Starting phenix.real_space_refine on Sun Oct 25 17:06:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9tu7_56251/10_2026/9tu7_56251.cif Found real_map, /net/cci-nas-00/data/ceres_data/9tu7_56251/10_2026/9tu7_56251.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9tu7_56251/10_2026/9tu7_56251.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9tu7_56251/10_2026/9tu7_56251.map" model { file = "/net/cci-nas-00/data/ceres_data/9tu7_56251/10_2026/9tu7_56251.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9tu7_56251/10_2026/9tu7_56251.cif" } resolution = 2.9 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= 0.002 sd= 0.015 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 5 6.06 5 P 46 5.49 5 S 69 5.16 5 C 10477 2.51 5 N 3025 2.21 5 O 3233 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.02s 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: 16855 Number of models: 1 Model: "" Number of chains: 4 Chain: "I" Number of atoms: 613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 613 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "Y" Number of atoms: 15937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2003, 15937 Classifications: {'peptide': 2003} Link IDs: {'PTRANS': 94, 'TRANS': 1908} Chain breaks: 4 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: "Y" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 36 Unusual residues: {' ZN': 5, 'AGS': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4088 SG CYS Y 437 29.375 51.205 104.488 1.00119.14 S ATOM 4126 SG CYS Y 442 29.932 47.743 106.314 1.00113.79 S ATOM 4347 SG CYS Y 467 29.952 47.809 102.680 1.00119.66 S ATOM 4361 SG CYS Y 469 26.726 48.603 104.631 1.00124.41 S ATOM 4436 SG CYS Y 479 42.125 69.476 106.186 1.00114.25 S ATOM 4452 SG CYS Y 482 42.821 67.959 109.542 1.00117.83 S ATOM 5213 SG CYS Y 586 39.464 69.528 109.017 1.00118.84 S ATOM 5232 SG CYS Y 589 42.437 71.754 109.273 1.00127.34 S ATOM 11263 SG CYS Y1423 27.640 76.429 60.364 1.00118.68 S ATOM 11289 SG CYS Y1426 27.386 72.981 58.729 1.00123.22 S ATOM 11373 SG CYS Y1439 28.852 75.789 56.758 1.00125.43 S ATOM 11395 SG CYS Y1442 25.155 75.825 57.590 1.00130.44 S ATOM 12068 SG CYS Y1526 57.690 90.786 66.532 1.00104.52 S ATOM 12088 SG CYS Y1529 60.542 88.709 67.875 1.00 98.49 S ATOM 12422 SG CYS Y1571 61.208 92.275 66.418 1.00122.31 S ATOM 13285 SG CYS Y1681 34.760 40.934 75.769 1.00142.80 S ATOM 13297 SG CYS Y1683 34.456 43.967 78.057 1.00139.75 S ATOM 13331 SG CYS Y1687 37.879 42.575 76.794 1.00135.54 S ATOM 13357 SG CYS Y1690 35.641 44.680 74.677 1.00134.11 S Time building chain proxies: 3.18, per 1000 atoms: 0.19 Number of scatterers: 16855 At special positions: 0 Unit cell: (105.387, 120.917, 144.213, 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 5 29.99 S 69 16.00 P 46 15.00 O 3233 8.00 N 3025 7.00 C 10477 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: 1.46 Conformation dependent library (CDL) restraints added in 722.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN Y2201 " pdb="ZN ZN Y2201 " - pdb=" SG CYS Y 442 " pdb="ZN ZN Y2201 " - pdb=" SG CYS Y 469 " pdb="ZN ZN Y2201 " - pdb=" SG CYS Y 467 " pdb="ZN ZN Y2201 " - pdb=" SG CYS Y 437 " pdb=" ZN Y2202 " pdb="ZN ZN Y2202 " - pdb=" SG CYS Y 482 " pdb="ZN ZN Y2202 " - pdb=" SG CYS Y 586 " pdb="ZN ZN Y2202 " - pdb=" SG CYS Y 589 " pdb="ZN ZN Y2202 " - pdb=" SG CYS Y 479 " pdb=" ZN Y2203 " pdb="ZN ZN Y2203 " - pdb=" SG CYS Y1426 " pdb="ZN ZN Y2203 " - pdb=" SG CYS Y1442 " pdb="ZN ZN Y2203 " - pdb=" SG CYS Y1439 " pdb="ZN ZN Y2203 " - pdb=" SG CYS Y1423 " pdb=" ZN Y2204 " pdb="ZN ZN Y2204 " - pdb=" NE2 HIS Y1554 " pdb="ZN ZN Y2204 " - pdb=" SG CYS Y1526 " pdb="ZN ZN Y2204 " - pdb=" SG CYS Y1529 " pdb="ZN ZN Y2204 " - pdb=" SG CYS Y1571 " pdb=" ZN Y2205 " pdb="ZN ZN Y2205 " - pdb=" SG CYS Y1687 " pdb="ZN ZN Y2205 " - pdb=" SG CYS Y1683 " pdb="ZN ZN Y2205 " - pdb=" SG CYS Y1690 " pdb="ZN ZN Y2205 " - pdb=" SG CYS Y1681 " Number of angles added : 27 3986 Ramachandran restraints generated. 1993 Oldfield, 0 Emsley, 1993 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3744 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 15 sheets defined 42.2% alpha, 9.5% beta 11 base pairs and 30 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'Y' and resid 7 through 28 removed outlier: 3.597A 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 70 through 75 Processing helix chain 'Y' and resid 80 through 87 Processing helix chain 'Y' and resid 94 through 108 removed outlier: 3.622A pdb=" N LYS Y 108 " --> pdb=" O ILE Y 104 " (cutoff:3.500A) Processing helix chain 'Y' and resid 120 through 141 Proline residue: Y 128 - end of helix Processing helix chain 'Y' and resid 155 through 171 removed outlier: 3.535A pdb=" N ILE Y 159 " --> pdb=" O LEU Y 155 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN Y 163 " --> pdb=" O ILE Y 159 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLU Y 164 " --> pdb=" O ASN Y 160 " (cutoff:3.500A) removed outlier: 4.478A 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: 3.789A pdb=" N ILE Y 238 " --> pdb=" O ASP Y 234 " (cutoff:3.500A) Processing helix chain 'Y' and resid 241 through 245 removed outlier: 3.925A pdb=" N MET Y 244 " --> pdb=" O SER Y 241 " (cutoff:3.500A) removed outlier: 4.583A 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 252 through 257 removed outlier: 4.005A pdb=" N ILE Y 257 " --> pdb=" O HIS Y 254 " (cutoff:3.500A) Processing helix chain 'Y' and resid 258 through 276 removed outlier: 3.684A 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 344 through 350 removed outlier: 3.848A pdb=" N LEU Y 348 " --> pdb=" O SER Y 344 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER Y 350 " --> pdb=" O THR Y 346 " (cutoff:3.500A) Processing helix chain 'Y' and resid 352 through 362 removed outlier: 3.988A 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: 4.147A 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: 3.752A pdb=" N ASN Y 450 " --> pdb=" O HIS Y 447 " (cutoff:3.500A) Processing helix chain 'Y' and resid 516 through 523 removed outlier: 3.716A pdb=" N TYR Y 520 " --> pdb=" O ASP Y 516 " (cutoff:3.500A) Processing helix chain 'Y' and resid 531 through 535 Processing helix chain 'Y' and resid 551 through 555 Processing helix chain 'Y' and resid 606 through 622 removed outlier: 3.517A pdb=" N PHE Y 610 " --> pdb=" O GLY Y 606 " (cutoff:3.500A) removed outlier: 3.563A 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 633 through 638 Processing helix chain 'Y' and resid 646 through 674 Processing helix chain 'Y' and resid 764 through 774 removed outlier: 3.707A pdb=" N GLY Y 773 " --> pdb=" O GLU Y 769 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N SER Y 774 " --> pdb=" O GLN Y 770 " (cutoff:3.500A) Processing helix chain 'Y' and resid 774 through 779 Processing helix chain 'Y' and resid 779 through 790 Processing helix chain 'Y' and resid 794 through 808 Processing helix chain 'Y' and resid 827 through 832 removed outlier: 4.093A pdb=" N ASP Y 831 " --> pdb=" O TYR Y 827 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS Y 832 " --> pdb=" O PRO Y 828 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 827 through 832' Processing helix chain 'Y' and resid 837 through 844 Processing helix chain 'Y' and resid 849 through 865 Processing helix chain 'Y' and resid 878 through 883 removed outlier: 3.714A pdb=" N MET Y 883 " --> pdb=" O PRO Y 880 " (cutoff:3.500A) Processing helix chain 'Y' and resid 910 through 916 removed outlier: 4.453A pdb=" N HIS Y 915 " --> pdb=" O ARG Y 912 " (cutoff:3.500A) Processing helix chain 'Y' and resid 917 through 927 Processing helix chain 'Y' and resid 934 through 953 Processing helix chain 'Y' and resid 954 through 956 No H-bonds