Starting phenix.real_space_refine on Sat Jul 4 03:06:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7oro_13044/07_2026/7oro_13044.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oro_13044/07_2026/7oro_13044.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/7oro_13044/07_2026/7oro_13044.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oro_13044/07_2026/7oro_13044.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7oro_13044/07_2026/7oro_13044.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7oro_13044/07_2026/7oro_13044.cif" model { file = "/net/cci-nas-00/data/ceres_data/7oro_13044/07_2026/7oro_13044.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oro_13044/07_2026/7oro_13044.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= 0.000 sd= 0.001 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 48 5.49 5 Mg 1 5.21 5 S 108 5.16 5 C 10962 2.51 5 N 2900 2.21 5 O 3396 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17416 Number of models: 1 Model: "" Number of chains: 6 Chain: "H" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 299 Classifications: {'RNA': 14} Modifications used: {'p5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 6, 'rna3p_pyr': 5} Link IDs: {'rna2p': 2, 'rna3p': 11} Chain: "S" Number of atoms: 297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 297 Classifications: {'RNA': 14} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 5, 'rna3p_pyr': 5} Link IDs: {'rna2p': 3, 'rna3p': 10} Chain: "T" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 231 Classifications: {'RNA': 11} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 4, 'rna3p_pyr': 5} Link IDs: {'rna2p': 1, 'rna3p': 9} Chain: "P" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 195 Classifications: {'RNA': 9} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 5, 'rna3p_pyr': 3} Link IDs: {'rna3p': 8} Chain: "A" Number of atoms: 16392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2008, 16392 Classifications: {'peptide': 2008} Link IDs: {'PTRANS': 67, 'TRANS': 1940} Chain breaks: 7 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16062 SG CYS A2064 61.365 30.363 27.421 1.00122.45 S Time building chain proxies: 3.74, per 1000 atoms: 0.21 Number of scatterers: 17416 At special positions: 0 Unit cell: (106.485, 130.53, 139.69, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 108 16.00 P 48 15.00 Mg 1 11.99 O 3396 8.00 N 2900 7.00 C 10962 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: 1.81 Conformation dependent library (CDL) restraints added in 946.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2301 " pdb="ZN ZN A2301 " - pdb=" NE2 HIS A2169 " pdb="ZN ZN A2301 " - pdb=" SG CYS A2064 " pdb="ZN ZN A2301 " - pdb=" NE2 HIS A2182 " 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3876 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 15 sheets defined 59.4% alpha, 8.9% beta 13 base pairs and 26 stacking pairs defined. Time for finding SS restraints: 2.36 Creating SS restraints... Processing helix chain 'A' and resid 2 through 16 Processing helix chain 'A' and resid 18 through 46 removed outlier: 3.865A pdb=" N LYS A 23 " --> pdb=" O ALA A 19 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ASP A 24 " --> pdb=" O CYS A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 63 Processing helix chain 'A' and resid 99 through 120 removed outlier: 4.619A pdb=" N ASP A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ILE A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 149 Processing helix chain 'A' and resid 158 through 172 Processing helix chain 'A' and resid 175 through 182 Processing helix chain 'A' and resid 200 through 203 Processing helix chain 'A' and resid 204 through 214 Processing helix chain 'A' and resid 215 through 227 Processing helix chain 'A' and resid 237 through 265 removed outlier: 4.745A pdb=" N LYS A 249 " --> pdb=" O GLU A 245 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N ASP A 250 " --> pdb=" O TYR A 246 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ILE A 262 " --> pdb=" O SER A 258 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N PHE A 263 " --> pdb=" O ALA A 259 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 292 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 319 through 333 Processing helix chain 'A' and resid 340 through 351 Processing helix chain 'A' and resid 356 through 373 Processing helix chain 'A' and resid 407 through 418 Processing helix chain 'A' and resid 447 through 466 Processing helix chain 'A' and resid 475 through 489 removed outlier: 5.916A pdb=" N SER A 483 " --> pdb=" O ASN A 479 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ARG A 484 " --> pdb=" O GLU A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 502 Processing helix chain 'A' and resid 502 through 522 removed outlier: 4.036A pdb=" N GLN A 506 " --> pdb=" O THR A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 620 Proline residue: A 608 - end of helix Processing helix chain 'A' and resid 626 through 639 removed outlier: 4.237A pdb=" N TYR A 636 " --> pdb=" O ASN A 632 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU A 639 " --> pdb=" O ILE A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 650 removed outlier: 3.986A pdb=" N LEU A 646 " --> pdb=" O THR A 642 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU A 648 " --> pdb=" O SER A 644 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLU A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 661 removed outlier: 4.249A pdb=" N TYR A 654 " --> pdb=" O GLU A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 673 Processing helix chain 'A' and resid 680 through 700 removed outlier: 3.633A pdb=" N PHE A 695 " --> pdb=" O LYS A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 704 removed outlier: 3.762A pdb=" N VAL A 704 " --> pdb=" O ARG A 701 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 701 through 704' Processing helix chain 'A' and resid 737 through 747 Processing helix chain 'A' and resid 748 through 752 removed outlier: 3.502A pdb=" N ASN A 752 " --> pdb=" O PHE A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 780 Processing helix chain 'A' and resid 795 through 814 removed outlier: 3.647A pdb=" N HIS A 814 " --> pdb=" O ASP A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 830 through 838 removed outlier: 3.511A pdb=" N THR A 833 " --> pdb=" O SER A 830 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE A 834 " --> pdb=" O ILE A 831 