Starting phenix.real_space_refine on Sat Jul 4 03:19:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ori_13038/07_2026/7ori_13038.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ori_13038/07_2026/7ori_13038.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7ori_13038/07_2026/7ori_13038.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ori_13038/07_2026/7ori_13038.cif" model { file = "/net/cci-nas-00/data/ceres_data/7ori_13038/07_2026/7ori_13038.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ori_13038/07_2026/7ori_13038.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ori_13038/07_2026/7ori_13038.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ori_13038/07_2026/7ori_13038.map" } resolution = 3.9 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 Anisotropic ADP refinement not supported. Converting 9 atoms to isotropic. 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 46 5.49 5 Mg 1 5.21 5 S 108 5.16 5 C 10917 2.51 5 N 2879 2.21 5 O 3374 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 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: 17326 Number of models: 1 Model: "" Number of chains: 5 Chain: "H" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 237 Classifications: {'RNA': 11} Modifications used: {'p5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 5, 'rna3p_pyr': 4} Link IDs: {'rna2p': 2, 'rna3p': 8} Chain: "T" Number of atoms: 439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 439 Classifications: {'RNA': 21} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 3, 'rna3p_pur': 7, 'rna3p_pyr': 9} Link IDs: {'rna2p': 4, 'rna3p': 16} Chain breaks: 1 Chain: "P" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 256 Classifications: {'RNA': 12} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 6, 'rna3p_pyr': 5} Link IDs: {'rna2p': 1, 'rna3p': 10} Chain: "A" Number of atoms: 16383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2007, 16383 Classifications: {'peptide': 2007} Link IDs: {'PTRANS': 67, 'TRANS': 1939} Chain breaks: 7 Chain: "A" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 11 Unusual residues: {' MG': 1, ' ZN': 1, 'POP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 15963 SG CYS A2064 66.994 30.063 27.886 1.00143.63 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" O POP A2303 " occ=0.74 ... (7 atoms not shown) pdb=" P2 POP A2303 " occ=0.74 Time building chain proxies: 3.71, per 1000 atoms: 0.21 Number of scatterers: 17326 At special positions: 0 Unit cell: (111.065, 132.82, 136.255, 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 46 15.00 Mg 1 11.99 O 3374 8.00 N 2879 7.00 C 10917 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: 1.79 Conformation dependent library (CDL) restraints added in 733.7 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 " 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3874 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 17 sheets defined 59.5% alpha, 8.8% beta 12 base pairs and 23 stacking pairs defined. Time for finding SS restraints: 2.68 Creating SS restraints... Processing helix chain 'A' and resid 2 through 16 Processing helix chain 'A' and resid 18 through 46 removed outlier: 3.588A pdb=" N LYS A 23 " --> pdb=" O ALA A 19 " (cutoff:3.500A) removed outlier: 4.319A 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 121 removed outlier: 4.773A pdb=" N ASP A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ILE A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 149 removed outlier: 3.666A pdb=" N LYS A 146 " --> pdb=" O SER A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 173 Processing helix chain 'A' and resid 175 through 182 Processing helix chain 'A' and resid 199 through 203 removed outlier: 3.757A pdb=" N TRP A 202 " --> pdb=" O PRO A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 214 Processing helix chain 'A' and resid 215 through 226 Processing helix chain 'A' and resid 237 through 265 removed outlier: 4.643A pdb=" N LYS A 249 " --> pdb=" O GLU A 245 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N ASP A 250 " --> pdb=" O TYR A 246 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ILE A 262 " --> pdb=" O SER A 258 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N PHE A 263 " --> pdb=" O ALA A 259 " (cutoff:3.500A) removed outlier: 4.391A 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 372 Processing helix chain 'A' and resid 407 through 417 Processing helix chain 'A' and resid 447 through 466 Processing helix chain 'A' and resid 475 through 489 removed outlier: 5.809A pdb=" N SER A 483 " --> pdb=" O ASN A 479 " (cutoff:3.500A) removed outlier: 6.051A 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 523 removed outlier: 3.800A pdb=" N GLN A 506 " --> pdb=" O THR A 502 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN A 523 " --> pdb=" O LEU A 519 " (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 640 removed outlier: 3.595A pdb=" N ILE A 630 " --> pdb=" O VAL A 626 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR A 636 " --> pdb=" O ASN A 632 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU A 639 " --> pdb=" O ILE A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 661 removed outlier: 3.882A pdb=" N LEU A 646 " --> pdb=" O THR A 642 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 648 " --> pdb=" O SER A 644 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) Proline residue: A 651 - end of helix removed outlier: 4.109A 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: 3.605A pdb=" N PHE A 695 " --> pdb=" O LYS A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 704 removed outlier: 4.008A 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: 3.521A 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 Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 830 through 838 removed outlier: 5.759A pdb=" N SER A 835 " --> pdb=" O THR A 832 " (cutoff:3.500A) removed outlier: 6.880A 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: 3.695A pdb=" N GLN A 932 " --> pdb=" O PRO A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 985 removed outlier: 4.214A pdb=" N LEU A 984 " --> pdb=" O GLU A 980 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASN A 985 " --> pdb=" O ARG A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1028 removed outlier: 4.315A pdb=" N LYS