 % 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: -0.47 (0.13), residues: 3868 helix: 0.79 (0.13), residues: 1516 sheet: -0.88 (0.22), residues: 515 loop : -1.04 (0.15), residues: 1837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG y 413 TYR 0.012 0.001 TYR y1070 PHE 0.026 0.001 PHE y1460 TRP 0.033 0.001 TRP y 101 HIS 0.005 0.001 HIS Y1554 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.15 (33269) covalent geometry : angle 0.58725 / 0.30 (45407) hydrogen bonds : bond 0.03754 / 2.45 ( 1269) hydrogen bonds : angle 4.83103 / 3.49 ( 3546) metal coordination : bond 0.01250 / 0.97 ( 40) metal coordination : angle 13.76668 / 10.33 ( 54) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 3311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 176 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 4 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7928 (pp30) REVERT: Y 224 MET cc_start: 0.9352 (mtt) cc_final: 0.9062 (mtt) REVERT: Y 268 LEU cc_start: 0.9627 (mt) cc_final: 0.9360 (tt) REVERT: Y 424 MET cc_start: 0.8741 (tmm) cc_final: 0.8450 (tmm) REVERT: Y 660 ASP cc_start: 0.9344 (m-30) cc_final: 0.9055 (m-30) REVERT: Y 891 MET cc_start: 0.8517 (tpp) cc_final: 0.8202 (tpp) REVERT: Y 904 ARG cc_start: 0.6774 (mtt180) cc_final: 0.6427 (mtp180) REVERT: Y 1589 MET cc_start: 0.8700 (ppp) cc_final: 0.8044 (ppp) REVERT: y 38 LEU cc_start: 0.9589 (mt) cc_final: 0.9293 (pp) REVERT: y 244 MET cc_start: 0.7997 (ppp) cc_final: 0.7537 (ppp) REVERT: y 1016 MET cc_start: 0.8938 (mmp) cc_final: 0.8459 (mmm) REVERT: y 1114 MET cc_start: 0.6300 (tpt) cc_final: 0.5355 (pmm) REVERT: y 1334 PHE cc_start: 0.9075 (t80) cc_final: 0.8806 (t80) REVERT: y 1523 TYR cc_start: 0.8646 (m-80) cc_final: 0.8047 (m-80) REVERT: y 1568 ASN cc_start: 0.8458 (t0) cc_final: 0.8137 (p0) outliers start: 1 outliers final: 0 residues processed: 177 average time/residue: 0.1758 time to fit residues: 53.9631 Evaluate side-chains 142 residues out of total 3311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 141 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: [106, 42, 123, 365, 232, 298, 78, 47, 264, 302, 297] chunk 106 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 123 optimal weight: 8.9990 chunk 365 optimal weight: 20.0000 chunk 232 optimal weight: 10.0000 chunk 298 optimal weight: 8.9990 chunk 78 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 264 optimal weight: 6.9990 chunk 302 optimal weight: 10.0000 chunk 297 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Y 4 GLN ** Y 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 698 GLN ** Y 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 770 GLN ** Y1083 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1521 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y1969 GLN ** y 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 770 GLN ** y 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y1075 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y1087 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y1097 ASN ** y1131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y1469 HIS y1667 HIS y1727 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.059152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.041142 restraints weight = 311124.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 73)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.042399 restraints weight = 177855.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.043199 restraints weight = 123222.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.043716 restraints weight = 97007.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.044031 restraints weight = 83582.999| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 33309 Z= 0.257 Angle : 0.841 40.604 45461 Z= 0.366 Chirality : 0.042 0.225 4954 Planarity : 0.005 0.106 5654 Dihedral : 14.314 168.469 5113 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 19.