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N SER A 835 " --> pdb=" O THR A 832 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N THR A 836 " --> pdb=" O THR A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 854 Processing helix chain 'A' and resid 894 through 900 Processing helix chain 'A' and resid 911 through 921 Processing helix chain 'A' and resid 928 through 940 removed outlier: 3.637A pdb=" N GLN A 932 " --> pdb=" O PRO A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 985 removed outlier: 4.097A pdb=" N LEU A 984 " --> pdb=" O GLU A 980 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASN A 985 " --> pdb=" O ARG A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1020 removed outlier: 4.396A pdb=" N LYS A 999 " --> pdb=" O ASP A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1020 through 1028 Processing helix chain 'A' and resid 1043 through 1049 Processing helix chain 'A' and resid 1071 through 1079 removed outlier: 3.869A pdb=" N TRP A1075 " --> pdb=" O TYR A1071 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A1076 " --> pdb=" O LYS A1072 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1099 Processing helix chain 'A' and resid 1106 through 1115 Processing helix chain 'A' and resid 1123 through 1129 Processing helix chain 'A' and resid 1148 through 1174 Processing helix chain 'A' and resid 1201 through 1220 removed outlier: 3.781A pdb=" N ILE A1205 " --> pdb=" O GLU A1201 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE A1220 " --> pdb=" O ALA A1216 " (cutoff:3.500A) Processing helix chain 'A' and resid 1252 through 1258 Processing helix chain 'A' and resid 1259 through 1261 No H-bonds generated for 'chain 'A' and resid 1259 through 1261' Processing helix chain 'A' and resid 1267 through 1285 removed outlier: 3.522A pdb=" N SER A1274 " --> pdb=" O GLU A1270 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG A1275 " --> pdb=" O ASP A1271 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N SER A1278 " --> pdb=" O SER A1274 " (cutoff:3.500A) Processing helix chain 'A' and resid 1288 through 1307 Processing helix chain 'A' and resid 1340 through 1347 Processing helix chain 'A' and resid 1350 through 1365 Processing helix chain 'A' and resid 1366 through 1370 Processing helix chain 'A' and resid 1373 through 1380 Processing helix chain 'A' and resid 1381 through 1384 Processing helix chain 'A' and resid 1385 through 1389 Processing helix chain 'A' and resid 1390 through 1403 Processing helix chain 'A' and resid 1418 through 1422 Processing helix chain 'A' and resid 1441 through 1453 Processing helix chain 'A' and resid 1455 through 1467 removed outlier: 3.963A pdb=" N GLU A1459 " --> pdb=" O GLY A1455 " (cutoff:3.500A) Processing helix chain 'A' and resid 1468 through 1472 Processing helix chain 'A' and resid 1477 through 1489 removed outlier: 3.946A pdb=" N TYR A1489 " --> pdb=" O VAL A1485 " (cutoff:3.500A) Processing helix chain 'A' and resid 1491 through 1499 removed outlier: 3.648A pdb=" N LYS A1495 " --> pdb=" O SER A1491 " (cutoff:3.500A) Processing helix chain 'A' and resid 1502 through 1513 Processing helix chain 'A' and resid 1520 through 1526 removed outlier: 3.906A pdb=" N ILE A1524 " --> pdb=" O ASP A1520 " (cutoff:3.500A) Processing helix chain 'A' and resid 1548 through 1563 removed outlier: 3.738A pdb=" N SER A1562 " --> pdb=" O ARG A1558 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU A1563 " --> pdb=" O ASP A1559 " (cutoff:3.500A) Processing helix chain 'A' and resid 1566 through 1578 Processing helix chain 'A' and resid 1581 through 1593 Processing helix chain 'A' and resid 1622 through 1632 Processing helix chain 'A' and resid 1641 through 1660 removed outlier: 3.638A pdb=" N ALA A1646 " --> pdb=" O PRO A1642 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG A1647 " --> pdb=" O THR A1643 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP A1648 " --> pdb=" O GLU A1644 " (cutoff:3.500A) Processing helix chain 'A' and resid 1660 through 1677 Processing helix chain 'A' and resid 1680 through 1700 Processing helix chain 'A' and resid 1717 through 1729 Processing helix chain 'A' and resid 1760 through 1779 Processing helix chain 'A' and resid 1782 through 1795 removed outlier: 4.683A pdb=" N ALA A1786 " --> pdb=" O LEU A1782 " (cutoff:3.500A) Processing helix chain 'A' and resid 1802 through 1811 Processing helix chain 'A' and resid 1818 through 1825 removed outlier: 3.532A pdb=" N THR A1825 " --> pdb=" O LEU A1821 " (cutoff:3.500A) Processing helix chain 'A' and resid 1830 through 1840 Processing helix chain 'A' and resid 1983 through 1991 Processing helix chain 'A' and resid 2014 through 2019 removed outlier: 3.980A pdb=" N VAL A2019 " --> pdb=" O SER A2016 " (cutoff:3.500A) Processing helix chain 'A' and resid 2033 through 2039 Processing helix chain 'A' and resid 2046 through 2052 Processing helix chain 'A' and resid 2054 through 2059 Processing helix chain 'A' and resid 2060 through 2062 No H-bonds generated for 'chain 'A' and resid 2060 through 2062' Processing helix chain 'A' and resid 2069 through 2074 Processing helix chain 'A' and resid 2109 through 2129 Processing helix chain 'A' and resid 2138 through 2155 Processing helix chain 'A' and resid 2158 through 2176 Processing helix chain 'A' and resid 2177 through 2183 Processing helix chain 'A' and resid 2200 through 2210 Processing helix chain 'A' and resid 2216 through 2238 removed outlier: 4.340A pdb=" N VAL A2221 " --> pdb=" O PRO A2217 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N MET A2222 " --> pdb=" O PRO A2218 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE A2238 " --> pdb=" O ILE A2234 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 84 removed outlier: 6.583A pdb=" N LEU A 138 " --> pdb=" O LYS A1617 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 293 through 295 removed outlier: 5.869A pdb=" N GLU A 293 " --> pdb=" O ILE A 442 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 386 through 388 removed outlier: 5.672A pdb=" N LEU A 392 " --> pdb=" O MET A 400 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLN A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ILE A 561 " --> pdb=" O SER A 591 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY A 586 " --> pdb=" O CYS A 583 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 386 through 388 removed outlier: 5.672A pdb=" N LEU A 392 " --> pdb=" O MET A 400 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLN A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 663 through 664 Processing sheet with id=AA6, first strand: chain 'A' and resid 716 through 717 removed outlier: 6.616A pdb=" N ILE A 709 " --> pdb=" O TYR A2099 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N SER A2101 " --> pdb=" O ILE A 709 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N LEU A 711 " --> pdb=" O SER A2101 " (cutoff:3.500A) removed outlier: 11.236A pdb=" N ARG A2103 " --> pdb=" O LEU A 711 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 727 through 728 Processing sheet with id=AA8, first strand: chain 'A' and resid 842 through 846 Processing sheet with id=AA9, first strand: chain 'A' and resid 959 through 963 removed outlier: 6.450A pdb=" N PHE A 945 " --> pdb=" O ILE A1104 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1236 through 1237 Processing sheet with id=AB2, first strand: chain 'A' and resid 1594 through 1596 Processing sheet with id=AB3, first strand: chain 'A' and resid 1606 through 1609 Processing sheet with id=AB4, first strand: chain 'A' and resid 1800 through 1801 Processing sheet with id=AB5, first strand: chain 'A' and resid 1999 through 2000 Processing sheet with id=AB6, first strand: chain 'A' and resid 2027 through 2028 902 hydrogen bonds defined for protein. 2598 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 32 hydrogen bonds 64 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 26 stacking parallelities Total time for adding SS restraints: 5.04 Time building geometry restraints manager: 2.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3408 1.33 - 1.45: 4392 1.45 - 1.57: 9798 1.57 - 1.69: 92 1.69 - 1.81: 179 Bond restraints: 17869 Sorted by residual: bond pdb=" CA SER A 664 " pdb=" CB SER A 664 " ideal model delta sigma weight residual 1.533 1.478 0.055 1.66e-02 3.63e+03 1.10e+01 bond pdb=" N LEU A1828 " pdb=" CA LEU A1828 " ideal model delta sigma weight residual 1.457 1.499 -0.041 1.29e-02 6.01e+03 1.03e+01 bond pdb=" CA SER A1192 " pdb=" CB SER A1192 " ideal model delta sigma weight residual 1.531 1.486 0.045 1.52e-02 4.33e+03 8.65e+00 bond pdb=" N ILE A 656 " pdb=" CA ILE A 656 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.21e-02 6.83e+03 8.55e+00 bond pdb=" N ILE A 938 " pdb=" CA ILE A 938 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.21e-02 6.83e+03 7.89e+00 ... (remaining 17864 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 23985 2.53 - 5.06: 322 5.06 - 7.59: 14 7.59 - 10.13: 1 10.13 - 12.66: 2 Bond angle restraints: 24324 Sorted by residual: angle pdb=" N GLU A1350 " pdb=" CA GLU A1350 " pdb=" C GLU A1350 " ideal model delta sigma weight residual 113.38 100.72 12.66 1.23e+00 6.61e-01 1.06e+02 angle pdb=" N PRO A2217 " pdb=" CA PRO A2217 " pdb=" C PRO A2217 " ideal model delta sigma weight residual 110.70 121.42 -10.72 1.22e+00 6.72e-01 7.72e+01 angle pdb=" CA GLY A1436 " pdb=" C GLY A1436 " pdb=" O GLY A1436 " ideal model delta sigma weight residual 122.01 117.57 4.44 9.70e-01 1.06e+00 2.09e+01 angle pdb=" CA PRO A2217 " pdb=" C PRO A2217 " pdb=" N PRO A2218 " ideal model delta sigma weight residual 117.93 123.29 -5.36 1.20e+00 6.94e-01 1.99e+01 angle pdb=" CA ASP A 35 " pdb=" CB ASP A 35 " pdb=" CG ASP A 35 " ideal model delta sigma weight residual 112.60 116.65 -4.05 1.00e+00 1.00e+00 1.64e+01 ... (remaining 24319 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.44: 9919 18.44 - 36.89: 717 36.89 - 55.33: 113 55.33 - 73.78: 23 73.78 - 92.22: 6 Dihedral angle restraints: 10778 sinusoidal: 4812 harmonic: 5966 Sorted by residual: dihedral pdb=" O4' G S 16 " pdb=" C1' G S 16 " pdb=" N9 G S 16 " pdb=" C4 G S 16 " ideal model delta sinusoidal sigma weight residual 70.00 -9.60 79.60 1 2.00e+01 2.50e-03 1.97e+01 dihedral pdb=" CA THR A2093 " pdb=" C THR A2093 " pdb=" N PRO A2094 " pdb=" CA PRO A2094 " ideal model delta harmonic sigma weight residual 180.00 158.34 21.66 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA TRP A1143 " pdb=" C TRP A1143 " pdb=" N LEU A1144 " pdb=" CA LEU A1144 " ideal model delta harmonic sigma weight residual -180.00 -159.53 -20.47 0 5.00e+00 4.00e-02 1.68e+01 ... (remaining 10775 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2352 0.062 - 0.124: 336 0.124 - 0.185: 43 0.185 - 0.247: 9 0.247 - 0.309: 5 Chirality restraints: 2745 Sorted by residual: chirality pdb=" CA ILE A 388 " pdb=" N ILE A 388 " pdb=" C ILE A 388 " pdb=" CB ILE A 388 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" CA PRO A2217 " pdb=" N PRO A2217 " pdb=" C PRO A2217 " pdb=" CB PRO A2217 " both_signs ideal model delta sigma weight residual False 2.72 2.42 0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CA ILE A2216 " pdb=" N ILE A2216 " pdb=" C ILE A2216 " pdb=" CB ILE A2216 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 2742 not shown) Planarity restraints: 2903 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A1641 " 0.054 5.00e-02 4.00e+02 8.13e-02 1.06e+01 pdb=" N PRO A1642 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO A1642 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO A1642 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A1349 " -0.015 2.00e-02 2.50e+03 3.14e-02 9.88e+00 pdb=" C LEU A1349 " 0.054 2.00e-02 2.50e+03 pdb=" O LEU A1349 " -0.021 2.00e-02 2.50e+03 pdb=" N GLU A1350 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A1826 " -0.013 2.00e-02 2.50e+03 2.72e-02 7.38e+00 pdb=" C GLY A1826 " 0.047 2.00e-02 2.50e+03 pdb=" O GLY A1826 " -0.017 2.00e-02 2.50e+03 pdb=" N ASP A1827 " -0.016 2.00e-02 2.50e+03 ... (remaining 2900 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 90 2.59 - 3.17: 14878 3.17 - 3.75: 28058 3.75 - 4.32: 40336 4.32 - 4.90: 65601 Nonbonded interactions: 148963 Sorted by model distance: nonbonded pdb=" OD1 ASP A1188 " pdb="MG MG A2302 " model vdw 2.015 2.170 nonbonded pdb=" O ILE A2118 " pdb=" OG1 THR A2122 " model vdw 2.210 3.040 nonbonded pdb=" OG SER A1443 " pdb=" OH TYR A1489 " model vdw 2.277 3.040 nonbonded pdb=" OD2 ASP A1413 " pdb=" OH TYR A1576 " model vdw 2.330 3.040 nonbonded pdb=" OG1 THR A2122 " pdb=" NZ LYS A2174 " model vdw 2.340 3.120 ... (remaining 148958 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: 1.610 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 23.610 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 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 : 0.006 0.497 17872 Z= 0.299 Angle : 0.677 12.658 24324 Z= 0.442 Chirality : 0.047 0.309 2745 