A 999 " --> pdb=" O ASP A 995 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N GLU A1022 " --> pdb=" O GLN A1018 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ILE A1023 " --> pdb=" O LYS A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1043 through 1049 Processing helix chain 'A' and resid 1070 through 1079 removed outlier: 3.968A pdb=" N PHE A1074 " --> pdb=" O PHE A1070 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N TRP A1075 " --> pdb=" O TYR A1071 " (cutoff:3.500A) removed outlier: 3.938A 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 1175 Processing helix chain 'A' and resid 1201 through 1220 removed outlier: 3.797A pdb=" N ILE A1205 " --> pdb=" O GLU A1201 " (cutoff:3.500A) removed outlier: 3.553A 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: 3.603A pdb=" N SER A1278 " --> pdb=" O SER A1274 " (cutoff:3.500A) Processing helix chain 'A' and resid 1288 through 1307 removed outlier: 3.530A pdb=" N TYR A1307 " --> pdb=" O THR A1303 " (cutoff:3.500A) Processing helix chain 'A' and resid 1330 through 1334 Processing helix chain 'A' and resid 1340 through 1348 Processing helix chain 'A' and resid 1350 through 1365 Processing helix chain 'A' and resid 1373 through 1381 Processing helix chain 'A' and resid 1382 through 1384 No H-bonds generated for 'chain 'A' and resid 1382 through 1384' 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 Processing helix chain 'A' and resid 1468 through 1472 Processing helix chain 'A' and resid 1477 through 1489 removed outlier: 3.843A pdb=" N TYR A1489 " --> pdb=" O VAL A1485 " (cutoff:3.500A) Processing helix chain 'A' and resid 1491 through 1499 removed outlier: 3.785A pdb=" N SER A1499 " --> pdb=" O LYS A1495 " (cutoff:3.500A) Processing helix chain 'A' and resid 1502 through 1513 Processing helix chain 'A' and resid 1521 through 1528 removed outlier: 4.004A pdb=" N TYR A1528 " --> pdb=" O ILE A1524 " (cutoff:3.500A) Processing helix chain 'A' and resid 1548 through 1563 removed outlier: 3.783A pdb=" N SER A1562 " --> pdb=" O ARG A1558 " (cutoff:3.500A) removed outlier: 3.534A 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 removed outlier: 3.724A pdb=" N LYS A1632 " --> pdb=" O ARG A1628 " (cutoff:3.500A) Processing helix chain 'A' and resid 1641 through 1660 Processing helix chain 'A' and resid 1660 through 1677 Processing helix chain 'A' and resid 1680 through 1699 Processing helix chain 'A' and resid 1717 through 1729 Processing helix chain 'A' and resid 1760 through 1779 Processing helix chain 'A' and resid 1780 through 1795 removed outlier: 4.488A pdb=" N SER A1785 " --> pdb=" O SER A1781 " (cutoff:3.500A) removed outlier: 5.072A 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 1815 through 1817 No H-bonds generated for 'chain 'A' and resid 1815 through 1817' Processing helix chain 'A' and resid 1818 through 1824 Processing helix chain 'A' and resid 1830 through 1840 removed outlier: 4.003A pdb=" N ASP A1834 " --> pdb=" O GLN A1830 " (cutoff:3.500A) Processing helix chain 'A' and resid 1983 through 1991 removed outlier: 3.575A pdb=" N TYR A1989 " --> pdb=" O ARG A1985 " (cutoff:3.500A) Processing helix chain 'A' and resid 2014 through 2019 removed outlier: 3.663A pdb=" N LYS A2017 " --> pdb=" O HIS A2014 " (cutoff:3.500A) removed outlier: 3.784A 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 2040 through 2044 removed outlier: 3.805A pdb=" N LEU A2043 " --> pdb=" O GLN A2040 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN A2044 " --> pdb=" O ASP A2041 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2040 through 2044' Processing helix chain 'A' and resid 2046 through 2052 Processing helix chain 'A' and resid 2054 through 2060 removed outlier: 3.540A pdb=" N PHE A2058 " --> pdb=" O ASN A2054 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LYS A2060 " --> pdb=" O ILE A2056 " (cutoff:3.500A) Processing helix chain 'A' and resid 2069 through 2075 removed outlier: 4.085A pdb=" N GLY A2073 " --> pdb=" O ASN A2069 " (cutoff:3.500A) 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 2175 Processing helix chain 'A' and resid 2177 through 2182 Processing helix chain 'A' and resid 2200 through 2210 removed outlier: 3.527A pdb=" N PHE A2204 " --> pdb=" O ASN A2200 " (cutoff:3.500A) Processing helix chain 'A' and resid 2219 through 2238 removed outlier: 3.832A 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: 6.698A pdb=" N LEU A 88 " --> pdb=" O GLU A 125 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N VAL A 127 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N ILE A 90 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ILE A 129 " --> pdb=" O ILE A 90 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ASP A 92 " --> pdb=" O ILE A 129 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N ILE A 131 " --> pdb=" O ASP A 92 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LYS A 94 " --> pdb=" O ILE A 131 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 293 through 295 removed outlier: 5.937A 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: 5.032A pdb=" N LEU A 392 " --> pdb=" O MET A 400 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU A 394 " --> pdb=" O GLN A 398 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N GLN A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ILE A 561 " --> pdb=" O SER A 591 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 386 through 388 removed outlier: 5.032A pdb=" N LEU A 392 " --> pdb=" O MET A 400 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU A 394 " --> pdb=" O GLN A 398 " (cutoff:3.500A) removed outlier: 7.065A 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 removed outlier: 3.501A pdb=" N SER A 663 " --> pdb=" O VAL A1231 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 710 through 711 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: 6.338A pdb=" N PHE A 945 " --> pdb=" O ILE A1104 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS A1101 " --> pdb=" O ILE A1139 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1242 through 1243 Processing sheet with id=AB2, first strand: chain 'A' and resid 1519 through 1520 Processing sheet with id=AB3, first strand: chain 'A' and resid 1594 through 1596 Processing sheet with id=AB4, first strand: chain 'A' and resid 1600 through 1601 Processing sheet with id=AB5, first strand: chain 'A' and resid 1606 through 1609 Processing sheet with id=AB6, first strand: chain 'A' and resid 1800 through 1801 Processing sheet with id=AB7, first strand: chain 'A' and resid 2027 through 2028 Processing sheet with id=AB8, first strand: chain 'A' and resid 2083 through 2089 893 hydrogen bonds defined for protein. 