generated for 'chain 'Y' and resid 954 through 956' Processing helix chain 'Y' and resid 966 through 971 Processing helix chain 'Y' and resid 1021 through 1025 Processing helix chain 'Y' and resid 1033 through 1043 removed outlier: 3.536A 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 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 1164 through 1169 removed outlier: 3.612A pdb=" N THR Y1169 " --> pdb=" O TRP Y1165 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1180 through 1200 removed outlier: 3.947A 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: 3.769A pdb=" N ASN Y1228 " --> pdb=" O LEU Y1224 " (cutoff:3.500A) removed outlier: 4.063A 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: 3.917A pdb=" N ASP Y1287 " --> pdb=" O ALA Y1283 " (cutoff:3.500A) removed outlier: 3.730A 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 1354 Processing helix chain 'Y' and resid 1374 through 1381 removed outlier: 4.279A 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 1666 Processing helix chain 'Y' and resid 1668 through 1680 Processing helix chain 'Y' and resid 1695 through 1703 removed outlier: 3.715A pdb=" N VAL Y1700 " --> pdb=" O GLN Y1697 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N ASN Y1701 " --> pdb=" O HIS Y1698 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1704 through 1710 Processing helix chain 'Y' and resid 1713 through 1720 Processing helix chain 'Y' and resid 1739 through 1750 Processing helix chain 'Y' and resid 1773 through 1785 removed outlier: 4.507A pdb=" N GLU Y1777 " --> pdb=" O PRO Y1773 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU Y1779 " --> pdb=" O PHE Y1775 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1800 through 1812 Processing helix chain 'Y' and resid 1824 through 1828 removed outlier: 3.827A pdb=" N LEU Y1828 " --> pdb=" O ALA Y1824 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 1824 through 1828' Processing helix chain 'Y' and resid 1888 through 1892 removed outlier: 3.515A pdb=" N LEU Y1891 " --> pdb=" O ALA Y1888 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU Y1892 " --> pdb=" O GLU Y1889 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 1888 through 1892' Processing helix chain 'Y' and resid 1913 through 1927 removed outlier: 4.352A pdb=" N SER Y1917 " --> pdb=" O GLU Y1913 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1927 through 1937 Processing helix chain 'Y' and resid 1952 through 1969 removed outlier: 3.651A pdb=" N GLN Y1969 " --> pdb=" O GLU Y1965 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2000 through 2013 removed outlier: 3.515A pdb=" N ARG Y2004 " --> pdb=" O ASN Y2000 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN Y2005 " --> pdb=" O GLU Y2001 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLN Y2006 " --> pdb=" O GLU Y2002 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL Y2007 " --> pdb=" O ASP Y2003 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU Y2012 " --> pdb=" O VAL Y2008 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2075 through 2086 removed outlier: 3.709A pdb=" N GLN Y2079 " --> pdb=" O ARG Y2075 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Y' and resid 380 through 382 removed outlier: 6.957A pdb=" N LEU Y 422 " --> pdb=" O SER Y1144 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N ALA Y1146 " --> pdb=" O LEU Y 422 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N MET Y 424 " --> pdb=" O ALA Y1146 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N THR Y1148 " --> pdb=" O MET Y 424 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLY Y 426 " --> pdb=" O THR Y1148 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N CYS Y1150 " --> pdb=" O GLY Y 426 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE Y 428 " --> pdb=" O CYS Y1150 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL Y1117 " --> pdb=" O ILE Y1147 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N LEU Y1149 " --> pdb=" O VAL Y1117 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N MET Y1119 " --> pdb=" O LEU Y1149 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU Y 641 " --> pdb=" O ALA Y1118 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LEU Y 640 " --> pdb=" O LEU Y1099 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N CYS Y1101 " --> pdb=" O LEU Y 640 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N THR Y 642 " --> pdb=" O CYS Y1101 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'Y' and resid 179 through 181 removed outlier: 6.699A pdb=" N ALA Y 180 " --> pdb=" O VAL Y 219 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ALA Y 149 " --> pdb=" O MET Y 218 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N THR Y 220 " --> pdb=" O ALA Y 149 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N PHE Y 151 " --> pdb=" O THR Y 220 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE Y 150 " --> pdb=" O VAL Y 249 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE Y 248 " --> pdb=" O ILE Y 288 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N THR Y 290 " --> pdb=" O ILE Y 248 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LEU Y 250 " --> pdb=" O THR Y 290 " (cutoff:3.500A) removed outlier: 9.006A pdb=" N ALA Y 292 " --> pdb=" O LEU Y 250 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N SER Y 110 " --> pdb=" O LYS Y 321 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N VAL Y 323 " --> pdb=" O SER Y 110 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU Y 112 " --> pdb=" O VAL Y 323 " (cutoff:3.500A) Processing sheet with id=AA3, 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 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 762 through 763 Processing sheet with id=AA5, first strand: chain 'Y' and resid 891 through 892 removed outlier: 6.293A pdb=" N MET Y 891 " --> pdb=" O GLN Y 906 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'Y' and resid 957 through 959 Processing sheet with id=AA7, first strand: chain 'Y' and resid 988 through 989 removed outlier: 3.688A 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 1373 removed outlier: 3.630A pdb=" N ALA Y1461 " --> pdb=" O GLY Y1398 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'Y' and resid 1386 through 1389 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 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=AB2, first strand: chain 'Y' and resid 1554 through 1555 removed outlier: 3.951A pdb=" N HIS Y1554 " --> pdb=" O CYS Y1571 " (cutoff:3.500A) Processing sheet with id=AB3, 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 1788 through 1792 removed outlier: 6.348A pdb=" N VAL Y1788 " --> pdb=" O GLN Y1819 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N LYS Y1821 " --> pdb=" O VAL Y1788 " (cutoff:3.500A) removed outlier: 6.097A 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: 6.774A pdb=" N TRP Y1848 " --> pdb=" O LEU Y1836 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLN Y1838 " --> pdb=" O GLN Y1846 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLN Y1846 " --> pdb=" O GLN Y1838 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Y' and resid 1901 through 1903 Processing sheet with id=AB5, first strand: chain 'Y' and resid 2025 through 2028 removed outlier: 4.135A pdb=" N GLU Y1944 " --> pdb=" O THR Y2042 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'Y' and resid 2063 through 2064 583 hydrogen bonds defined for protein. 