Planarity : 0.004 0.081 2903 Dihedral : 12.691 92.223 6902 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.22 % Allowed : 0.92 % Favored : 98.87 % 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: 1.47 (0.19), residues: 1992 helix: 2.03 (0.16), residues: 1080 sheet: 0.71 (0.41), residues: 151 loop : -0.50 (0.22), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1690 TYR 0.016 0.001 TYR A2181 PHE 0.024 0.001 PHE A1768 TRP 0.011 0.001 TRP A2160 HIS 0.004 0.001 HIS A 760 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.27 (17869) covalent geometry : angle 0.67683 / 0.44 (24324) hydrogen bonds : bond 0.11938 / 7.09 ( 918) hydrogen bonds : angle 5.36079 / 3.62 ( 2662) metal coordination : bond 0.28721 / 14.36 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 176 time to evaluate : 0.721 Fit side-chains REVERT: A 763 MET cc_start: 0.9065 (mmt) cc_final: 0.8857 (mmp) REVERT: A 2070 ILE cc_start: 0.7895 (pt) cc_final: 0.7659 (mt) outliers start: 4 outliers final: 0 residues processed: 178 average time/residue: 0.7519 time to fit residues: 147.6887 Evaluate side-chains 125 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 8.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 0.0570 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 overall best weight: 1.7904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 51 ASN A 166 GLN A 397 GLN A 620 HIS A 985 ASN A1007 GLN A1181 ASN A1334 ASN A1448 GLN A1515 HIS A2040 GLN ** A2049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2141 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.100900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.073523 restraints weight = 30812.381| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 2.12 r_work: 0.2856 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.1047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 17872 Z= 0.205 Angle : 0.555 9.672 24324 Z= 0.298 Chirality : 0.042 0.179 2745 Planarity : 0.004 0.052 2903 Dihedral : 7.882 99.157 2740 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.71 % Favored : 97.24 % Rotamer: Outliers : 1.24 % Allowed : 7.18 % Favored : 91.58 % 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: 1.34 (0.19), residues: 1992 helix: 1.87 (0.16), residues: 1089 sheet: 0.54 (0.42), residues: 142 loop : -0.45 (0.23), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1829 TYR 0.016 0.002 TYR A 669 PHE 0.022 0.002 PHE A1768 TRP 0.009 0.001 TRP A1143 HIS 0.009 0.001 HIS A2169 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.21 (17869) covalent geometry : angle 0.55536 / 0.30 (24324) hydrogen bonds : bond 0.04979 / 2.99 ( 918) hydrogen bonds : angle 4.36521 / 2.87 ( 2662) metal coordination : bond 0.00259 / 0.15 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 0.758 Fit side-chains REVERT: A 1095 MET cc_start: 0.9155 (mtp) cc_final: 0.8949 (mtt) REVERT: A 1657 GLU cc_start: 0.8326 (mp0) cc_final: 0.8120 (mp0) REVERT: A 1671 MET cc_start: 0.7363 (ttt) cc_final: 0.7080 (ttm) REVERT: A 1690 ARG cc_start: 0.8405 (mtp180) cc_final: 0.8037 (ttm-80) REVERT: A 2044 ASN cc_start: 0.9003 (t0) cc_final: 0.8765 (t0) REVERT: A 2070 ILE cc_start: 0.8005 (pt) cc_final: 0.7748 (mt) REVERT: A 2204 PHE cc_start: 0.6505 (OUTLIER) cc_final: 0.5979 (t80) outliers start: 23 outliers final: 10 residues processed: 143 average time/residue: 0.6743 time to fit residues: 108.0117 Evaluate side-chains 131 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ARG Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 497 HIS Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 1478 MET Chi-restraints excluded: chain A residue 1616 LEU Chi-restraints excluded: chain A residue 1685 LEU Chi-restraints excluded: chain A residue 1987 LEU Chi-restraints excluded: chain A residue 2093 THR Chi-restraints excluded: chain A residue 2204 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 196 optimal weight: 7.9990 chunk 134 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 1 optimal weight: 8.9990 chunk 172 optimal weight: 0.8980 chunk 143 optimal weight: 2.9990 chunk 202 optimal weight: 6.9990 chunk 160 optimal weight: 0.9980 chunk 199 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 51 ASN A 319 ASN A1502 ASN ** A2049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2141 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.100781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.073553 restraints weight = 31144.004| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 2.13 r_work: 0.2852 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 17872 Z= 0.175 Angle : 0.518 8.761 24324 Z= 0.278 Chirality : 0.041 0.180 2745 Planarity : 0.004 0.043 2903 Dihedral : 7.869 98.572 2740 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.56 % Favored : 97.39 % Rotamer: Outliers : 1.83 % Allowed : 8.69 % Favored : 89.48 % 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: 1.32 (0.19), residues: 1992 helix: 1.87 (0.16), residues: 1089 sheet: 0.71 (0.43), residues: 132 loop : -0.53 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A1439 TYR 0.014 0.001 TYR A 504 PHE 0.022 0.001 PHE A1768 TRP 0.010 0.001 TRP A1143 HIS 0.008 0.001 HIS A2169 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.18 (17869) covalent geometry : angle 0.51754 / 0.28 (24324) hydrogen bonds : bond 0.04627 / 2.78 ( 918) hydrogen bonds : angle 4.21589 / 2.76 ( 2662) metal coordination : bond 0.00200 / 0.12 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 134 time to evaluate : 0.658 Fit side-chains REVERT: A 166 GLN cc_start: 0.7976 (OUTLIER) cc_final: 0.7724 (mm-40) REVERT: A 231 TYR cc_start: 0.8165 (OUTLIER) cc_final: 0.7757 (t80) REVERT: A 732 PHE cc_start: 0.9683 (OUTLIER) cc_final: 0.8338 (p90) REVERT: A 1018 GLN cc_start: 0.8705 (tm-30) cc_final: 0.8492 (tm-30) REVERT: A 1671 MET cc_start: 0.7403 (ttt) cc_final: 0.7112 (ttm) REVERT: A 1690 ARG cc_start: 0.8395 (mtp180) cc_final: 0.8068 (ttm-80) REVERT: A 1982 ILE cc_start: 0.6815 (OUTLIER) cc_final: 0.6572 (mm) REVERT: A 2044 ASN cc_start: 0.9031 (t0) cc_final: 0.8804 (t0) REVERT: A 2070 ILE cc_start: 0.7977 (pt) cc_final: 0.7765 (mt) REVERT: A 2108 MET cc_start: 0.8292 (ptp) cc_final: 0.7996 (ptm) REVERT: A 2203 MET cc_start: 0.5801 (tmm) cc_final: 0.4901 (ttt) REVERT: A 2204 PHE cc_start: 0.6493 (OUTLIER) cc_final: 0.5825 (t80) outliers start: 34 outliers final: 13 residues processed: 150 average time/residue: 0.6731 time to fit residues: 113.0071 Evaluate side-chains 138 