2571 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 29 hydrogen bonds 58 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 23 stacking parallelities Total time for adding SS restraints: 4.65 Time building geometry restraints manager: 2.19 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: 4167 1.33 - 1.45: 3696 1.45 - 1.57: 9639 1.57 - 1.69: 86 1.69 - 1.81: 179 Bond restraints: 17767 Sorted by residual: bond pdb=" N VAL A1239 " pdb=" CA VAL A1239 " ideal model delta sigma weight residual 1.459 1.501 -0.042 1.25e-02 6.40e+03 1.13e+01 bond pdb=" N PHE A1242 " pdb=" CA PHE A1242 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.19e-02 7.06e+03 7.32e+00 bond pdb=" N VAL A 134 " pdb=" CA VAL A 134 " ideal model delta sigma weight residual 1.461 1.493 -0.031 1.17e-02 7.31e+03 7.21e+00 bond pdb=" N TYR A1528 " pdb=" CA TYR A1528 " ideal model delta sigma weight residual 1.454 1.485 -0.030 1.16e-02 7.43e+03 6.88e+00 bond pdb=" N LEU A1241 " pdb=" CA LEU A1241 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.24e-02 6.50e+03 6.81e+00 ... (remaining 17762 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 23885 2.41 - 4.82: 264 4.82 - 7.22: 15 7.22 - 9.63: 2 9.63 - 12.04: 1 Bond angle restraints: 24167 Sorted by residual: angle pdb=" C ASP A 137 " pdb=" CA ASP A 137 " pdb=" CB ASP A 137 " ideal model delta sigma weight residual 109.48 116.63 -7.15 1.68e+00 3.54e-01 1.81e+01 angle pdb=" P1 POP A2303 " pdb=" O POP A2303 " pdb=" P2 POP A2303 " ideal model delta sigma weight residual 120.50 132.54 -12.04 3.00e+00 1.11e-01 1.61e+01 angle pdb=" CA ARG A 136 " pdb=" C ARG A 136 " pdb=" O ARG A 136 " ideal model delta sigma weight residual 122.64 118.25 4.39 1.25e+00 6.40e-01 1.23e+01 angle pdb=" O LYS A1370 " pdb=" C LYS A1370 " pdb=" N ARG A1371 " ideal model delta sigma weight residual 122.12 125.67 -3.55 1.06e+00 8.90e-01 1.12e+01 angle pdb=" N GLN A 387 " pdb=" CA GLN A 387 " pdb=" C GLN A 387 " ideal model delta sigma weight residual 108.23 113.92 -5.69 1.72e+00 3.38e-01 1.10e+01 ... (remaining 24162 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.40: 10025 23.40 - 46.81: 608 46.81 - 70.21: 76 70.21 - 93.61: 13 93.61 - 117.02: 3 Dihedral angle restraints: 10725 sinusoidal: 4762 harmonic: 5963 Sorted by residual: dihedral pdb=" O4 POP A2303 " pdb=" O POP A2303 " pdb=" P2 POP A2303 " pdb=" P1 POP A2303 " ideal model delta sinusoidal sigma weight residual -57.42 59.60 -117.02 1 2.00e+01 2.50e-03 3.49e+01 dihedral pdb=" O2 POP A2303 " pdb=" O POP A2303 " pdb=" P1 POP A2303 " pdb=" P2 POP A2303 " ideal model delta sinusoidal sigma weight residual -88.77 -176.65 87.88 1 2.00e+01 2.50e-03 2.31e+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 -156.62 -23.38 0 5.00e+00 4.00e-02 2.19e+01 ... (remaining 10722 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2401 0.063 - 0.126: 283 0.126 - 0.188: 33 0.188 - 0.251: 4 0.251 - 0.314: 3 Chirality restraints: 2724 Sorted by residual: chirality pdb=" CA ASN A1334 " pdb=" N ASN A1334 " pdb=" C ASN A1334 " pdb=" CB ASN A1334 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CA ASP A1799 " pdb=" N ASP A1799 " pdb=" C ASP A1799 " pdb=" CB ASP A1799 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CB ILE A 421 " pdb=" CA ILE A 421 " pdb=" CG1 ILE A 421 " pdb=" CG2 ILE A 421 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 2721 not shown) Planarity restraints: 2898 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 135 " -0.011 2.00e-02 2.50e+03 2.28e-02 5.21e+00 pdb=" C SER A 135 " 0.039 2.00e-02 2.50e+03 pdb=" O SER A 135 " -0.015 2.00e-02 2.50e+03 pdb=" N ARG A 136 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 939 " -0.010 2.00e-02 2.50e+03 2.07e-02 4.31e+00 pdb=" C ASP A 939 " 0.036 2.00e-02 2.50e+03 pdb=" O ASP A 939 " -0.014 2.00e-02 2.50e+03 pdb=" N HIS A 940 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 668 " -0.009 2.00e-02 2.50e+03 1.85e-02 3.41e+00 pdb=" C ASP A 668 " 0.032 2.00e-02 2.50e+03 pdb=" O ASP A 668 " -0.012 2.00e-02 2.50e+03 pdb=" N TYR A 669 " -0.011 2.00e-02 2.50e+03 ... (remaining 2895 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 73 2.51 - 3.11: 13193 3.11 - 3.70: 28189 3.70 - 4.30: 39542 4.30 - 4.90: 64510 Nonbonded interactions: 145507 Sorted by model distance: nonbonded pdb=" OD1 ASP A2178 " pdb="ZN ZN A2301 " model vdw 1.911 2.230 nonbonded pdb=" O2' U T 30 " pdb=" O2 U T 30 " model vdw 2.244 3.040 nonbonded pdb=" O PHE A 210 " pdb=" OG SER A 213 " model vdw 2.271 3.040 nonbonded pdb=" O GLU A1469 " pdb=" OG1 THR A1473 " model vdw 2.279 3.040 nonbonded pdb=" O GLU A1654 " pdb=" ND2 ASN A1658 " model vdw 2.281 3.120 ... (remaining 145502 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=0.74 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 22.940 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.500 ------------------------------------------------------------------------------- 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 : 0.005 0.494 17770 Z= 0.217 Angle : 0.581 12.039 24167 Z= 0.342 Chirality : 0.043 0.314 2724 Planarity : 0.003 0.038 2898 Dihedral : 14.371 117.017 6851 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.30 % Allowed : 1.24 % Favored : 97.46 % 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: 1.23 (0.19), residues: 1991 helix: 1.91 (0.16), residues: 1076 sheet: 1.20 (0.45), residues: 137 loop : -0.84 (0.22), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 136 TYR 0.012 0.001 TYR A1528 PHE 0.019 0.001 PHE A1795 TRP 0.012 0.001 TRP A1293 HIS 0.007 0.001 HIS A1156 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.18 (17767) covalent geometry : angle 0.58111 / 0.34 (24167) hydrogen bonds : bond 0.12072 / 7.19 ( 907) hydrogen bonds : angle 5.06076 / 3.36 ( 2629) metal coordination : bond 0.28501 / 14.25 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 163 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 ASN cc_start: 0.8859 (OUTLIER) cc_final: 0.8635 (t0) REVERT: A 400 MET cc_start: 0.8668 (tpt) cc_final: 0.8359 (tpt) REVERT: A 510 ASP cc_start: 0.8233 (m-30) cc_final: 0.7890 (m-30) REVERT: A 696 ASP cc_start: 0.8430 (m-30) cc_final: 0.7747 (p0) REVERT: A 1056 GLU cc_start: 0.8373 (mm-30) cc_final: 0.7258 (mm-30) REVERT: A 1236 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8077 (mtpt) REVERT: A 1240 SER cc_start: 0.9167 (m) cc_final: 0.8856 (p) REVERT: A 1439 ARG cc_start: 0.7880 (mmp80) cc_final: 0.7558 (mmm160) REVERT: A 1472 VAL cc_start: 0.9668 (m) cc_final: 0.9404 (p) REVERT: A 2227 LYS cc_start: 0.7791 (OUTLIER) cc_final: 0.7577 (tptp) outliers start: 24 outliers final: 6 residues processed: 184 average time/residue: 0.1421 time to fit residues: 40.3290 Evaluate side-chains 134 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 125 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 312 HIS Chi-restraints excluded: chain A residue 313 ASN Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 1198 ASP Chi-restraints excluded: chain A residue 1236 LYS Chi-restraints excluded: chain A residue 2090 ILE Chi-restraints excluded: chain A residue 2134 ASN Chi-restraints excluded: chain A residue 2227 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.0060 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 6.9990 chunk 200 optimal weight: 0.9980 chunk 77 optimal weight: 0.0980 chunk 122 optimal weight: 0.6980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 ASN A 523 GLN ** A 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 622 ASN A 760 HIS ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1280 GLN A1334 ASN A1704 HIS ** A1743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2209 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.061340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.049685 restraints weight = 65798.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.051407 restraints weight = 32715.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.052598 restraints weight = 20250.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.053344 restraints weight = 14379.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.053915 restraints weight = 11394.311| |-----------------------------------------------------------------------------| r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2824 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2824 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.0959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 17770 Z= 0.109 Angle : 0.509 5.869 24167 Z= 0.269 Chirality : 0.040 0.188 2724 Planarity : 0.004 0.053 2898 Dihedral : 8.870 107.345 2716 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.70 % Allowed : 7.56 % Favored : 91.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.19), residues: 1991 helix: 1.99 (0.16), residues: 1098 sheet: 1.20 (0.45), residues: 137 loop : -0.81 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 813 TYR 0.022 0.001 TYR A1696 PHE 0.018 0.001 PHE A1795 TRP 0.010 0.001 TRP A1735 HIS 0.006 0.001 HIS A1156 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (17767) covalent geometry : angle 0.50942 / 0.27 (24167) hydrogen bonds : bond 0.03684 / 2.20 ( 907) hydrogen bonds : angle 4.21717 / 2.80 ( 2629) metal coordination : bond 0.01155 / 0.73 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 154 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 214 MET cc_start: 0.8306 (mpp) cc_final: 0.7920 (mpp) REVERT: A 365 MET cc_start: 0.8448 (tpp) cc_final: 0.8120 (tpp) REVERT: A 400 MET cc_start: 0.8688 (tpt) cc_final: 0.8302 (tpt) REVERT: A 450 MET cc_start: 0.9596 (mmp) cc_final: 0.9389 (mmm) REVERT: A 510 ASP cc_start: 0.8277 (m-30) cc_final: 0.7918 (m-30) REVERT: A 524 TYR cc_start: 0.8335 (m-10) cc_final: 0.8039 (m-10) REVERT: A 696 ASP cc_start: 0.8552 (m-30) cc_final: 0.7823 (p0) REVERT: A 900 MET cc_start: 0.8293 (tmm) cc_final: 0.7982 (tmm) REVERT: A 1056 GLU cc_start: 0.8269 (mm-30) cc_final: 0.7564 (mm-30) REVERT: A 1457 MET cc_start: 0.7440 (mmm) cc_final: 0.7143 (mmm) REVERT: A 2037 MET cc_start: 0.8797 (mpp) cc_final: 0.8560 (mpp) REVERT: A 2177 MET cc_start: 0.7979 (tpp) cc_final: 0.7763 (tpp) outliers start: 13 outliers final: 6 residues processed: 163 average time/residue: 0.1291 time to fit residues: 33.5966 Evaluate side-chains 141 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 135 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 964 GLU Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1350 GLU Chi-restraints excluded: chain A residue 2090 ILE Chi-restraints excluded: chain A residue 2227 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 23 optimal weight: 0.0060 chunk 203 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 147 optimal weight: 5.9990 chunk 129 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 64 optimal weight: 0.0050 chunk 70 optimal weight: 1.9990 chunk 80 optimal weight: 7.9990 chunk 181 optimal weight: 6.9990 overall best weight: 2.0016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 539 ASN ** A 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1505 GLN ** A1743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.059324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.047629 restraints weight = 67816.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.049326 restraints weight = 33439.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.050499 restraints weight = 20655.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.051283 restraints weight = 14657.