1626 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 26 hydrogen bonds 52 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 30 stacking parallelities Total time for adding SS restraints: 4.87 Time building geometry restraints manager: 1.93 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: 5708 1.36 - 1.51: 5199 1.51 - 1.66: 6311 1.66 - 1.80: 85 1.80 - 1.95: 16 Bond restraints: 17319 Sorted by residual: bond pdb=" O3B AGS Y2206 " pdb=" PB AGS Y2206 " ideal model delta sigma weight residual 1.673 1.582 0.091 2.00e-02 2.50e+03 2.06e+01 bond pdb=" O3A AGS Y2206 " pdb=" PA AGS Y2206 " ideal model delta sigma weight residual 1.664 1.584 0.080 2.00e-02 2.50e+03 1.61e+01 bond pdb=" C3' DT I 18 " pdb=" C2' DT I 18 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.15e+01 bond pdb=" C3' DC I 25 " pdb=" C2' DC I 25 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.75e+00 bond pdb=" C3' DC I 12 " pdb=" C2' DC I 12 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.49e+00 ... (remaining 17314 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 23420 2.41 - 4.82: 203 4.82 - 7.23: 26 7.23 - 9.64: 12 9.64 - 12.05: 3 Bond angle restraints: 23664 Sorted by residual: angle pdb=" N3 DT I 11 " pdb=" C4 DT I 11 " pdb=" O4 DT I 11 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.87e+01 angle pdb=" N3 DT G 30 " pdb=" C4 DT G 30 " pdb=" O4 DT G 30 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.81e+01 angle pdb=" N3 DT I 18 " pdb=" C4 DT I 18 " pdb=" O4 DT I 18 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.77e+01 angle pdb=" N3 DT I 13 " pdb=" C4 DT I 13 " pdb=" O4 DT I 13 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT I 30 " pdb=" C4 DT I 30 " pdb=" O4 DT I 30 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.73e+01 ... (remaining 23659 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.31: 9832 34.31 - 68.62: 457 68.62 - 102.94: 30 102.94 - 137.25: 4 137.25 - 171.56: 1 Dihedral angle restraints: 10324 sinusoidal: 4520 harmonic: 5804 Sorted by residual: dihedral pdb=" O2B AGS Y2206 " pdb=" O3B AGS Y2206 " pdb=" PB AGS Y2206 " pdb=" PG AGS Y2206 " ideal model delta sinusoidal sigma weight residual 7.37 -125.77 133.14 1 3.00e+01 1.11e-03 1.80e+01 dihedral pdb=" O1A AGS Y2206 " pdb=" O3A AGS Y2206 " pdb=" PA AGS Y2206 " pdb=" PB AGS Y2206 " ideal model delta sinusoidal sigma weight residual 82.37 -50.03 132.40 1 3.00e+01 1.11e-03 1.79e+01 dihedral pdb=" CA MET Y1107 " pdb=" C MET Y1107 " pdb=" N GLY Y1108 " pdb=" CA GLY Y1108 " ideal model delta harmonic sigma weight residual 180.00 158.89 21.11 0 5.00e+00 4.00e-02 1.78e+01 ... (remaining 10321 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2162 0.052 - 0.104: 340 0.104 - 0.156: 67 0.156 - 0.207: 2 0.207 - 0.259: 1 Chirality restraints: 2572 Sorted by residual: chirality pdb=" C3' AGS Y2206 " pdb=" C2' AGS Y2206 " pdb=" C4' AGS Y2206 " pdb=" O3' AGS Y2206 " both_signs ideal model delta sigma weight residual False -2.37 -2.63 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA TRP Y 101 " pdb=" N TRP Y 101 " pdb=" C TRP Y 101 " pdb=" CB TRP Y 101 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.50e-01 chirality pdb=" P DT I 13 " pdb=" OP1 DT I 13 " pdb=" OP2 DT I 13 " pdb=" O5' DT I 13 " both_signs ideal model delta sigma weight residual True 2.34 -2.51 -0.17 2.00e-01 2.50e+01 7.31e-01 ... (remaining 2569 not shown) Planarity restraints: 2934 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET Y1474 " 0.014 2.00e-02 2.50e+03 2.82e-02 7.93e+00 pdb=" C MET Y1474 " -0.049 2.00e-02 2.50e+03 pdb=" O MET Y1474 " 0.018 2.00e-02 2.50e+03 pdb=" N PRO Y1475 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG Y1957 " -0.150 9.50e-02 1.11e+02 6.73e-02 2.81e+00 pdb=" NE ARG Y1957 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG Y1957 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG Y1957 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG Y1957 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE Y2102 " 0.008 2.00e-02 2.50e+03 1.62e-02 2.62e+00 pdb=" C ILE Y2102 " -0.028 2.00e-02 2.50e+03 pdb=" O ILE Y2102 " 0.011 2.00e-02 2.50e+03 pdb=" N ALA Y2103 " 0.009 2.00e-02 2.50e+03 ... (remaining 2931 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 708 2.72 - 3.26: 16839 3.26 - 3.81: 28384 3.81 - 4.35: 34511 4.35 - 4.90: 58337 Nonbonded interactions: 138779 Sorted by model distance: nonbonded pdb=" N GLU Y 49 " pdb=" OE1 GLU Y 49 " model vdw 2.171 3.120 nonbonded pdb=" OG1 THR Y 644 " pdb=" OD1 ASN Y1120 " model vdw 2.182 3.040 nonbonded pdb=" N GLU Y1860 " pdb=" OE1 GLU Y1860 " model vdw 2.201 3.120 nonbonded pdb=" O THR Y 117 " pdb=" O2B AGS Y2206 " model vdw 2.213 3.040 nonbonded pdb=" OG1 THR Y1855 " pdb=" O LEU Y1861 " model vdw 2.221 3.040 ... (remaining 138774 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.420 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 20.570 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 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:8.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 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 : 0.005 0.091 17339 Z= 0.256 Angle : 0.616 12.047 23691 Z= 0.345 Chirality : 0.041 0.259 2572 Planarity : 0.004 0.067 2934 Dihedral : 17.980 171.562 6580 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.11 % Favored : 96.84 % Rotamer: Outliers : 1.35 % Allowed : 16.41 % Favored : 82.24 % 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 (0.19), residues: 1993 helix: 1.53 (0.20), residues: 732 sheet: -0.27 (0.28), residues: 296 loop : -0.81 (0.19), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Y 318 TYR 0.012 0.001 TYR Y1945 PHE 0.025 0.001 PHE Y1919 TRP 0.019 0.001 TRP Y1930 HIS 0.003 0.001 HIS Y1521 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.26 (17319) covalent geometry : angle 0.60340 / 0.34 (23664) hydrogen bonds : bond 0.13250 / 14.51 ( 609) hydrogen bonds : angle 5.24442 / 6.15 ( 1678) metal coordination : bond 0.00913 / 1.30 ( 20) metal coordination : angle 3.74670 / 5.73 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3986 Ramachandran restraints generated. 1993 Oldfield, 0 Emsley, 1993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3986 Ramachandran restraints generated. 1993 Oldfield, 0 Emsley, 1993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 62 time to evaluate : 0.579 Fit side-chains REVERT: Y 1474 MET cc_start: 0.9197 (ppp) cc_final: 0.8705 (ptp) REVERT: Y 1709 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8693 (mm) REVERT: Y 1903 ASN cc_start: 0.7438 (OUTLIER) cc_final: 0.6308 (p0) REVERT: Y 1949 TYR cc_start: 0.8629 (m-80) cc_final: 0.8229 (m-80) REVERT: Y 1971 MET cc_start: 0.8208 (mmp) cc_final: 0.7646 (mpm) outliers start: 23 outliers final: 19 residues processed: 82 average time/residue: 0.5631 time to fit residues: 52.4318 Evaluate side-chains 81 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 60 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 103 THR Chi-restraints excluded: chain Y residue 124 CYS Chi-restraints excluded: chain Y residue 163 GLN Chi-restraints excluded: chain Y residue 193 ILE Chi-restraints excluded: chain Y residue 282 ASP Chi-restraints excluded: chain Y residue 332 VAL Chi-restraints excluded: chain Y residue 417 LEU Chi-restraints excluded: chain Y residue 496 ASP Chi-restraints excluded: chain Y residue 582 ASN Chi-restraints excluded: chain Y residue 816 THR Chi-restraints excluded: chain Y residue 823 VAL Chi-restraints excluded: chain Y residue 990 ASP Chi-restraints excluded: chain Y residue 1012 VAL Chi-restraints excluded: chain Y residue 1437 VAL Chi-restraints excluded: chain Y residue 1493 VAL Chi-restraints excluded: chain Y residue 1553 THR Chi-restraints excluded: chain Y residue 1709 LEU Chi-restraints excluded: chain Y residue 1903 ASN Chi-restraints excluded: chain Y residue 1946 SER Chi-restraints excluded: chain Y residue 1951 ASN Chi-restraints excluded: chain Y residue 1980 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: [98, 194, 107, 10, 66, 130, 124, 103, 200, 77, 122] chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 9.