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ARG Chi-restraints excluded: chain A residue 166 GLN Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 497 HIS Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 732 PHE Chi-restraints excluded: chain A residue 1112 ASN Chi-restraints excluded: chain A residue 1478 MET Chi-restraints excluded: chain A residue 1616 LEU Chi-restraints excluded: chain A residue 1685 LEU Chi-restraints excluded: chain A residue 1982 ILE Chi-restraints excluded: chain A residue 1987 LEU Chi-restraints excluded: chain A residue 2093 THR Chi-restraints excluded: chain A residue 2141 ASN Chi-restraints excluded: chain A residue 2204 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 7 optimal weight: 0.0770 chunk 109 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 176 optimal weight: 0.0970 chunk 100 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 187 optimal weight: 9.9990 chunk 21 optimal weight: 4.9990 chunk 119 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 overall best weight: 1.0140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 51 ASN A 760 HIS A1502 ASN A2049 ASN A2141 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.101531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.074498 restraints weight = 31192.752| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 2.11 r_work: 0.2873 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17872 Z= 0.137 Angle : 0.485 8.519 24324 Z= 0.260 Chirality : 0.039 0.181 2745 Planarity : 0.004 0.041 2903 Dihedral : 7.809 97.598 2740 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.66 % Favored : 97.29 % Rotamer: Outliers : 1.78 % Allowed : 10.20 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.19), residues: 1992 helix: 1.95 (0.16), residues: 1089 sheet: 0.70 (0.44), residues: 132 loop : -0.53 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A1439 TYR 0.012 0.001 TYR A 669 PHE 0.021 0.001 PHE A1768 TRP 0.011 0.001 TRP A1143 HIS 0.006 0.001 HIS A2169 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (17869) covalent geometry : angle 0.48479 / 0.26 (24324) hydrogen bonds : bond 0.04210 / 2.53 ( 918) hydrogen bonds : angle 4.08747 / 2.68 ( 2662) metal coordination : bond 0.00088 / 0.06 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 0.672 Fit side-chains REVERT: A 166 GLN cc_start: 0.7992 (mp10) cc_final: 0.7735 (mm-40) REVERT: A 231 TYR cc_start: 0.8172 (OUTLIER) cc_final: 0.7770 (t80) REVERT: A 424 HIS cc_start: 0.6348 (OUTLIER) cc_final: 0.5698 (m-70) REVERT: A 534 MET cc_start: 0.9053 (OUTLIER) cc_final: 0.8762 (mtp) REVERT: A 732 PHE cc_start: 0.9674 (OUTLIER) cc_final: 0.8405 (p90) REVERT: A 1671 MET cc_start: 0.7347 (ttt) cc_final: 0.7063 (ttm) REVERT: A 1690 ARG cc_start: 0.8396 (mtp180) cc_final: 0.8031 (ttm-80) REVERT: A 1817 ASP cc_start: 0.8602 (m-30) cc_final: 0.8129 (p0) REVERT: A 1982 ILE cc_start: 0.6741 (OUTLIER) cc_final: 0.6491 (mm) REVERT: A 2044 ASN cc_start: 0.9037 (t0) cc_final: 0.8800 (t0) REVERT: A 2108 MET cc_start: 0.8212 (ptp) cc_final: 0.7874 (ptm) REVERT: A 2203 MET cc_start: 0.5964 (tmm) cc_final: 0.5589 (ttt) outliers start: 33 outliers final: 13 residues processed: 151 average time/residue: 0.6270 time to fit residues: 106.4411 Evaluate side-chains 136 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ARG Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 497 HIS Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 732 PHE Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1478 MET Chi-restraints excluded: chain A residue 1502 ASN Chi-restraints excluded: chain A residue 1616 LEU Chi-restraints excluded: chain A residue 1685 LEU Chi-restraints excluded: chain A residue 1702 THR Chi-restraints excluded: chain A residue 1825 THR Chi-restraints excluded: chain A residue 1982 ILE Chi-restraints excluded: chain A residue 1987 LEU Chi-restraints excluded: chain A residue 2040 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 1 optimal weight: 8.9990 chunk 194 optimal weight: 9.9990 chunk 139 optimal weight: 0.1980 chunk 121 optimal weight: 2.9990 chunk 21 optimal weight: 0.0870 chunk 95 optimal weight: 2.9990 chunk 178 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 202 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 overall best weight: 1.2562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.101087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.075094 restraints weight = 30850.863| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 2.04 r_work: 0.2871 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17872 Z= 0.154 Angle : 0.495 8.396 24324 Z= 0.265 Chirality : 0.040 0.178 2745 Planarity : 0.004 0.052 2903 Dihedral : 7.798 97.433 2740 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.66 % Favored : 97.29 % Rotamer: Outliers : 1.67 % Allowed : 11.17 % Favored : 87.16 % 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: 1.38 (0.19), residues: 1992 helix: 1.95 (0.16), residues: 1089 sheet: 0.69 (0.44), residues: 132 loop : -0.55 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A1439 TYR 0.012 0.001 TYR A 669 PHE 0.022 0.001 PHE A1768 TRP 0.010 0.001 TRP A1143 HIS 0.006 0.001 HIS A 760 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 (17869) covalent geometry : angle 0.49512 / 0.27 (24324) hydrogen bonds : bond 0.04310 / 2.60 ( 918) hydrogen bonds : angle 4.05492 / 2.65 ( 2662) metal coordination : bond 0.00140 / 0.09 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 126 time to evaluate : 0.712 Fit side-chains REVERT: A 166 GLN cc_start: 0.7982 (mp10) cc_final: 0.7721 (mm-40) REVERT: A 195 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8630 (mptp) REVERT: A 231 TYR cc_start: 0.8187 (OUTLIER) cc_final: 0.7792 (t80) REVERT: A 412 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8621 (mp) REVERT: A 424 HIS cc_start: 0.6350 (OUTLIER) cc_final: 0.5710 (m-70) REVERT: A 534 MET cc_start: 0.9057 (OUTLIER) cc_final: 0.8822 (mtp) REVERT: A 732 PHE cc_start: 0.9671 (OUTLIER) cc_final: 0.8401 (p90) REVERT: A 1671 MET cc_start: 0.7373 (ttt) cc_final: 0.7088 (ttm) REVERT: A 1690 ARG cc_start: 0.8392 (mtp180) cc_final: 0.8002 (ttm-80) REVERT: A 1817 ASP cc_start: 0.8607 (m-30) cc_final: 0.8162 (p0) REVERT: A 1982 ILE cc_start: 0.6757 (OUTLIER) cc_final: 0.6539 (mm) REVERT: A 1989 TYR cc_start: 0.8415 (t80) cc_final: 0.8196 (t80) REVERT: A 2108 MET cc_start: 0.8157 (ptp) cc_final: 0.7810 (ptm) outliers start: 31 outliers final: 10 residues processed: 147 average time/residue: 0.6563 time to fit residues: 108.0765 Evaluate side-chains 135 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 497 HIS Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 732 PHE Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1478 MET Chi-restraints excluded: chain A residue 1616 LEU Chi-restraints excluded: chain A residue 1702 THR Chi-restraints excluded: chain A residue 1825 THR Chi-restraints excluded: chain A residue 1982 ILE Chi-restraints excluded: chain A residue 1987 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 36 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 148 optimal weight: 6.9990 chunk 145 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 192 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 80 optimal weight: 0.3980 chunk 28 optimal weight: 4.9990 chunk 158 optimal weight: 1.