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.051799 restraints weight = 11521.100| |-----------------------------------------------------------------------------| r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2769 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2769 r_free = 0.2769 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2769 r_free = 0.2769 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2769 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17770 Z= 0.179 Angle : 0.521 6.687 24167 Z= 0.272 Chirality : 0.040 0.168 2724 Planarity : 0.004 0.054 2898 Dihedral : 8.399 108.573 2699 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.40 % Allowed : 9.34 % Favored : 89.25 % 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: 1.42 (0.19), residues: 1991 helix: 2.06 (0.16), residues: 1100 sheet: 1.10 (0.45), residues: 138 loop : -0.80 (0.22), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 813 TYR 0.017 0.001 TYR A1696 PHE 0.015 0.001 PHE A1768 TRP 0.008 0.001 TRP A1293 HIS 0.007 0.001 HIS A 760 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.18 (17767) covalent geometry : angle 0.52071 / 0.27 (24167) hydrogen bonds : bond 0.03746 / 2.23 ( 907) hydrogen bonds : angle 4.19831 / 2.78 ( 2629) metal coordination : bond 0.00271 / 0.15 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 0.709 Fit side-chains REVERT: A 7 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.8101 (pm20) REVERT: A 214 MET cc_start: 0.8426 (mpp) cc_final: 0.7919 (mpp) REVERT: A 365 MET cc_start: 0.8523 (tpp) cc_final: 0.8202 (tpp) REVERT: A 400 MET cc_start: 0.8644 (tpt) cc_final: 0.8294 (tpt) REVERT: A 510 ASP cc_start: 0.8344 (m-30) cc_final: 0.7966 (m-30) REVERT: A 696 ASP cc_start: 0.8584 (m-30) cc_final: 0.7931 (p0) REVERT: A 900 MET cc_start: 0.8331 (tmm) cc_final: 0.7940 (tmm) REVERT: A 946 THR cc_start: 0.9473 (t) cc_final: 0.9259 (t) REVERT: A 1056 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7543 (mm-30) REVERT: A 1271 ASP cc_start: 0.8589 (m-30) cc_final: 0.8321 (m-30) REVERT: A 1415 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.8116 (ttp) REVERT: A 1457 MET cc_start: 0.7476 (mmm) cc_final: 0.7190 (mmm) REVERT: A 1496 GLU cc_start: 0.8943 (tm-30) cc_final: 0.8675 (tm-30) REVERT: A 2037 MET cc_start: 0.9011 (mpp) cc_final: 0.8705 (mpp) REVERT: A 2180 MET cc_start: 0.8896 (ttt) cc_final: 0.8509 (tpp) outliers start: 26 outliers final: 16 residues processed: 146 average time/residue: 0.1261 time to fit residues: 29.7116 Evaluate side-chains 146 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 964 GLU Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1287 CYS Chi-restraints excluded: chain A residue 1350 GLU Chi-restraints excluded: chain A residue 1415 MET Chi-restraints excluded: chain A residue 1472 VAL Chi-restraints excluded: chain A residue 1566 THR Chi-restraints excluded: chain A residue 1689 THR Chi-restraints excluded: chain A residue 1799 ASP Chi-restraints excluded: chain A residue 2005 ASP Chi-restraints excluded: chain A residue 2090 ILE Chi-restraints excluded: chain A residue 2227 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 45 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 chunk 194 optimal weight: 10.0000 chunk 102 optimal weight: 8.9990 chunk 65 optimal weight: 0.6980 chunk 120 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 175 optimal weight: 0.5980 chunk 31 optimal weight: 10.0000 chunk 172 optimal weight: 0.6980 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 ASN ** A 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.059269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.047667 restraints weight = 67432.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.049334 restraints weight = 33748.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.050493 restraints weight = 21002.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.051252 restraints weight = 14928.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.051704 restraints weight = 11782.989| |-----------------------------------------------------------------------------| r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2765 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2765 r_free = 0.2765 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2765 r_free = 0.2765 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.2765 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17770 Z= 0.159 Angle : 0.504 9.427 24167 Z= 0.264 Chirality : 0.039 0.158 2724 Planarity : 0.003 0.055 2898 Dihedral : 8.304 109.341 2699 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.40 % Allowed : 10.96 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.19), residues: 1991 helix: 2.07 (0.16), residues: 1099 sheet: 1.17 (0.45), residues: 137 loop : -0.82 (0.22), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1424 TYR 0.017 0.001 TYR A1696 PHE 0.014 0.001 PHE A1795 TRP 0.007 0.001 TRP A1293 HIS 0.008 0.001 HIS A 760 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (17767) covalent geometry : angle 0.50369 / 0.26 (24167) hydrogen bonds : bond 0.03603 / 2.15 ( 907) hydrogen bonds : angle 4.11440 / 2.71 ( 2629) metal coordination : bond 0.00266 / 0.15 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.8050 (pm20) REVERT: A 214 MET cc_start: 0.8440 (mpp) cc_final: 0.8040 (mpp) REVERT: A 400 MET cc_start: 0.8542 (tpt) cc_final: 0.8208 (tpt) REVERT: A 510 ASP cc_start: 0.8300 (m-30) cc_final: 0.7935 (m-30) REVERT: A 900 MET cc_start: 0.8397 (tmm) cc_final: 0.7933 (tmm) REVERT: A 934 MET cc_start: 0.9555 (mmp) cc_final: 0.9329 (mmp) REVERT: A 946 THR cc_start: 0.9496 (t) cc_final: 0.9289 (t) REVERT: A 1056 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7678 (mm-30) REVERT: A 1160 MET cc_start: 0.9215 (mmp) cc_final: 0.8864 (mmp) REVERT: A 1169 GLU cc_start: 0.8859 (tp30) cc_final: 0.8443 (tp30) REVERT: A 1271 ASP cc_start: 0.8590 (m-30) cc_final: 0.8326 (m-30) REVERT: A 1415 MET cc_start: 0.8357 (OUTLIER) cc_final: 0.8035 (ttp) REVERT: A 1457 MET cc_start: 0.7401 (mmm) cc_final: 0.7125 (mmm) REVERT: A 1496 GLU cc_start: 0.8938 (tm-30) cc_final: 0.8699 (tm-30) REVERT: A 2037 MET cc_start: 0.9029 (mpp) cc_final: 0.8734 (mpp) REVERT: A 2180 MET cc_start: 0.8874 (ttt) cc_final: 0.8301 (tpp) outliers start: 26 outliers final: 18 residues processed: 148 average time/residue: 0.1247 time to fit residues: 29.9950 Evaluate side-chains 145 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 964 GLU Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1283 ILE Chi-restraints excluded: chain A residue 1287 CYS Chi-restraints excluded: chain A residue 1350 GLU Chi-restraints excluded: chain A residue 1415 MET Chi-restraints excluded: chain A residue 1472 VAL Chi-restraints excluded: chain A residue 1526 ASP Chi-restraints excluded: chain A residue 1566 THR Chi-restraints excluded: chain A residue 1603 MET Chi-restraints excluded: chain A residue 1689 THR Chi-restraints excluded: chain A residue 1799 ASP Chi-restraints excluded: chain A residue 2005 ASP Chi-restraints excluded: chain A residue 2090 ILE Chi-restraints excluded: chain A residue 2227 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 99 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 193 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 77 optimal weight: 0.4980 chunk 61 optimal weight: 0.7980 chunk 1 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 chunk 109 optimal weight: 3.