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.79 % Favored : 94.18 % Rotamer: Outliers : 0.03 % Allowed : 2.02 % Favored : 97.95 % 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: -0.72 (0.13), residues: 3868 helix: 0.56 (0.13), residues: 1522 sheet: -1.15 (0.22), residues: 515 loop : -1.11 (0.15), residues: 1831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG Y1841 TYR 0.019 0.002 TYR Y 804 PHE 0.023 0.002 PHE y 621 TRP 0.079 0.002 TRP y 101 HIS 0.013 0.002 HIS y 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00536 / 0.26 (33269) covalent geometry : angle 0.68898 / 0.36 (45407) hydrogen bonds : bond 0.04151 / 2.73 ( 1269) hydrogen bonds : angle 5.08495 / 3.66 ( 3546) metal coordination : bond 0.01671 / 1.22 ( 40) metal coordination : angle 14.01321 / 10.68 ( 54) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 3311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 162 time to evaluate : 1.035 Fit side-chains revert: symmetry clash REVERT: Y 4 GLN cc_start: 0.8232 (OUTLIER) cc_final: 0.7923 (pp30) REVERT: Y 218 MET cc_start: 0.9209 (ttt) cc_final: 0.8670 (tpp) REVERT: Y 224 MET cc_start: 0.9375 (mtt) cc_final: 0.9102 (mtt) REVERT: Y 268 LEU cc_start: 0.9657 (mt) cc_final: 0.9338 (tt) REVERT: Y 891 MET cc_start: 0.8605 (tpp) cc_final: 0.8297 (tpp) REVERT: Y 904 ARG cc_start: 0.6923 (mtt180) cc_final: 0.6671 (mtp180) REVERT: Y 1589 MET cc_start: 0.8692 (ppp) cc_final: 0.8067 (ppp) REVERT: y 38 LEU cc_start: 0.9655 (mt) cc_final: 0.9374 (pp) REVERT: y 244 MET cc_start: 0.8046 (ppp) cc_final: 0.7628 (ppp) REVERT: y 409 MET cc_start: 0.8183 (mpp) cc_final: 0.7759 (mpp) REVERT: y 663 LYS cc_start: 0.9721 (mmtt) cc_final: 0.9332 (mmmm) REVERT: y 1114 MET cc_start: 0.6380 (tpt) cc_final: 0.5250 (pmm) REVERT: y 1281 ILE cc_start: 0.8030 (mm) cc_final: 0.7770 (mm) REVERT: y 1523 TYR cc_start: 0.8686 (m-80) cc_final: 0.8330 (m-10) outliers start: 1 outliers final: 0 residues processed: 163 average time/residue: 0.1728 time to fit residues: 48.6068 Evaluate side-chains 134 residues out of total 3311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 133 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: [44, 255, 264, 151, 289, 186, 266, 23, 208, 302, 333] chunk 44 optimal weight: 0.0270 chunk 255 optimal weight: 20.0000 chunk 264 optimal weight: 4.9990 chunk 151 optimal weight: 30.0000 chunk 289 optimal weight: 0.2980 chunk 186 optimal weight: 6.9990 chunk 266 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 208 optimal weight: 9.9990 chunk 302 optimal weight: 9.9990 chunk 333 optimal weight: 1.9990 overall best weight: 1.8644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Y 4 GLN ** Y 688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 698 GLN ** Y 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1083 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1521 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y2005 GLN ** y 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y1075 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y1087 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y1131 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 = 0.3696 r_free = 0.3696 target = 0.060368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.042514 restraints weight = 301921.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.043791 restraints weight = 170726.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.044648 restraints weight = 117209.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.045188 restraints weight = 91773.