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.100628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.074184 restraints weight = 31309.500| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.05 r_work: 0.2882 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 17872 Z= 0.168 Angle : 0.511 10.393 24324 Z= 0.273 Chirality : 0.040 0.177 2745 Planarity : 0.004 0.052 2903 Dihedral : 7.812 97.416 2740 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.96 % Favored : 96.99 % Rotamer: Outliers : 2.16 % Allowed : 11.28 % Favored : 86.56 % 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: 1.33 (0.19), residues: 1992 helix: 1.93 (0.16), residues: 1089 sheet: 0.64 (0.44), residues: 132 loop : -0.60 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A1439 TYR 0.014 0.001 TYR A 504 PHE 0.023 0.001 PHE A1768 TRP 0.010 0.001 TRP A1143 HIS 0.007 0.001 HIS A 760 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 (17869) covalent geometry : angle 0.51145 / 0.27 (24324) hydrogen bonds : bond 0.04453 / 2.68 ( 918) hydrogen bonds : angle 4.06142 / 2.66 ( 2662) metal coordination : bond 0.00191 / 0.12 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 127 time to evaluate : 0.668 Fit side-chains REVERT: A 195 LYS cc_start: 0.8979 (OUTLIER) cc_final: 0.8606 (mptp) REVERT: A 231 TYR cc_start: 0.8306 (OUTLIER) cc_final: 0.7878 (t80) REVERT: A 412 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8641 (mp) REVERT: A 424 HIS cc_start: 0.6296 (OUTLIER) cc_final: 0.5693 (m-70) REVERT: A 534 MET cc_start: 0.9026 (OUTLIER) cc_final: 0.8815 (mtp) REVERT: A 732 PHE cc_start: 0.9677 (OUTLIER) cc_final: 0.8376 (p90) REVERT: A 1056 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8232 (mm-30) REVERT: A 1080 ASP cc_start: 0.8488 (OUTLIER) cc_final: 0.7940 (t0) REVERT: A 1502 ASN cc_start: 0.8210 (OUTLIER) cc_final: 0.7986 (m-40) REVERT: A 1671 MET cc_start: 0.7352 (ttt) cc_final: 0.7055 (ttm) REVERT: A 1690 ARG cc_start: 0.8425 (mtp180) cc_final: 0.8072 (ttm-80) REVERT: A 1817 ASP cc_start: 0.8607 (m-30) cc_final: 0.8189 (OUTLIER) REVERT: A 1982 ILE cc_start: 0.6865 (OUTLIER) cc_final: 0.6652 (mm) REVERT: A 1989 TYR cc_start: 0.8295 (t80) cc_final: 0.8064 (t80) REVERT: A 2108 MET cc_start: 0.8095 (ptp) cc_final: 0.7755 (ptm) REVERT: A 2202 VAL cc_start: 0.6877 (OUTLIER) cc_final: 0.6619 (p) REVERT: A 2203 MET cc_start: 0.5439 (tmm) cc_final: 0.4658 (ttp) outliers start: 40 outliers final: 15 residues processed: 149 average time/residue: 0.6336 time to fit residues: 105.9711 Evaluate side-chains 143 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 118 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 144 ARG Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 497 HIS Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 732 PHE Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1080 ASP Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1478 MET Chi-restraints excluded: chain A residue 1502 ASN Chi-restraints excluded: chain A residue 1616 LEU Chi-restraints excluded: chain A residue 1702 THR Chi-restraints excluded: chain A residue 1708 VAL Chi-restraints excluded: chain A residue 1825 THR Chi-restraints excluded: chain A residue 1982 ILE Chi-restraints excluded: chain A residue 1987 LEU Chi-restraints excluded: chain A residue 2000 ILE Chi-restraints excluded: chain A residue 2202 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 41 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 chunk 129 optimal weight: 0.6980 chunk 154 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 177 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 173 optimal weight: 0.9980 chunk 80 optimal weight: 0.3980 chunk 101 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.101050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.074215 restraints weight = 30959.657| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 2.10 r_work: 0.2870 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 17872 Z= 0.136 Angle : 0.495 9.401 24324 Z= 0.263 Chirality : 0.039 0.209 2745 Planarity : 0.004 0.063 2903 Dihedral : 7.755 96.621 2740 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.76 % Favored : 97.19 % Rotamer: Outliers : 1.67 % Allowed : 12.20 % Favored : 86.13 % 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: 1.41 (0.19), residues: 1992 helix: 2.01 (0.16), residues: 1089 sheet: 0.65 (0.45), residues: 132 loop : -0.57 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG A1439 TYR 0.011 0.001 TYR A 677 PHE 0.034 0.001 PHE A2207 TRP 0.011 0.001 TRP A1143 HIS 0.006 0.001 HIS A 760 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (17869) covalent geometry : angle 0.49458 / 0.26 (24324) hydrogen bonds : bond 0.04106 / 2.47 ( 918) hydrogen bonds : angle 4.00174 / 2.63 ( 2662) metal coordination : bond 0.00068 / 0.