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 940 HIS A 952 GLN ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.058759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.047217 restraints weight = 66751.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.048875 restraints weight = 33432.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.050014 restraints weight = 20824.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.050750 restraints weight = 14841.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.051279 restraints weight = 11763.994| |-----------------------------------------------------------------------------| r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2753 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2753 r_free = 0.2753 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2753 r_free = 0.2753 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2753 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 17770 Z= 0.178 Angle : 0.516 7.464 24167 Z= 0.271 Chirality : 0.039 0.168 2724 Planarity : 0.003 0.051 2898 Dihedral : 8.308 109.726 2699 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.94 % Allowed : 12.37 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.19), residues: 1991 helix: 2.04 (0.16), residues: 1100 sheet: 0.97 (0.44), residues: 144 loop : -0.84 (0.23), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1439 TYR 0.016 0.001 TYR A1696 PHE 0.012 0.001 PHE A1795 TRP 0.008 0.001 TRP A 281 HIS 0.006 0.001 HIS A 760 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.18 (17767) covalent geometry : angle 0.51619 / 0.27 (24167) hydrogen bonds : bond 0.03697 / 2.20 ( 907) hydrogen bonds : angle 4.14586 / 2.73 ( 2629) metal coordination : bond 0.00458 / 0.26 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 130 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.8054 (pm20) REVERT: A 214 MET cc_start: 0.8485 (mpp) cc_final: 0.8069 (mpp) REVERT: A 365 MET cc_start: 0.8401 (tpp) cc_final: 0.8117 (tpp) REVERT: A 400 MET cc_start: 0.8534 (tpt) cc_final: 0.8185 (tpt) REVERT: A 424 HIS cc_start: 0.5071 (OUTLIER) cc_final: 0.4523 (t-170) REVERT: A 450 MET cc_start: 0.9650 (mmt) cc_final: 0.9429 (mmm) REVERT: A 510 ASP cc_start: 0.8322 (m-30) cc_final: 0.7944 (m-30) REVERT: A 696 ASP cc_start: 0.8457 (m-30) cc_final: 0.7929 (p0) REVERT: A 900 MET cc_start: 0.8339 (tmm) cc_final: 0.7836 (tmm) REVERT: A 946 THR cc_start: 0.9508 (t) cc_final: 0.9306 (t) REVERT: A 1006 GLU cc_start: 0.8386 (mm-30) cc_final: 0.8077 (mm-30) REVERT: A 1056 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7507 (mm-30) REVERT: A 1169 GLU cc_start: 0.8868 (tp30) cc_final: 0.8356 (tp30) REVERT: A 1271 ASP cc_start: 0.8553 (m-30) cc_final: 0.8311 (m-30) REVERT: A 1457 MET cc_start: 0.7542 (mmm) cc_final: 0.7265 (mmm) REVERT: A 1496 GLU cc_start: 0.8952 (tm-30) cc_final: 0.8537 (tm-30) REVERT: A 2180 MET cc_start: 0.8881 (ttt) cc_final: 0.8307 (tpp) outliers start: 36 outliers final: 19 residues processed: 152 average time/residue: 0.1226 time to fit residues: 29.9965 Evaluate side-chains 149 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 964 GLU Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1110 LEU Chi-restraints excluded: chain A residue 1283 ILE Chi-restraints excluded: chain A residue 1287 CYS Chi-restraints excluded: chain A residue 1350 GLU Chi-restraints excluded: chain A residue 1472 VAL Chi-restraints excluded: chain A residue 1526 ASP Chi-restraints excluded: chain A residue 1566 THR Chi-restraints excluded: chain A residue 1603 MET Chi-restraints excluded: chain A residue 1665 MET Chi-restraints excluded: chain A residue 1799 ASP Chi-restraints excluded: chain A residue 2005 ASP Chi-restraints excluded: chain A residue 2090 ILE Chi-restraints excluded: chain A residue 2227 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 44 optimal weight: 0.3980 chunk 100 optimal weight: 0.9980 chunk 115 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 chunk 176 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 193 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 154 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1334 ASN ** A2169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.058703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.047222 restraints weight = 66526.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.048884 restraints weight = 33402.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.050024 restraints weight = 20751.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.050810 restraints weight = 14787.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.051263 restraints weight = 11583.588| |-----------------------------------------------------------------------------| r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2756 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2756 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17770 Z= 0.165 Angle : 0.512 7.727 24167 Z= 0.268 Chirality : 0.039 0.166 2724 Planarity : 0.003 0.052 2898 Dihedral : 8.310 110.055 2699 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.73 % Allowed : 13.23 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.19), residues: 1991 helix: 2.04 (0.16), residues: 1101 sheet: 0.94 (0.44), residues: 144 loop : -0.84 (0.23), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1439 TYR 0.016 0.001 TYR A1696 PHE 0.019 0.001 PHE A1507 TRP 0.009 0.001 TRP A2219 HIS 0.006 0.001 HIS A 760 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (17767) covalent geometry : angle 0.51203 / 0.27 (24167) hydrogen bonds : bond 0.03638 / 2.17 ( 907) hydrogen bonds : angle 4.10298 / 2.70 ( 2629) metal coordination : bond 0.00386 / 0.22 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 133 time to evaluate : 0.691 Fit side-chains revert: symmetry clash REVERT: A 7 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.8021 (pm20) REVERT: A 214 MET cc_start: 0.8482 (mpp) cc_final: 0.8191 (mpp) REVERT: A 365 MET cc_start: 0.8492 (tpp) cc_final: 0.8175 (tpp) REVERT: A 400 MET cc_start: 0.8444 (tpt) cc_final: 0.8076 (tpt) REVERT: A 424 HIS cc_start: 0.5081 (OUTLIER) cc_final: 0.4469 (t-170) REVERT: A 450 MET cc_start: 0.9649 (mmt) cc_final: 0.9441 (mmm) REVERT: A 510 ASP cc_start: 0.8307 (m-30) cc_final: 0.7945 (m-30) REVERT: A 696 ASP cc_start: 0.8428 (m-30) cc_final: 0.7985 (p0) REVERT: A 900 MET cc_start: 0.8342 (tmm) cc_final: 0.6926 (tmm) REVERT: A 946 THR cc_start: 0.9515 (t) cc_final: 0.9314 (t) REVERT: A 1056 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7524 (mm-30) REVERT: A 1169 GLU cc_start: 0.8861 (tp30) cc_final: 0.8336 (tp30) REVERT: A 1237 GLU cc_start: 0.8370 (tm-30) cc_final: 0.8127 (tm-30) REVERT: A 1496 GLU cc_start: 0.8952 (tm-30) cc_final: 0.8553 (tm-30) REVERT: A 2037 MET cc_start: 0.8962 (mpp) cc_final: 0.8666 (mpp) REVERT: A 2180 MET cc_start: 0.8873 (ttt) cc_final: 0.8291 (tpp) outliers start: 32 outliers final: 21 residues processed: 153 average time/residue: 0.1213 time to fit residues: 30.4762 Evaluate side-chains 151 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 964 GLU Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1110 LEU Chi-restraints excluded: chain A residue 1283 ILE Chi-restraints excluded: chain A residue 1287 CYS Chi-restraints excluded: chain A residue 1350 GLU Chi-restraints excluded: chain A residue 1472 VAL Chi-restraints excluded: chain A residue 1526 ASP Chi-restraints excluded: chain A residue 1566 THR Chi-restraints excluded: chain A residue 1573 ILE Chi-restraints excluded: chain A residue 1603 MET Chi-restraints excluded: chain A residue 1689 THR Chi-restraints excluded: chain A residue 1799 ASP Chi-restraints excluded: chain A residue 2005 ASP Chi-restraints excluded: chain A residue 2090 ILE Chi-restraints excluded: chain A residue 2227 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 174 optimal weight: 0.6980 chunk 155 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 55 optimal weight: 0.3980 chunk 30 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2169 HIS ** 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 = 0.2980 r_free = 0.2980 target = 0.059320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.047810 restraints weight = 66170.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.049481 restraints weight = 33247.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.050637 restraints weight = 20685.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.051387 restraints weight = 14694.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.051918 restraints weight = 11606.897| |-----------------------------------------------------------------------------| r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2773 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2773 r_free = 0.2773 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2773 r_free = 0.2773 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2773 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17770 Z= 0.127 Angle : 0.501 7.665 24167 Z= 0.262 Chirality : 0.039 0.173 2724 Planarity : 0.003 0.051 2898 Dihedral : 8.277 110.282 2699 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.84 % Allowed : 13.66 % Favored : 84.50 % 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: 1991 helix: 2.07 (0.16), residues: 1103 sheet: 0.93 (0.45), residues: 134 loop : -0.81 (0.23), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1602 TYR 0.016 0.001 TYR A1696 PHE 0.022 0.001 PHE A1507 TRP 0.007 0.001 TRP A2219 HIS 0.006 0.001 HIS A 760 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (17767) covalent geometry : angle 0.50057 / 0.26 (24167) hydrogen bonds : bond 0.03526 / 2.10 ( 907) hydrogen bonds : angle 4.05900 / 2.67 ( 2629) metal coordination : bond 0.00176 / 0.10 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 132 time to evaluate : 0.814 Fit side-chains revert: symmetry clash REVERT: A 7 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.8033 (pm20) REVERT: A 214 MET cc_start: 0.8498 (mpp) cc_final: 0.8153 (mpp) REVERT: A 365 MET cc_start: 0.8537 (tpp) cc_final: 0.8212 (tpp) REVERT: A 400 MET cc_start: 0.8461 (tpt) cc_final: 0.8106 (tpt) REVERT: A 424 HIS cc_start: 0.5103 (OUTLIER) cc_final: 0.4522 (t-170) REVERT: A 450 MET cc_start: 0.9645 (mmt) cc_final: 0.9444 (mmm) REVERT: A 510 ASP cc_start: 0.8341 (m-30) cc_final: 0.7975 (m-30) REVERT: A 696 ASP cc_start: 0.8449 (m-30) cc_final: 0.7942 (p0) REVERT: A 900 MET cc_start: 0.8282 (tmm) cc_final: 0.6958 (tmm) REVERT: A 946 THR cc_start: 0.9471 (t) cc_final: 0.9265 (t) REVERT: A 1056 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7479 (mm-30) REVERT: A 1169 GLU cc_start: 0.8914 (tp30) cc_final: 0.8375 (tp30) REVERT: A 1237 GLU cc_start: 0.8353 (tm-30) cc_final: 0.8089 (tm-30) REVERT: A 1343 MET cc_start: 0.9354 (mmm) cc_final: 0.8950 (tpp) REVERT: A 1409 MET cc_start: 0.8573 (mtt) cc_final: 0.8070 (mtm) REVERT: A 1457 MET cc_start: 0.7391 (mmm) cc_final: 0.7114 (mmm) REVERT: A 1496 GLU cc_start: 0.8995 (tm-30) cc_final: 0.8579 (tm-30) REVERT: A 2037 MET cc_start: 0.8964 (mpp) cc_final: 0.8660 (mpp) REVERT: A 2180 MET cc_start: 0.8881 (ttt) cc_final: 0.8321 (tpp) outliers start: 34 outliers final: 19 residues processed: 154 average time/residue: 0.1215 time to fit residues: 30.7765 Evaluate side-chains 146 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 787 THR Chi-restraints excluded: chain A residue 964 GLU Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1110 LEU Chi-restraints excluded: chain A residue 1283 ILE Chi-restraints excluded: chain A residue 1287 CYS Chi-restraints excluded: chain A residue 1472 VAL Chi-restraints excluded: chain A residue 1526 ASP Chi-restraints excluded: chain A residue 1566 THR Chi-restraints excluded: chain A residue 1573 ILE Chi-restraints excluded: chain A residue 1603 MET Chi-restraints excluded: chain A residue 1665 MET Chi-restraints excluded: chain A residue 1799 ASP Chi-restraints excluded: chain A residue 2005 ASP Chi-restraints excluded: chain A residue 2090 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 30 optimal weight: 4.9990 chunk 68 optimal weight: 8.9990 chunk 55 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 137 optimal weight: 1.9990 chunk 140 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 143 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 11 optimal weight: 8.