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.045522 restraints weight = 78404.061| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 33309 Z= 0.131 Angle : 0.766 37.086 45461 Z= 0.319 Chirality : 0.041 0.263 4954 Planarity : 0.004 0.059 5654 Dihedral : 14.255 172.912 5113 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.68 % Favored : 95.29 % Rotamer: Outliers : 0.03 % Allowed : 1.09 % Favored : 98.88 % 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: -0.56 (0.14), residues: 3868 helix: 0.69 (0.13), residues: 1516 sheet: -1.09 (0.22), residues: 520 loop : -1.00 (0.15), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG y 413 TYR 0.018 0.001 TYR Y 804 PHE 0.019 0.001 PHE y1460 TRP 0.073 0.002 TRP Y 101 HIS 0.016 0.001 HIS Y1689 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (33269) covalent geometry : angle 0.60156 / 0.31 (45407) hydrogen bonds : bond 0.03750 / 2.45 ( 1269) hydrogen bonds : angle 4.83418 / 3.48 ( 3546) metal coordination : bond 0.01142 / 0.93 ( 40) metal coordination : angle 13.76385 / 10.41 ( 54) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 3311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 177 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 224 MET cc_start: 0.9110 (mtt) cc_final: 0.8787 (mtt) REVERT: Y 268 LEU cc_start: 0.9531 (mt) cc_final: 0.9266 (tt) REVERT: Y 891 MET cc_start: 0.8755 (tpp) cc_final: 0.8470 (tpp) REVERT: Y 1589 MET cc_start: 0.8546 (ppp) cc_final: 0.8123 (ppp) REVERT: y 38 LEU cc_start: 0.9578 (mt) cc_final: 0.9243 (pp) REVERT: y 244 MET cc_start: 0.7747 (ppp) cc_final: 0.7265 (ppp) REVERT: y 272 MET cc_start: 0.8807 (tmm) cc_final: 0.8572 (tmm) REVERT: y 409 MET cc_start: 0.8436 (mpp) cc_final: 0.7827 (mpp) REVERT: y 945 MET cc_start: 0.7826 (ptp) cc_final: 0.7426 (ttp) REVERT: y 1016 MET cc_start: 0.8613 (mmp) cc_final: 0.8345 (mmm) REVERT: y 1114 MET cc_start: 0.5747 (tpt) cc_final: 0.5199 (pmm) REVERT: y 1334 PHE cc_start: 0.8947 (t80) cc_final: 0.8724 (t80) REVERT: y 1523 TYR cc_start: 0.8555 (m-80) cc_final: 0.7992 (m-10) outliers start: 1 outliers final: 0 residues processed: 178 average time/residue: 0.1734 time to fit residues: 53.2310 Evaluate side-chains 138 residues out of total 3311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: [205, 294, 95, 196, 387, 155, 237, 67, 56, 263, 350] chunk 205 optimal weight: 1.9990 chunk 294 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 196 optimal weight: 5.9990 chunk 387 optimal weight: 50.0000 chunk 155 optimal weight: 7.9990 chunk 237 optimal weight: 5.9990 chunk 67 optimal weight: 20.0000 chunk 56 optimal weight: 5.9990 chunk 263 optimal weight: 0.0270 chunk 350 optimal weight: 10.0000 overall best weight: 2.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Y 4 GLN ** Y 688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 698 GLN ** Y 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1083 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1521 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y2005 GLN ** y 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y1075 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y1087 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y1131 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 = 0.3693 r_free = 0.3693 target = 0.060116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.042122 restraints weight = 301278.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.043405 restraints weight = 171095.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.044236 restraints weight = 117824.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.044752 restraints weight = 92430.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.045089 restraints weight = 79355.684| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 33309 Z= 0.151 Angle : 0.766 38.063 45461 Z= 0.321 Chirality : 0.041 0.251 4954 Planarity : 0.004 0.070 5654 Dihedral : 14.232 176.667 5113 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.09 % Favored : 94.88 % Rotamer: Outliers : 0.03 % Allowed : 0.85 % Favored : 99.12 % 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: -0.53 (0.14), residues: 3868 helix: 0.73 (0.13), residues: 1510 sheet: -1.06 (0.22), residues: 509 loop : -1.01 (0.15), residues: 1849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG y 413 TYR 0.021 0.001 TYR Y 804 PHE 0.019 0.001 PHE Y1213 TRP 0.066 0.002 TRP Y 764 HIS 0.021 0.001 HIS Y1689 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (33269) covalent