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Y 565 HIS Y1120 ASN Y1830 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.079177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.053863 restraints weight = 42532.506| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 2.84 r_work: 0.2731 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.0501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17339 Z= 0.133 Angle : 0.535 7.680 23691 Z= 0.278 Chirality : 0.039 0.208 2572 Planarity : 0.004 0.039 2934 Dihedral : 16.394 173.664 2751 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.76 % Favored : 97.19 % Rotamer: Outliers : 1.35 % Allowed : 15.71 % Favored : 82.94 % 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: 0.41 (0.19), residues: 1993 helix: 1.77 (0.20), residues: 724 sheet: -0.17 (0.29), residues: 284 loop : -0.72 (0.19), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Y 232 TYR 0.009 0.001 TYR Y1302 PHE 0.023 0.001 PHE Y 125 TRP 0.017 0.001 TRP Y1226 HIS 0.004 0.001 HIS Y1521 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (17319) covalent geometry : angle 0.52351 / 0.28 (23664) hydrogen bonds : bond 0.04393 / 4.86 ( 609) hydrogen bonds : angle 4.36687 / 4.91 ( 1678) metal coordination : bond 0.00710 / 0.93 ( 20) metal coordination : angle 3.25347 / 4.95 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3986 Ramachandran restraints generated. 1993 Oldfield, 0 Emsley, 1993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3986 Ramachandran restraints generated. 1993 Oldfield, 0 Emsley, 1993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 65 time to evaluate : 0.638 Fit side-chains REVERT: Y 281 THR cc_start: 0.9550 (OUTLIER) cc_final: 0.9118 (p) REVERT: Y 414 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.8315 (tt0) REVERT: Y 1105 MET cc_start: 0.9156 (mmm) cc_final: 0.8903 (mtp) REVERT: Y 1341 GLU cc_start: 0.8106 (tm-30) cc_final: 0.7565 (tm-30) REVERT: Y 1474 MET cc_start: 0.9292 (ppp) cc_final: 0.8970 (ptp) REVERT: Y 1709 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8507 (mm) REVERT: Y 1731 ASP cc_start: 0.8638 (m-30) cc_final: 0.8289 (t0) REVERT: Y 1776 LYS cc_start: 0.9237 (mppt) cc_final: 0.8902 (mmtt) REVERT: Y 1949 TYR cc_start: 0.8804 (m-80) cc_final: 0.8463 (m-80) REVERT: Y 1971 MET cc_start: 0.8077 (mmp) cc_final: 0.7578 (mpm) outliers start: 23 outliers final: 9 residues processed: 85 average time/residue: 0.5301 time to fit residues: 51.2938 Evaluate side-chains 75 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 124 CYS Chi-restraints excluded: chain Y residue 281 THR Chi-restraints excluded: chain Y residue 414 GLU Chi-restraints excluded: chain Y residue 417 LEU Chi-restraints excluded: chain Y residue 438 SER Chi-restraints excluded: chain Y residue 1012 VAL Chi-restraints excluded: chain Y residue 1437 VAL Chi-restraints excluded: chain Y residue 1493 VAL Chi-restraints excluded: chain Y residue 1553 THR Chi-restraints excluded: chain Y residue 1709 LEU Chi-restraints excluded: chain Y residue 1946 SER Chi-restraints excluded: chain Y residue 2006 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: [111, 116, 187, 28, 171, 41, 10, 58, 165, 137, 61] chunk 111 optimal weight: 0.0570 chunk 116 optimal weight: 4.9990 chunk 187 optimal weight: 8.9990 chunk 28 optimal weight: 0.9980 chunk 171 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 165 optimal weight: 0.5980 chunk 137 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Y 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 917 ASN ** Y1121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y1830 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.079561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.054289 restraints weight = 43112.167| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 2.87 r_work: 0.2742 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.0685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17339 Z= 0.115 Angle : 0.513 8.207 23691 Z= 0.266 Chirality : 0.038 0.202 2572 Planarity : 0.003 0.045 2934 Dihedral : 15.985 173.966 2729 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.81 % Favored : 97.14 % Rotamer: Outliers : 1.76 % Allowed : 15.71 % Favored : 82.53 % 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: 0.45 (0.19), residues: 1993 helix: 1.83 (0.20), residues: 724 sheet: -0.12 (0.29), residues: 283 loop : -0.72 (0.19), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Y 318 TYR 0.010 0.001 TYR Y1302 PHE 0.022 0.001 PHE Y 125 TRP 0.018 0.001 TRP Y1226 HIS 0.004 0.001 HIS Y1576 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 (17319) covalent geometry : angle 0.50287 / 0.27 (23664) hydrogen bonds : bond 0.03826 / 4.24 ( 609) hydrogen bonds : angle 4.18441 / 4.65 ( 1678) metal coordination : bond 0.00552 / 0.75 ( 20) metal coordination : angle 3.08682 / 4.72 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3986 Ramachandran restraints generated. 1993 Oldfield, 0 Emsley, 1993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3986 Ramachandran restraints generated. 1993 Oldfield, 0 Emsley, 1993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 65 time to evaluate : 0.569 Fit side-chains REVERT: Y 123 GLU cc_start: 0.8357 (mp0) cc_final: 0.7724 (mp0) REVERT: Y 281 THR cc_start: 0.9548 (OUTLIER) cc_final: 0.9127 (p) REVERT: Y 414 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8274 (tt0) REVERT: Y 645 ASP cc_start: 0.8870 (m-30) cc_final: 0.8350 (m-30) REVERT: Y 917 ASN cc_start: 0.8720 (OUTLIER) cc_final: 0.8269 (t0) REVERT: Y 1341 GLU cc_start: 0.8124 (tm-30) cc_final: 0.7643 (tm-30) REVERT: Y 1709 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8499 (mm) REVERT: Y 1731 ASP cc_start: 0.8638 (m-30) cc_final: 0.8266 (t0) REVERT: Y 1776 LYS cc_start: 0.9207 (mppt) cc_final: 0.8880 (mmtt) REVERT: Y 1948 ARG cc_start: 0.8234 (pmt170) cc_final: 0.8033 (pmt170) REVERT: Y 1949 TYR cc_start: 0.8796 (m-80) cc_final: 0.8432 (m-80) REVERT: Y 1971 MET cc_start: 0.8022 (mmp) cc_final: 0.7550 (mpm) REVERT: Y 1998 TRP cc_start: 0.7433 (OUTLIER) cc_final: 0.6935 (m-10) outliers start: 30 outliers final: 12 residues processed: 93 average time/residue: 0.5231 time to fit residues: 55.3121 Evaluate side-chains 79 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 31 SER Chi-restraints excluded: chain Y residue 124 CYS Chi-restraints excluded: chain Y residue 163 GLN Chi-restraints excluded: chain Y residue 281 THR Chi-restraints excluded: chain Y residue 332 VAL Chi-restraints excluded: chain Y residue 414 GLU Chi-restraints excluded: chain Y residue 417 LEU Chi-restraints excluded: chain Y residue 438 SER Chi-restraints excluded: chain Y residue 917 ASN Chi-restraints excluded: chain Y residue 990 ASP Chi-restraints excluded: chain Y residue 1012 VAL Chi-restraints excluded: chain Y residue 1437 VAL Chi-restraints excluded: chain Y residue 1493 VAL Chi-restraints excluded: chain Y residue 1553 THR Chi-restraints excluded: chain Y residue 1709 LEU Chi-restraints excluded: chain Y residue 1813 MET Chi-restraints excluded: chain Y residue 1998 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: [40, 165, 139, 38, 130, 56, 202, 147, 57, 87, 112] chunk 40 optimal weight: 3.9990 chunk 165 optimal weight: 0.9980 chunk 139 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 202 optimal weight: 10.0000 chunk 147 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 87 optimal weight: 0.0870 chunk 112 optimal weight: 0.7980 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Y 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y1830 GLN Y1942 