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 123 time to evaluate : 0.728 Fit side-chains REVERT: A 231 TYR cc_start: 0.8315 (OUTLIER) cc_final: 0.7971 (t80) REVERT: A 412 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8595 (mp) REVERT: A 424 HIS cc_start: 0.6371 (OUTLIER) cc_final: 0.5764 (m-70) REVERT: A 534 MET cc_start: 0.9021 (OUTLIER) cc_final: 0.8816 (mtp) REVERT: A 686 MET cc_start: 0.9180 (OUTLIER) cc_final: 0.8424 (mtt) REVERT: A 732 PHE cc_start: 0.9673 (OUTLIER) cc_final: 0.8366 (p90) REVERT: A 971 MET cc_start: 0.9150 (OUTLIER) cc_final: 0.8512 (mtp) REVERT: A 1056 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8243 (mm-30) REVERT: A 1080 ASP cc_start: 0.8523 (OUTLIER) cc_final: 0.7968 (t0) REVERT: A 1671 MET cc_start: 0.7411 (ttt) cc_final: 0.7135 (ttm) REVERT: A 1690 ARG cc_start: 0.8391 (mtp180) cc_final: 0.8049 (ttm-80) REVERT: A 1817 ASP cc_start: 0.8599 (m-30) cc_final: 0.8167 (OUTLIER) REVERT: A 1989 TYR cc_start: 0.8360 (t80) cc_final: 0.8121 (t80) REVERT: A 2151 LEU cc_start: 0.7780 (tp) cc_final: 0.7553 (tt) REVERT: A 2203 MET cc_start: 0.5486 (tmm) cc_final: 0.5041 (ttp) outliers start: 31 outliers final: 12 residues processed: 142 average time/residue: 0.6919 time to fit residues: 109.6931 Evaluate side-chains 138 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 497 HIS Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 732 PHE Chi-restraints excluded: chain A residue 971 MET Chi-restraints excluded: chain A residue 1016 THR Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1080 ASP Chi-restraints excluded: chain A residue 1478 MET Chi-restraints excluded: chain A residue 1616 LEU Chi-restraints excluded: chain A residue 1702 THR Chi-restraints excluded: chain A residue 1708 VAL Chi-restraints excluded: chain A residue 1987 LEU Chi-restraints excluded: chain A residue 2000 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 148 optimal weight: 1.9990 chunk 169 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 8 optimal weight: 7.9990 chunk 78 optimal weight: 2.9990 chunk 10 optimal weight: 0.0070 chunk 195 optimal weight: 7.9990 chunk 158 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 41 optimal weight: 0.4980 overall best weight: 1.1004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.100789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.074039 restraints weight = 31395.738| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 2.07 r_work: 0.2876 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 17872 Z= 0.143 Angle : 0.506 8.784 24324 Z= 0.269 Chirality : 0.040 0.178 2745 Planarity : 0.004 0.071 2903 Dihedral : 7.733 96.246 2740 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.86 % Favored : 97.09 % Rotamer: Outliers : 1.73 % Allowed : 12.47 % Favored : 85.81 % 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: 1.40 (0.19), residues: 1992 helix: 2.00 (0.16), residues: 1090 sheet: 0.66 (0.45), residues: 132 loop : -0.57 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG A1439 TYR 0.011 0.001 TYR A 669 PHE 0.027 0.001 PHE A2207 TRP 0.010 0.001 TRP A1143 HIS 0.006 0.001 HIS A 760 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (17869) covalent geometry : angle 0.50573 / 0.27 (24324) hydrogen bonds : bond 0.04165 / 2.50 ( 918) hydrogen bonds : angle 3.99758 / 2.63 ( 2662) metal coordination : bond 0.00171 / 0.11 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 120 time to evaluate : 0.668 Fit side-chains REVERT: A 143 ASP cc_start: 0.8166 (p0) cc_final: 0.7890 (p0) REVERT: A 166 GLN cc_start: 0.7969 (mp10) cc_final: 0.7719 (mm-40) REVERT: A 231 TYR cc_start: 0.8323 (OUTLIER) cc_final: 0.7981 (t80) REVERT: A 412 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8640 (mp) REVERT: A 424 HIS cc_start: 0.6376 (OUTLIER) cc_final: 0.5771 (m-70) REVERT: A 686 MET cc_start: 0.9197 (OUTLIER) cc_final: 0.8450 (mtt) REVERT: A 732 PHE cc_start: 0.9664 (OUTLIER) cc_final: 0.8362 (p90) REVERT: A 971 MET cc_start: 0.9202 (OUTLIER) cc_final: 0.8549 (mtp) REVERT: A 1056 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8215 (mm-30) REVERT: A 1080 ASP cc_start: 0.8480 (OUTLIER) cc_final: 0.7934 (t0) REVERT: A 1671 MET cc_start: 0.7384 (ttt) cc_final: 0.7101 (ttm) REVERT: A 1690 ARG cc_start: 0.8400 (mtp180) cc_final: 0.8069 (ttm-80) REVERT: A 1817 ASP cc_start: 0.8598 (m-30) cc_final: 0.8162 (OUTLIER) REVERT: A 1989 TYR cc_start: 0.8308 (t80) cc_final: 0.8068 (t80) REVERT: A 2108 MET cc_start: 0.8214 (ptp) cc_final: 0.7903 (ptm) REVERT: A 2151 LEU cc_start: 0.7834 (tp) cc_final: 0.7553 (tt) REVERT: A 2177 MET cc_start: 0.7233 (tpt) cc_final: 0.6910 (tmt) REVERT: A 2203 MET cc_start: 0.5448 (tmm) cc_final: 0.4623 (ttt) outliers start: 32 outliers final: 15 residues processed: 142 average time/residue: 0.6480 time to fit residues: 102.9965 Evaluate side-chains 139 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 497 HIS Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 732 PHE Chi-restraints excluded: chain A residue 938 ILE Chi-restraints excluded: chain A residue 971 MET Chi-restraints excluded: chain A residue 1016 THR Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1080 ASP Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1478 MET Chi-restraints excluded: chain A residue 1702 THR Chi-restraints excluded: chain A residue 1708 VAL Chi-restraints excluded: chain A residue 1825 THR Chi-restraints excluded: chain A residue 1987 LEU Chi-restraints excluded: chain A residue 2000 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 105 optimal weight: 0.4980 chunk 153 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 118 optimal weight: 4.9990 chunk 175 optimal weight: 2.9990 chunk 198 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 chunk 167 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.099685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.072895 restraints weight = 31659.350| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.07 r_work: 0.2851 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 17872 Z= 0.186 Angle : 0.539 9.447 24324 Z= 0.285 Chirality : 0.041 0.177 2745 Planarity : 0.004 0.072 2903 Dihedral : 7.769 96.894 2740 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.91 % Favored : 97.04 % Rotamer: Outliers : 1.46 % Allowed : 12.84 % Favored : 85.70 % 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: 1.27 (0.19), residues: 1992 helix: 1.87 (0.16), residues: 1089 sheet: 0.60 (0.45), residues: 132 loop : -0.60 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A1439 TYR 0.015 0.001 TYR A 669 PHE 0.039 0.001 PHE A2207 TRP 0.008 0.001 TRP A1143 HIS 0.008 0.001 HIS A 760 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.19 (17869) covalent geometry : angle 0.53904 / 0.29 (24324) hydrogen bonds : bond 0.04578 / 2.75 ( 918) hydrogen bonds : angle 4.09508 / 2.69 ( 2662) metal coordination : bond 0.00326 / 0.20 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 118 time to evaluate : 0.740 Fit side-chains REVERT: A 162 PHE cc_start: 0.8334 (m-80) cc_final: 0.8129 (m-80) REVERT: A 166 GLN cc_start: 0.7978 (mp10) cc_final: 0.7727 (mm-40) REVERT: A 231 TYR cc_start: 0.8367 (OUTLIER) cc_final: 0.8041 (t80) REVERT: A 412 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8641 (mp) REVERT: A 