geometry : angle 0.60409 / 0.31 (45407) hydrogen bonds : bond 0.03717 / 2.43 ( 1269) hydrogen bonds : angle 4.84148 / 3.50 ( 3546) metal coordination : bond 0.01225 / 1.00 ( 40) metal coordination : angle 13.68311 / 10.40 ( 54) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 3311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 176 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 4 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.7856 (pp30) REVERT: Y 224 MET cc_start: 0.9190 (mtt) cc_final: 0.8039 (mtt) REVERT: Y 268 LEU cc_start: 0.9532 (mt) cc_final: 0.9278 (tt) REVERT: Y 891 MET cc_start: 0.8705 (tpp) cc_final: 0.8399 (tpp) REVERT: Y 1119 MET cc_start: 0.8316 (mmt) cc_final: 0.8101 (mmt) REVERT: Y 1589 MET cc_start: 0.8596 (ppp) cc_final: 0.8182 (ppp) REVERT: y 38 LEU cc_start: 0.9578 (mt) cc_final: 0.9262 (pp) REVERT: y 244 MET cc_start: 0.7915 (ppp) cc_final: 0.7446 (ppp) REVERT: y 272 MET cc_start: 0.8751 (tmm) cc_final: 0.8524 (tmm) REVERT: y 409 MET cc_start: 0.8451 (mpp) cc_final: 0.7826 (mpp) REVERT: y 945 MET cc_start: 0.8026 (ptp) cc_final: 0.7633 (ttp) REVERT: y 1016 MET cc_start: 0.8686 (mmp) cc_final: 0.8360 (mmm) REVERT: y 1114 MET cc_start: 0.5911 (tpt) cc_final: 0.5377 (pmm) REVERT: y 1334 PHE cc_start: 0.9013 (t80) cc_final: 0.8794 (t80) REVERT: y 1523 TYR cc_start: 0.8575 (m-80) cc_final: 0.8196 (m-10) outliers start: 1 outliers final: 0 residues processed: 177 average time/residue: 0.1702 time to fit residues: 52.1606 Evaluate side-chains 138 residues out of total 3311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 137 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: [365, 317, 74, 15, 51, 141, 240, 265, 239, 234, 382] chunk 365 optimal weight: 8.9990 chunk 317 optimal weight: 8.9990 chunk 74 optimal weight: 0.9990 chunk 15 optimal weight: 0.0670 chunk 51 optimal weight: 0.9990 chunk 141 optimal weight: 5.9990 chunk 240 optimal weight: 6.9990 chunk 265 optimal weight: 20.0000 chunk 239 optimal weight: 20.0000 chunk 234 optimal weight: 5.9990 chunk 382 optimal weight: 6.9990 overall best weight: 2.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Y 4 GLN ** Y 688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 698 GLN ** Y 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1083 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y2005 GLN ** y 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y1075 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y1131 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 = 0.3693 r_free = 0.3693 target = 0.060147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.042206 restraints weight = 305312.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.043494 restraints weight = 172598.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.044339 restraints weight = 118643.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.044875 restraints weight = 92704.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.045215 restraints weight = 79282.813| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 33309 Z= 0.148 Angle : 0.770 37.868 45461 Z= 0.324 Chirality : 0.041 0.256 4954 Planarity : 0.004 0.068 5654 Dihedral : 14.223 179.865 5113 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.99 % Favored : 94.98 % Rotamer: Outliers : 0.03 % Allowed : 0.24 % Favored : 99.73 % 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: -0.52 (0.14), residues: 3868 helix: 0.76 (0.13), residues: 1503 sheet: -1.09 (0.22), residues: 505 loop : -1.00 (0.15), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG y 413 TYR 0.017 0.001 TYR Y 804 PHE 0.021 0.001 PHE Y1213 TRP 0.055 0.002 TRP Y 101 HIS 0.019 0.001 HIS Y1689 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 (33269) covalent geometry : angle 0.61064 / 0.31 (45407) hydrogen bonds : bond 0.03701 / 2.43 ( 1269) hydrogen bonds : angle 4.84337 / 3.51 ( 3546) metal coordination : bond 0.01211 / 0.99 ( 40) metal coordination : angle 13.63697 / 10.36 ( 54) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7736 Ramachandran restraints generated. 