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.079351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.054088 restraints weight = 42690.231| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 2.84 r_work: 0.2738 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.0795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17339 Z= 0.131 Angle : 0.525 9.953 23691 Z= 0.268 Chirality : 0.038 0.205 2572 Planarity : 0.003 0.044 2934 Dihedral : 15.785 173.774 2728 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.66 % Favored : 97.29 % Rotamer: Outliers : 1.82 % Allowed : 16.06 % Favored : 82.12 % 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: 0.47 (0.19), residues: 1993 helix: 1.82 (0.20), residues: 727 sheet: -0.15 (0.29), residues: 285 loop : -0.69 (0.19), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Y 318 TYR 0.011 0.001 TYR Y1302 PHE 0.022 0.001 PHE Y 125 TRP 0.018 0.001 TRP Y1226 HIS 0.004 0.001 HIS Y1576 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (17319) covalent geometry : angle 0.51437 / 0.27 (23664) hydrogen bonds : bond 0.03638 / 4.04 ( 609) hydrogen bonds : angle 4.10970 / 4.57 ( 1678) metal coordination : bond 0.00663 / 0.92 ( 20) metal coordination : angle 3.15873 / 4.78 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3986 Ramachandran restraints generated. 1993 Oldfield, 0 Emsley, 1993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3986 Ramachandran restraints generated. 1993 Oldfield, 0 Emsley, 1993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 63 time to evaluate : 0.600 Fit side-chains REVERT: Y 123 GLU cc_start: 0.8383 (mp0) cc_final: 0.7728 (mp0) REVERT: Y 281 THR cc_start: 0.9549 (OUTLIER) cc_final: 0.9131 (p) REVERT: Y 407 ASP cc_start: 0.8305 (p0) cc_final: 0.7919 (p0) REVERT: Y 414 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8264 (tt0) REVERT: Y 645 ASP cc_start: 0.8890 (m-30) cc_final: 0.8366 (m-30) REVERT: Y 1709 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8526 (mm) REVERT: Y 1731 ASP cc_start: 0.8578 (m-30) cc_final: 0.8214 (t0) REVERT: Y 1776 LYS cc_start: 0.9236 (mppt) cc_final: 0.8905 (mmtt) REVERT: Y 1949 TYR cc_start: 0.8786 (m-80) cc_final: 0.8439 (m-80) REVERT: Y 1959 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8825 (pp) REVERT: Y 1971 MET cc_start: 0.8017 (mmp) cc_final: 0.7693 (mpm) REVERT: Y 1998 TRP cc_start: 0.7530 (OUTLIER) cc_final: 0.7024 (m-10) outliers start: 31 outliers final: 15 residues processed: 90 average time/residue: 0.5070 time to fit residues: 52.1644 Evaluate side-chains 82 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 62 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 31 SER Chi-restraints excluded: chain Y residue 119 SER Chi-restraints excluded: chain Y residue 124 CYS Chi-restraints excluded: chain Y residue 163 GLN Chi-restraints excluded: chain Y residue 281 THR Chi-restraints excluded: chain Y residue 332 VAL Chi-restraints excluded: chain Y residue 393 THR Chi-restraints excluded: chain Y residue 414 GLU Chi-restraints excluded: chain Y residue 417 LEU Chi-restraints excluded: chain Y residue 438 SER Chi-restraints excluded: chain Y residue 990 ASP Chi-restraints excluded: chain Y residue 1012 VAL Chi-restraints excluded: chain Y residue 1437 VAL Chi-restraints excluded: chain Y residue 1493 VAL Chi-restraints excluded: chain Y residue 1553 THR Chi-restraints excluded: chain Y residue 1709 LEU Chi-restraints excluded: chain Y residue 1813 MET Chi-restraints excluded: chain Y residue 1959 LEU Chi-restraints excluded: chain Y residue 1998 TRP Chi-restraints excluded: chain Y residue 2059 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: [156, 18, 28, 74, 199, 73, 94, 86, 83, 12, 112] chunk 156 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 74 optimal weight: 0.9980 chunk 199 optimal weight: 10.0000 chunk 73 optimal weight: 0.0010 chunk 94 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 chunk 83 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 112 optimal weight: 0.7980 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Y 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y1830 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.079774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.054485 restraints weight = 42558.887| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 2.84 r_work: 0.2753 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.0892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 17339 Z= 0.110 Angle : 0.510 8.779 23691 Z= 0.261 Chirality : 0.038 0.226 2572 Planarity : 0.003 0.048 2934 Dihedral : 15.631 178.198 2728 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.36 % Favored : 97.59 % Rotamer: Outliers : 1.82 % Allowed : 16.53 % Favored : 81.65 % 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: 0.56 (0.19), residues: 1993 helix: 1.89 (0.20), residues: 728 sheet: -0.04 (0.29), residues: 285 loop : -0.67 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Y 318 TYR 0.011 0.001 TYR Y1302 PHE 0.021 0.001 PHE Y 125 TRP 0.017 0.001 TRP Y1226 HIS 0.003 0.001 HIS Y1576 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (17319) covalent geometry : angle 0.49989 / 0.26 (23664) hydrogen bonds : bond 0.03453 / 3.85 ( 609) hydrogen bonds : angle 4.02620 / 4.48 ( 1678) metal coordination : bond 0.00480 / 0.65 ( 20) metal coordination : angle 3.01918 / 4.63 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3986 Ramachandran restraints generated. 1993 Oldfield, 0 Emsley, 1993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3986 Ramachandran restraints generated. 1993 Oldfield, 0 Emsley, 1993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 62 time to evaluate : 0.516 Fit side-chains REVERT: Y 123 GLU cc_start: 0.8360 (mp0) cc_final: 0.7708 (mp0) REVERT: Y 281 THR cc_start: 0.9545 (OUTLIER) cc_final: 0.9125 (p) REVERT: Y 407 ASP cc_start: 0.8228 (p0) cc_final: 0.7900 (p0) REVERT: Y 414 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8228 (tt0) REVERT: Y 645 ASP cc_start: 0.8872 (m-30) cc_final: 0.8340 (m-30) REVERT: Y 1474 MET cc_start: 0.8952 (ptp) cc_final: 0.8705 (ppp) REVERT: Y 1709 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8508 (mm) REVERT: Y 1731 ASP cc_start: 0.8618 (m-30) cc_final: 0.8230 (t0) REVERT: Y 1776 LYS cc_start: 0.9243 (mppt) cc_final: 0.8956 (mmtt) REVERT: Y 1948 ARG cc_start: 0.8330 (pmt170) cc_final: 0.7741 (pmm-80) REVERT: Y 1949 TYR cc_start: 0.8753 (m-80) cc_final: 0.8375 (m-80) REVERT: Y 1959 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8830 (pp) REVERT: Y 1971 MET cc_start: 0.7950 (mmp) cc_final: 0.7639 (mpm) REVERT: Y 1998 TRP cc_start: 0.7487 (OUTLIER) cc_final: 0.7161 (m-10) outliers start: 31 outliers final: 18 residues processed: 91 average time/residue: 0.5061 time to fit residues: 52.5438 Evaluate side-chains 82 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 59 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 31 SER Chi-restraints excluded: chain Y residue 119 SER Chi-restraints excluded: chain Y residue 124 CYS Chi-restraints excluded: chain Y residue 163 GLN Chi-restraints excluded: chain Y residue 281 THR Chi-restraints excluded: chain Y residue 332 VAL Chi-restraints excluded: chain Y residue 393 THR Chi-restraints excluded: chain Y residue 414 GLU Chi-restraints excluded: chain Y residue 417 LEU Chi-restraints excluded: chain Y residue 438 SER Chi-restraints excluded: chain Y residue 823 VAL Chi-restraints excluded: chain Y residue 1012 VAL Chi-restraints excluded: chain Y residue 1437 VAL Chi-restraints excluded: chain Y residue 1493 VAL Chi-restraints excluded: chain Y residue 1553 THR Chi-restraints excluded: chain Y residue 1700 VAL Chi-restraints excluded: chain Y residue 1709 LEU Chi-restraints excluded: chain Y residue 