424 HIS cc_start: 0.6440 (OUTLIER) cc_final: 0.5733 (m-70) REVERT: A 732 PHE cc_start: 0.9684 (OUTLIER) cc_final: 0.8355 (p90) REVERT: A 971 MET cc_start: 0.9208 (OUTLIER) cc_final: 0.8677 (mtp) REVERT: A 1056 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8230 (mm-30) REVERT: A 1080 ASP cc_start: 0.8487 (OUTLIER) cc_final: 0.7932 (t0) REVERT: A 1671 MET cc_start: 0.7388 (ttt) cc_final: 0.7095 (ttm) REVERT: A 1690 ARG cc_start: 0.8386 (mtp180) cc_final: 0.8039 (ttm-80) REVERT: A 1817 ASP cc_start: 0.8669 (m-30) cc_final: 0.8194 (OUTLIER) REVERT: A 1989 TYR cc_start: 0.8309 (t80) cc_final: 0.8066 (t80) REVERT: A 2108 MET cc_start: 0.8176 (ptp) cc_final: 0.7823 (ptm) REVERT: A 2177 MET cc_start: 0.7327 (tpt) cc_final: 0.6975 (tmt) REVERT: A 2202 VAL cc_start: 0.6912 (OUTLIER) cc_final: 0.6684 (p) outliers start: 27 outliers final: 17 residues processed: 136 average time/residue: 0.6472 time to fit residues: 98.9582 Evaluate side-chains 140 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 116 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 497 HIS Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 732 PHE Chi-restraints excluded: chain A residue 938 ILE Chi-restraints excluded: chain A residue 971 MET Chi-restraints excluded: chain A residue 1016 THR Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1080 ASP Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1343 MET Chi-restraints excluded: chain A residue 1478 MET Chi-restraints excluded: chain A residue 1702 THR Chi-restraints excluded: chain A residue 1708 VAL Chi-restraints excluded: chain A residue 1825 THR Chi-restraints excluded: chain A residue 1987 LEU Chi-restraints excluded: chain A residue 2000 ILE Chi-restraints excluded: chain A residue 2202 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 33 optimal weight: 0.7980 chunk 79 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 145 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 66 optimal weight: 0.0980 chunk 182 optimal weight: 0.5980 chunk 190 optimal weight: 0.8980 chunk 134 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 51 ASN A 332 GLN A1615 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.101887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.075133 restraints weight = 31012.199| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.09 r_work: 0.2894 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 17872 Z= 0.111 Angle : 0.499 11.900 24324 Z= 0.262 Chirality : 0.039 0.178 2745 Planarity : 0.004 0.085 2903 Dihedral : 7.674 96.156 2740 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.51 % Favored : 97.44 % Rotamer: Outliers : 1.35 % Allowed : 13.38 % Favored : 85.27 % 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: 1.47 (0.19), residues: 1992 helix: 2.04 (0.16), residues: 1090 sheet: 0.70 (0.45), residues: 132 loop : -0.53 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.000 ARG A1439 TYR 0.011 0.001 TYR A 669 PHE 0.028 0.001 PHE A2207 TRP 0.012 0.001 TRP A1143 HIS 0.005 0.001 HIS A 760 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (17869) covalent geometry : angle 0.49895 / 0.26 (24324) hydrogen bonds : bond 0.03815 / 2.29 ( 918) hydrogen bonds : angle 3.95177 / 2.60 ( 2662) metal coordination : bond 0.00096 / 0.06 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 0.724 Fit side-chains REVERT: A 166 GLN cc_start: 0.7981 (mp10) cc_final: 0.7715 (mm110) REVERT: A 412 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8601 (mp) REVERT: A 424 HIS cc_start: 0.6349 (OUTLIER) cc_final: 0.5784 (m-70) REVERT: A 686 MET cc_start: 0.9248 (OUTLIER) cc_final: 0.8575 (mtt) REVERT: A 718 GLN cc_start: 0.7517 (tt0) cc_final: 0.6817 (tm-30) REVERT: A 732 PHE cc_start: 0.9655 (OUTLIER) cc_final: 0.8384 (p90) REVERT: A 1056 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8195 (mm-30) REVERT: A 1671 MET cc_start: 0.7379 (ttt) cc_final: 0.7104 (ttm) REVERT: A 1690 ARG cc_start: 0.8349 (mtp180) cc_final: 0.8023 (ttm-80) REVERT: A 1813 TYR cc_start: 0.8672 (m-80) cc_final: 0.8174 (m-80) REVERT: A 1817 ASP cc_start: 0.8590 (m-30) cc_final: 0.8128 (OUTLIER) REVERT: A 1989 TYR cc_start: 0.8349 (t80) cc_final: 0.8117 (t80) REVERT: A 2108 MET cc_start: 0.8062 (ptp) cc_final: 0.7721 (ptm) REVERT: A 2203 MET cc_start: 0.5704 (tmm) cc_final: 0.5190 (ttp) outliers start: 25 outliers final: 12 residues processed: 144 average time/residue: 0.5977 time to fit residues: 96.6790 Evaluate side-chains 137 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 732 PHE Chi-restraints excluded: chain A residue 938 ILE Chi-restraints excluded: chain A residue 1016 THR Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1478 MET Chi-restraints excluded: chain A residue 1702 THR Chi-restraints excluded: chain A residue 1708 VAL Chi-restraints excluded: chain A residue 1825 THR Chi-restraints excluded: chain A residue 2000 ILE Chi-restraints excluded: chain A residue 2202 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 176 optimal weight: 0.0670 chunk 196 optimal weight: 10.0000 chunk 155 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 112 optimal weight: 0.6980 chunk 201 optimal weight: 0.9990 chunk 133 optimal weight: 5.9990 chunk 62 optimal weight: 0.5980 chunk 44 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.101717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.075254 restraints weight = 31432.821| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 2.08 r_work: 0.2902 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17872 Z= 0.115 Angle : 0.504 11.546 24324 Z= 0.264 Chirality : 0.039 0.177 2745 Planarity : 0.004 0.085 2903 Dihedral : 7.622 95.483 2740 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.51 % Favored : 97.44 % Rotamer: Outliers : 0.97 % Allowed : 14.30 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.19), residues: 1992 helix: 2.06 (0.16), residues: 1090 sheet: 0.73 (0.45), residues: 132 loop : -0.52 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.000 ARG A1439 TYR 0.011 0.001 TYR A 714 PHE 0.043 0.001 PHE A2207 TRP 0.011 0.001 TRP A1143 HIS 0.005 0.001 HIS A 760 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (17869) covalent geometry : angle 0.50388 / 0.26 (24324) hydrogen bonds : bond 0.03813 / 2.29 ( 918) hydrogen bonds : angle 3.92545 / 2.58 ( 2662) metal coordination : bond 0.00051 / 0.03 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5537.42 seconds wall clock time: 95 minutes 41.56 seconds (5741.56 seconds total)