3868 Oldfield, 0 Emsley, 3868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 3311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 175 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 4 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.8102 (pp30) REVERT: Y 71 MET cc_start: 0.8827 (ptm) cc_final: 0.8581 (ptm) REVERT: Y 224 MET cc_start: 0.9112 (mtt) cc_final: 0.8543 (mtt) REVERT: Y 268 LEU cc_start: 0.9625 (mt) cc_final: 0.9356 (tt) REVERT: Y 891 MET cc_start: 0.8595 (tpp) cc_final: 0.8287 (tpp) REVERT: Y 1119 MET cc_start: 0.8663 (mmt) cc_final: 0.8367 (mmt) REVERT: Y 1589 MET cc_start: 0.8710 (ppp) cc_final: 0.8204 (ppp) REVERT: y 38 LEU cc_start: 0.9627 (mt) cc_final: 0.9336 (pp) REVERT: y 244 MET cc_start: 0.8077 (ppp) cc_final: 0.7640 (ppp) REVERT: y 431 LEU cc_start: 0.9546 (tp) cc_final: 0.9258 (tp) REVERT: y 945 MET cc_start: 0.8190 (ptp) cc_final: 0.7834 (ttp) REVERT: y 1016 MET cc_start: 0.8910 (mmp) cc_final: 0.8342 (mmm) REVERT: y 1072 LEU cc_start: 0.8893 (tp) cc_final: 0.8469 (tp) REVERT: y 1114 MET cc_start: 0.6196 (tpt) cc_final: 0.5417 (pmm) REVERT: y 1334 PHE cc_start: 0.9138 (t80) cc_final: 0.8886 (t80) REVERT: y 1523 TYR cc_start: 0.8737 (m-80) cc_final: 0.8359 (m-10) outliers start: 1 outliers final: 0 residues processed: 176 average time/residue: 0.1713 time to fit residues: 52.1026 Evaluate side-chains 134 residues out of total 3311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 133 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: [279, 222, 118, 7, 315, 68, 281, 89, 37, 121, 302] chunk 279 optimal weight: 4.9990 chunk 222 optimal weight: 40.0000 chunk 118 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 315 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 281 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 121 optimal weight: 8.9990 chunk 302 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Y 4 GLN ** Y 688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 698 GLN ** Y 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1083 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y2005 GLN y 14 GLN ** y 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y1075 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y1087 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y1131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.060056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.042154 restraints weight = 303710.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.043422 restraints weight = 172178.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.044285 restraints weight = 118566.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.044798 restraints weight = 92670.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.045143 restraints weight = 79264.288| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 33309 Z= 0.147 Angle : 0.771 37.839 45461 Z= 0.324 Chirality : 0.041 0.251 4954 Planarity : 0.004 0.059 5654 Dihedral : 14.192 176.938 5113 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.02 % Favored : 94.96 % Rotamer: Outliers : 0.03 % Allowed : 0.54 % Favored : 99.43 % 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: -0.52 (0.14), residues: 3868 helix: 0.77 (0.13), residues: 1502 sheet: -1.14 (0.22), residues: 502 loop : -0.99 (0.15), residues: 1864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG y 413 TYR 0.020 0.001 TYR y 671 PHE 0.036 0.001 PHE y 621 TRP 0.052 0.002 TRP Y 101 HIS 0.017 0.001 HIS Y1689 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.15 (33269) covalent geometry : angle 0.61199 / 0.31 (45407) hydrogen bonds : bond 0.03705 / 2.42 ( 1269) hydrogen bonds : angle 4.85274 / 3.52 ( 3546) metal coordination : bond 0.01197 / 0.98 ( 40) metal coordination : angle 13.60690 / 10.34 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6093.36 seconds wall clock time: 105 minutes 50.35 seconds (6350.35 seconds total)