1813 MET Chi-restraints excluded: chain Y residue 1959 LEU Chi-restraints excluded: chain Y residue 1998 TRP Chi-restraints excluded: chain Y residue 2006 GLN Chi-restraints excluded: chain Y residue 2059 LEU Chi-restraints excluded: chain Y residue 2102 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: [128, 4, 191, 46, 178, 187, 162, 164, 82, 111, 107] chunk 128 optimal weight: 4.9990 chunk 4 optimal weight: 0.6980 chunk 191 optimal weight: 0.3980 chunk 46 optimal weight: 0.7980 chunk 178 optimal weight: 0.6980 chunk 187 optimal weight: 5.9990 chunk 162 optimal weight: 3.9990 chunk 164 optimal weight: 0.7980 chunk 82 optimal weight: 0.5980 chunk 111 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Y 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 917 ASN ** Y1121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y1830 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.079904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.054635 restraints weight = 42431.737| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 2.84 r_work: 0.2757 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 17339 Z= 0.108 Angle : 0.500 8.617 23691 Z= 0.256 Chirality : 0.038 0.214 2572 Planarity : 0.003 0.051 2934 Dihedral : 15.447 174.067 2728 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.61 % Favored : 97.34 % Rotamer: Outliers : 1.93 % Allowed : 16.59 % Favored : 81.48 % 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: 0.62 (0.19), residues: 1993 helix: 1.94 (0.20), residues: 728 sheet: -0.01 (0.30), residues: 273 loop : -0.62 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Y 318 TYR 0.011 0.001 TYR Y1302 PHE 0.021 0.001 PHE Y1919 TRP 0.017 0.001 TRP Y1226 HIS 0.003 0.001 HIS Y1576 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (17319) covalent geometry : angle 0.49011 / 0.26 (23664) hydrogen bonds : bond 0.03341 / 3.71 ( 609) hydrogen bonds : angle 3.95416 / 4.41 ( 1678) metal coordination : bond 0.00463 / 0.62 ( 20) metal coordination : angle 2.96805 / 4.54 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3986 Ramachandran restraints generated. 1993 Oldfield, 0 Emsley, 1993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3986 Ramachandran restraints generated. 1993 Oldfield, 0 Emsley, 1993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 64 time to evaluate : 0.543 Fit side-chains REVERT: Y 123 GLU cc_start: 0.8359 (mp0) cc_final: 0.7711 (mp0) REVERT: Y 281 THR cc_start: 0.9544 (OUTLIER) cc_final: 0.9129 (p) REVERT: Y 296 GLU cc_start: 0.8420 (tm-30) cc_final: 0.8069 (tm-30) REVERT: Y 407 ASP cc_start: 0.8177 (p0) cc_final: 0.7924 (p0) REVERT: Y 645 ASP cc_start: 0.8857 (m-30) cc_final: 0.8363 (m-30) REVERT: Y 917 ASN cc_start: 0.8546 (OUTLIER) cc_final: 0.8184 (t0) REVERT: Y 1709 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8503 (mm) REVERT: Y 1731 ASP cc_start: 0.8593 (m-30) cc_final: 0.8207 (t0) REVERT: Y 1776 LYS cc_start: 0.9244 (mppt) cc_final: 0.8982 (mmtt) REVERT: Y 1948 ARG cc_start: 0.8357 (pmt170) cc_final: 0.7713 (pmm-80) REVERT: Y 1959 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8902 (pp) REVERT: Y 1971 MET cc_start: 0.7942 (mmp) cc_final: 0.7613 (mpm) outliers start: 33 outliers final: 17 residues processed: 95 average time/residue: 0.5010 time to fit residues: 54.1003 Evaluate side-chains 85 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 64 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 31 SER Chi-restraints excluded: chain Y residue 119 SER Chi-restraints excluded: chain Y residue 124 CYS Chi-restraints excluded: chain Y residue 163 GLN Chi-restraints excluded: chain Y residue 281 THR Chi-restraints excluded: chain Y residue 332 VAL Chi-restraints excluded: chain Y residue 393 THR Chi-restraints excluded: chain Y residue 417 LEU Chi-restraints excluded: chain Y residue 438 SER Chi-restraints excluded: chain Y residue 823 VAL Chi-restraints excluded: chain Y residue 917 ASN Chi-restraints excluded: chain Y residue 990 ASP Chi-restraints excluded: chain Y residue 1012 VAL Chi-restraints excluded: chain Y residue 1493 VAL Chi-restraints excluded: chain Y residue 1553 THR Chi-restraints excluded: chain Y residue 1709 LEU Chi-restraints excluded: chain Y residue 1813 MET Chi-restraints excluded: chain Y residue 1959 LEU Chi-restraints excluded: chain Y residue 1980 CYS Chi-restraints excluded: chain Y residue 2059 LEU Chi-restraints excluded: chain Y residue 2102 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: [151, 118, 69, 189, 163, 178, 113, 33, 97, 30, 68] chunk 151 optimal weight: 0.5980 chunk 118 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 189 optimal weight: 8.9990 chunk 163 optimal weight: 3.9990 chunk 178 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 97 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Y 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.079792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.054453 restraints weight = 42454.801| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 2.86 r_work: 0.2751 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.1049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17339 Z= 0.124 Angle : 0.534 14.526 23691 Z= 0.267 Chirality : 0.038 0.215 2572 Planarity : 0.003 0.052 2934 Dihedral : 15.407 174.084 2727 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.61 % Favored : 97.34 % Rotamer: Outliers : 1.82 % Allowed : 16.76 % Favored : 81.42 % 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: 0.64 (0.19), residues: 1993 helix: 1.97 (0.20), residues: 726 sheet: -0.02 (0.30), residues: 273 loop : -0.61 (0.19), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG Y 318 TYR 0.011 0.001 TYR Y1302 PHE 0.021 0.001 PHE Y 125 TRP 0.038 0.001 TRP Y1998 HIS 0.003 0.001 HIS Y1521 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (17319) covalent geometry : angle 0.52391 / 0.27 (23664) hydrogen bonds : bond 0.03321 / 3.68 ( 609) hydrogen bonds : angle 3.96129 / 4.41 ( 1678) metal coordination : bond 0.00565 / 0.78 ( 20) metal coordination : angle 3.02909 / 4.60 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3986 Ramachandran restraints generated. 1993 Oldfield, 0 Emsley, 1993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3986 Ramachandran restraints generated. 1993 Oldfield, 0 Emsley, 1993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 66 time to evaluate : 0.632 Fit side-chains REVERT: Y 123 GLU cc_start: 0.8374 (mp0) cc_final: 0.7719 (mp0) REVERT: Y 281 THR cc_start: 0.9548 (OUTLIER) cc_final: 0.9132 (p) REVERT: Y 296 GLU cc_start: 0.8434 (tm-30) cc_final: 0.8080 (tm-30) REVERT: Y 407 ASP cc_start: 0.8204 (p0) cc_final: 0.7971 (p0) REVERT: Y 645 ASP cc_start: 0.8875 (m-30) cc_final: 0.8344 (m-30) REVERT: Y 1709 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8530 (mm) REVERT: Y 1731 ASP cc_start: 0.8591 (m-30) cc_final: 0.8210 (t0) REVERT: Y 1776 LYS cc_start: 0.9239 (mppt) cc_final: 0.8950 (mmtt) REVERT: Y 1948 ARG cc_start: 0.8367 (pmt170) cc_final: 0.7766 (pmm-80) REVERT: Y 1971 MET cc_start: 0.7948 (mmp) cc_final: 0.7617 (mpm) REVERT: Y 1998 TRP cc_start: 0.7387 (OUTLIER) cc_final: 0.6686 (m-10) outliers start: 31 outliers final: 20 residues processed: 94 average time/residue: 0.5348 time to fit residues: 57.2243 Evaluate side-chains 88 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 65 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 31 SER Chi-restraints excluded: chain Y residue 119 SER Chi-restraints excluded: chain Y residue 124 CYS Chi-restraints excluded: chain Y residue 163 GLN Chi-restraints excluded: chain Y residue 281 THR Chi-restraints excluded: chain Y residue 332 VAL Chi-restraints excluded: chain Y residue 393 THR Chi-restraints excluded: chain Y residue 417 LEU Chi-restraints excluded: chain Y residue 438 SER Chi-restraints excluded: chain Y residue 823 VAL Chi-restraints excluded: chain Y residue 990 ASP Chi-restraints excluded: chain Y residue 1012 VAL Chi-restraints excluded: chain Y residue 1437 VAL Chi-restraints excluded: chain Y residue 1493 VAL Chi-restraints excluded: chain Y residue 1553 THR Chi-restraints excluded: chain Y residue 1700 VAL Chi-restraints excluded: chain Y residue 1709 LEU Chi-restraints excluded: chain Y residue 1813 MET Chi-restraints excluded: chain Y residue 1980 CYS Chi-restraints excluded: chain Y residue 1998 TRP Chi-restraints excluded: chain Y residue 2006 GLN Chi-restraints excluded: chain Y residue 2059 LEU Chi-restraints excluded: chain Y residue 2102 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: [0, 81, 1, 57, 151, 147, 157, 177, 167, 56, 18] chunk 0 optimal weight: 50.0000 chunk 81 optimal weight: 2.9990 chunk 1 optimal weight: 9.9990 chunk 57 optimal weight: 0.7980 chunk 151 optimal weight: 3.9990 chunk 147 optimal weight: 0.8980 chunk 157 optimal weight: 0.9980 chunk 177 optimal weight: 6.9990 chunk 167 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Y 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y1830 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.079900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.054315 restraints weight = 42822.365| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 2.90 r_work: 0.2746 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17339 Z= 0.121 Angle : 0.532 12.882 23691 Z= 0.268 Chirality : 0.038 0.217 2572 Planarity : 0.003 0.057 2934 Dihedral : 15.387 173.975 2727 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.71 % Favored : 97.24 % Rotamer: Outliers : 1.76 % Allowed : 17.12 % Favored : 81.13 % 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: 0.67 (0.19), residues: 1993 helix: 2.00 (0.20), residues: 726 sheet: 0.00 (0.30), residues: 273 loop : -0.59 (0.19), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG Y 318 TYR 0.011 0.001 TYR Y1302 PHE 0.022 0.001 PHE Y1919 TRP 0.036 0.001 TRP Y1998 HIS 0.006 0.001 HIS Y2051 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (17319) covalent geometry : angle 0.52229 / 0.27 (23664) hydrogen bonds : bond 0.03325 / 3.67 ( 609) hydrogen bonds : angle 3.95938 / 4.40 ( 1678) metal coordination : bond 0.00548 / 0.75 ( 20) metal coordination : angle 3.02941 / 4.61 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3986 Ramachandran restraints generated. 1993 Oldfield, 0 Emsley, 1993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3986 Ramachandran restraints generated. 1993 Oldfield, 0 Emsley, 1993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 65 time to evaluate : 0.594 Fit side-chains REVERT: Y 123 GLU cc_start: 0.8376 (mp0) cc_final: 0.7721 (mp0) REVERT: Y 281 THR cc_start: 0.9548 (OUTLIER) cc_final: 0.9137 (p) REVERT: Y 296 GLU cc_start: 0.8444 (tm-30) cc_final: 0.8090 (tm-30) REVERT: Y 407 ASP cc_start: 0.8231 (p0) cc_final: 0.7981 (p0) REVERT: Y 645 ASP cc_start: 0.8860 (m-30) cc_final: 0.8324 (m-30) REVERT: Y 1709 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8522 (mm) REVERT: Y 1731 ASP cc_start: 0.8586 (m-30) cc_final: 0.8196 (t0) REVERT: Y 1776 LYS cc_start: 0.9245 (mppt) cc_final: 0.8963 (mmtt) REVERT: Y 1860 GLU cc_start: 0.8441 (pm20) cc_final: 0.7954 (tp30) REVERT: Y 1903 ASN cc_start: 0.7441 (OUTLIER) cc_final: 0.6244 (p0) REVERT: Y 1948 ARG cc_start: 0.8421 (pmt170) cc_final: 0.7830 (pmm-80) REVERT: Y 1959 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8894 (pp) REVERT: Y 1971 MET cc_start: 0.7905 (mmp) cc_final: 0.7652 (mpm) REVERT: Y 1998 TRP cc_start: 0.7466 (OUTLIER) cc_final: 0.7221 (m-10) outliers start: 30 outliers final: 19 residues processed: 92 average time/residue: 0.4877 time to fit residues: 51.6077 Evaluate side-chains 87 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 63 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 31 SER Chi-restraints excluded: chain Y residue 119 SER Chi-restraints excluded: chain Y residue 124 CYS Chi-restraints excluded: chain Y residue 163 GLN Chi-restraints excluded: chain Y residue 281 THR Chi-restraints excluded: chain Y residue 332 VAL Chi-restraints excluded: chain Y residue 393 THR Chi-restraints excluded: chain Y residue 417 LEU Chi-restraints excluded: chain Y residue 438 SER Chi-restraints excluded: chain Y residue 823 VAL Chi-restraints excluded: chain Y residue 990 ASP Chi-restraints excluded: chain Y residue 1012 VAL Chi-restraints excluded: chain Y residue 1437 VAL Chi-restraints excluded: chain Y residue 1493 VAL Chi-restraints excluded: chain Y residue 1553 THR Chi-restraints excluded: chain Y residue 1700 VAL Chi-restraints excluded: chain Y residue 1709 LEU Chi-restraints excluded: chain Y residue 1813 MET Chi-restraints excluded: chain Y residue 1903 ASN Chi-restraints excluded: chain Y residue 1959 LEU Chi-restraints excluded: chain Y residue 1980 CYS Chi-restraints excluded: chain Y residue 1998 TRP Chi-restraints excluded: chain Y residue 2059 LEU Chi-restraints excluded: chain Y residue 2102 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: [122, 67, 180, 75, 133, 199, 14, 119, 58, 200, 62] chunk 122 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 180 optimal weight: 0.0020 chunk 75 optimal weight: 0.7980 chunk 133 optimal weight: 3.9990 chunk 199 optimal weight: 0.5980 chunk 14 optimal weight: 5.9990 chunk 119 optimal weight: 0.9980 chunk 58 optimal weight: 0.0020 chunk 200 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Y 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y1764 GLN Y1830 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.080295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.054986 restraints weight = 42502.662| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 2.86 r_work: 0.2763 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 17339 Z= 0.103 Angle : 0.537 13.841 23691 Z= 0.268 Chirality : 0.038 0.224 2572 Planarity : 0.004 0.059 2934 Dihedral : 15.369 174.217 2727 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.76 % Allowed : 17.06 % Favored : 81.18 % 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: 0.69 (0.19), residues: 1993 helix: 2.02 (0.20), residues: 726 sheet: 0.02 (0.30), residues: 273 loop : -0.58 (0.19), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG Y 318 TYR 0.012 0.001 TYR Y1302 PHE 0.020 0.001 PHE Y 125 TRP 0.033 0.001 TRP Y1998 HIS 0.005 0.001 HIS Y2051 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (17319) covalent geometry : angle 0.52827 / 0.27 (23664) hydrogen bonds : bond 0.03210 / 3.56 ( 609) hydrogen bonds : angle 3.92332 / 4.36 ( 1678) metal coordination : bond 0.00390 / 0.52 ( 20) metal coordination : angle 2.88056 / 4.43 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3986 Ramachandran restraints generated. 1993 Oldfield, 0 Emsley, 1993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3986 Ramachandran restraints generated. 1993 Oldfield, 0 Emsley, 1993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 64 time to evaluate : 0.461 Fit side-chains REVERT: Y 123 GLU cc_start: 0.8376 (mp0) cc_final: 0.7681 (mp0) REVERT: Y 281 THR cc_start: 0.9541 (OUTLIER) cc_final: 0.9131 (p) REVERT: Y 296 GLU cc_start: 0.8449 (tm-30) cc_final: 0.8087 (tm-30) REVERT: Y 407 ASP cc_start: 0.8206 (p0) cc_final: 0.7965 (p0) REVERT: Y 645 ASP cc_start: 0.8832 (m-30) cc_final: 0.8337 (m-30) REVERT: Y 1709 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8524 (mm) REVERT: Y 1731 ASP cc_start: 0.8559 (m-30) cc_final: 0.8177 (t0) REVERT: Y 1776 LYS cc_start: 0.9234 (mppt) cc_final: 0.8953 (mmtt) REVERT: Y 1860 GLU cc_start: 0.8422 (pm20) cc_final: 0.7961 (tp30) REVERT: Y 1903 ASN cc_start: 0.7387 (OUTLIER) cc_final: 0.6239 (p0) REVERT: Y 1937 HIS cc_start: 0.9091 (OUTLIER) cc_final: 0.8128 (t70) REVERT: Y 1948 ARG cc_start: 0.8437 (pmt170) cc_final: 0.7863 (pmm-80) REVERT: Y 1959 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8884 (pp) REVERT: Y 1971 MET cc_start: 0.7994 (mmp) cc_final: 0.7751 (mpm) REVERT: Y 1998 TRP cc_start: 0.7414 (OUTLIER) cc_final: 0.7207 (m-10) outliers start: 30 outliers final: 19 residues processed: 90 average time/residue: 0.4863 time to fit residues: 50.0499 Evaluate side-chains 89 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 64 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 31 SER Chi-restraints excluded: chain Y residue 119 SER Chi-restraints excluded: chain Y residue 124 CYS Chi-restraints excluded: chain Y residue 163 GLN Chi-restraints excluded: chain Y residue 193 ILE Chi-restraints excluded: chain Y residue 281 THR Chi-restraints excluded: chain Y residue 332 VAL Chi-restraints excluded: chain Y residue 393 THR Chi-restraints excluded: chain Y residue 417 LEU Chi-restraints excluded: chain Y residue 438 SER Chi-restraints excluded: chain Y residue 823 VAL Chi-restraints excluded: chain Y residue 990 ASP Chi-restraints excluded: chain Y residue 1012 VAL Chi-restraints excluded: chain Y residue 1437 VAL Chi-restraints excluded: chain Y residue 1493 VAL Chi-restraints excluded: chain Y residue 1553 THR Chi-restraints excluded: chain Y residue 1700 VAL Chi-restraints excluded: chain Y residue 1709 LEU Chi-restraints excluded: chain Y residue 1903 ASN Chi-restraints excluded: chain Y residue 1937 HIS Chi-restraints excluded: chain Y residue 1959 LEU Chi-restraints excluded: chain Y residue 1980 CYS Chi-restraints excluded: chain Y residue 1998 TRP Chi-restraints excluded: chain Y residue 2059 LEU Chi-restraints excluded: chain Y residue 2102 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: [167, 1, 92, 160, 48, 43, 194, 25, 115, 33, 125] chunk 167 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 92 optimal weight: 0.7980 chunk 160 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 194 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 115 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Y 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y1764 GLN Y1830 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.079961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.054618 restraints weight = 42364.938| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 2.86 r_work: 0.2755 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17339 Z= 0.125 Angle : 0.539 14.862 23691 Z= 0.268 Chirality : 0.038 0.223 2572 Planarity : 0.003 0.062 2934 Dihedral : 15.388 174.008 2727 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.58 % Allowed : 17.29 % Favored : 81.13 % 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 (0.19), residues: 1993 helix: 2.04 (0.20), residues: 726 sheet: 0.06 (0.30), residues: 285 loop : -0.58 (0.19), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG Y 318 TYR 0.011 0.001 TYR Y1302 PHE 0.025 0.001 PHE Y1919 TRP 0.030 0.001 TRP Y1998 HIS 0.005 0.001 HIS Y1576 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (17319) covalent geometry : angle 0.53024 / 0.27 (23664) hydrogen bonds : bond 0.03268 / 3.61 ( 609) hydrogen bonds : angle 3.92294 / 4.36 ( 1678) metal coordination : bond 0.00568 / 0.78 ( 20) metal coordination : angle 2.99221 / 4.52 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3986 Ramachandran restraints generated. 1993 Oldfield, 0 Emsley, 1993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3986 Ramachandran restraints generated. 1993 Oldfield, 0 Emsley, 1993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 64 time to evaluate : 0.599 Fit side-chains REVERT: Y 123 GLU cc_start: 0.8410 (mp0) cc_final: 0.7726 (mp0) REVERT: Y 281 THR cc_start: 0.9543 (OUTLIER) cc_final: 0.9138 (p) REVERT: Y 296 GLU cc_start: 0.8448 (tm-30) cc_final: 0.8084 (tm-30) REVERT: Y 318 ARG cc_start: 0.8705 (mtm110) cc_final: 0.8499 (ptp-110) REVERT: Y 407 ASP cc_start: 0.8214 (p0) cc_final: 0.8011 (p0) REVERT: Y 645 ASP cc_start: 0.8848 (m-30) cc_final: 0.8352 (m-30) REVERT: Y 1709 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8513 (mm) REVERT: Y 1731 ASP cc_start: 0.8564 (m-30) cc_final: 0.8167 (t0) REVERT: Y 1776 LYS cc_start: 0.9243 (mppt) cc_final: 0.8962 (mmtt) REVERT: Y 1903 ASN cc_start: 0.7429 (OUTLIER) cc_final: 0.6262 (p0) REVERT: Y 1937 HIS cc_start: 0.8971 (OUTLIER) cc_final: 0.7853 (t70) REVERT: Y 1948 ARG cc_start: 0.8443 (pmt170) cc_final: 0.7871 (pmm-80) REVERT: Y 1959 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8899 (pp) REVERT: Y 1971 MET cc_start: 0.7962 (mmp) cc_final: 0.7743 (mpm) outliers start: 27 outliers final: 18 residues processed: 88 average time/residue: 0.5105 time to fit residues: 51.3266 Evaluate side-chains 86 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 63 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 31 SER Chi-restraints excluded: chain Y residue 119 SER Chi-restraints excluded: chain Y residue 124 CYS Chi-restraints excluded: chain Y residue 163 GLN Chi-restraints excluded: chain Y residue 281 THR Chi-restraints excluded: chain Y residue 332 VAL Chi-restraints excluded: chain Y residue 393 THR Chi-restraints excluded: chain Y residue 417 LEU Chi-restraints excluded: chain Y residue 438 SER Chi-restraints excluded: chain Y residue 823 VAL Chi-restraints excluded: chain Y residue 1012 VAL Chi-restraints excluded: chain Y residue 1437 VAL Chi-restraints excluded: chain Y residue 1493 VAL Chi-restraints excluded: chain Y residue 1553 THR Chi-restraints excluded: chain Y residue 1700 VAL Chi-restraints excluded: chain Y residue 1709 LEU Chi-restraints excluded: chain Y residue 1903 ASN Chi-restraints excluded: chain Y residue 1937 HIS Chi-restraints excluded: chain Y residue 1959 LEU Chi-restraints excluded: chain Y residue 1980 CYS Chi-restraints excluded: chain Y residue 2006 GLN Chi-restraints excluded: chain Y residue 2059 LEU Chi-restraints excluded: chain Y residue 2102 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: [77, 147, 16, 73, 102, 31, 56, 96, 146, 136, 78] chunk 77 optimal weight: 0.3980 chunk 147 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Y 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 917 ASN ** Y1121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y1764 GLN Y1830 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.079660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.054381 restraints weight = 42428.221| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 2.85 r_work: 0.2742 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17339 Z= 0.148 Angle : 0.566 14.822 23691 Z= 0.279 Chirality : 0.039 0.221 2572 Planarity : 0.004 0.059 2934 Dihedral : 15.434 174.325 2727 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.58 % Allowed : 17.41 % Favored : 81.01 % 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: 0.73 (0.19), residues: 1993 helix: 2.03 (0.20), residues: 726 sheet: 0.07 (0.30), residues: 285 loop : -0.56 (0.19), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG Y 318 TYR 0.011 0.001 TYR Y1302 PHE 0.020 0.001 PHE Y 125 TRP 0.063 0.001 TRP Y1998 HIS 0.005 0.001 HIS Y1576 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (17319) covalent geometry : angle 0.55582 / 0.28 (23664) hydrogen bonds : bond 0.03380 / 3.75 ( 609) hydrogen bonds : angle 3.93948 / 4.39 ( 1678) metal coordination : bond 0.00731 / 1.02 ( 20) metal coordination : angle 3.17940 / 4.79 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4060.52 seconds wall clock time: 70 minutes 14.58 seconds (4214.58 seconds total)