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2169 HIS ** 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 = 0.2982 r_free = 0.2982 target = 0.059494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.047960 restraints weight = 66603.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.049644 restraints weight = 33327.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.050791 restraints weight = 20637.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.051579 restraints weight = 14685.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.052029 restraints weight = 11537.051| |-----------------------------------------------------------------------------| r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2775 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2775 r_free = 0.2775 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2775 r_free = 0.2775 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2775 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17770 Z= 0.134 Angle : 0.511 8.640 24167 Z= 0.266 Chirality : 0.039 0.150 2724 Planarity : 0.003 0.053 2898 Dihedral : 8.174 110.173 2695 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.51 % Allowed : 13.77 % Favored : 84.72 % 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: 1.42 (0.19), residues: 1991 helix: 2.07 (0.16), residues: 1105 sheet: 1.15 (0.46), residues: 127 loop : -0.84 (0.23), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 600 TYR 0.015 0.001 TYR A1696 PHE 0.022 0.001 PHE A1507 TRP 0.007 0.001 TRP A 281 HIS 0.005 0.001 HIS A 760 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (17767) covalent geometry : angle 0.51129 / 0.27 (24167) hydrogen bonds : bond 0.03517 / 2.10 ( 907) hydrogen bonds : angle 4.06095 / 2.68 ( 2629) metal coordination : bond 0.00269 / 0.15 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 129 time to evaluate : 0.707 Fit side-chains revert: symmetry clash REVERT: A 7 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.8036 (pm20) REVERT: A 214 MET cc_start: 0.8527 (mpp) cc_final: 0.8189 (mpp) REVERT: A 400 MET cc_start: 0.8395 (tpt) cc_final: 0.8024 (tpt) REVERT: A 424 HIS cc_start: 0.5095 (OUTLIER) cc_final: 0.4516 (t-170) REVERT: A 450 MET cc_start: 0.9641 (mmt) cc_final: 0.9432 (mmm) REVERT: A 510 ASP cc_start: 0.8293 (m-30) cc_final: 0.7927 (m-30) REVERT: A 696 ASP cc_start: 0.8424 (m-30) cc_final: 0.7974 (p0) REVERT: A 900 MET cc_start: 0.8272 (tmm) cc_final: 0.6944 (tmm) REVERT: A 946 THR cc_start: 0.9470 (t) cc_final: 0.9252 (t) REVERT: A 1056 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7483 (mm-30) REVERT: A 1169 GLU cc_start: 0.8912 (tp30) cc_final: 0.8368 (tp30) REVERT: A 1237 GLU cc_start: 0.8336 (tm-30) cc_final: 0.8060 (tm-30) REVERT: A 1343 MET cc_start: 0.9208 (mmm) cc_final: 0.8941 (tpp) REVERT: A 1415 MET cc_start: 0.9112 (ptm) cc_final: 0.8837 (ptt) REVERT: A 1457 MET cc_start: 0.7441 (mmm) cc_final: 0.7165 (mmm) REVERT: A 1496 GLU cc_start: 0.9006 (tm-30) cc_final: 0.8595 (tm-30) REVERT: A 2037 MET cc_start: 0.8965 (mpp) cc_final: 0.8676 (mpp) outliers start: 28 outliers final: 19 residues processed: 146 average time/residue: 0.1253 time to fit residues: 29.7677 Evaluate side-chains 147 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 787 THR Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1110 LEU Chi-restraints excluded: chain A residue 1260 VAL Chi-restraints excluded: chain A residue 1283 ILE Chi-restraints excluded: chain A residue 1287 CYS Chi-restraints excluded: chain A residue 1350 GLU Chi-restraints excluded: chain A residue 1472 VAL Chi-restraints excluded: chain A residue 1526 ASP Chi-restraints excluded: chain A residue 1566 THR Chi-restraints excluded: chain A residue 1689 THR Chi-restraints excluded: chain A residue 1799 ASP Chi-restraints excluded: chain A residue 2005 ASP Chi-restraints excluded: chain A residue 2085 THR Chi-restraints excluded: chain A residue 2090 ILE Chi-restraints excluded: chain A residue 2227 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 171 optimal weight: 1.9990 chunk 156 optimal weight: 4.9990 chunk 151 optimal weight: 0.8980 chunk 66 optimal weight: 0.0570 chunk 70 optimal weight: 0.6980 chunk 115 optimal weight: 7.9990 chunk 68 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 163 optimal weight: 3.9990 chunk 167 optimal weight: 1.9990 overall best weight: 0.9100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1308 ASN A2169 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.060006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.048396 restraints weight = 65811.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.050110 restraints weight = 32535.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.051285 restraints weight = 20069.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.052063 restraints weight = 14208.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.052526 restraints weight = 11146.637| |-----------------------------------------------------------------------------| r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2789 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2789 r_free = 0.2789 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2789 r_free = 0.2789 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2789 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.140 17770 Z= 0.119 Angle : 0.513 8.968 24167 Z= 0.266 Chirality : 0.038 0.147 2724 Planarity : 0.003 0.052 2898 Dihedral : 8.154 110.166 2695 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.51 % Allowed : 14.04 % Favored : 84.45 % 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: 1.46 (0.19), residues: 1991 helix: 2.11 (0.16), residues: 1104 sheet: 1.20 (0.46), residues: 127 loop : -0.83 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 600 TYR 0.015 0.001 TYR A1696 PHE 0.022 0.001 PHE A1507 TRP 0.008 0.001 TRP A1143 HIS 0.007 0.001 HIS A 940 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (17767) covalent geometry : angle 0.51294 / 0.27 (24167) hydrogen bonds : bond 0.03419 / 2.04 ( 907) hydrogen bonds : angle 4.00186 / 2.64 ( 2629) metal coordination : bond 0.08094 / 4.05 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 134 time to evaluate : 0.664 Fit side-chains REVERT: A 7 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.8032 (pm20) REVERT: A 214 MET cc_start: 0.8505 (mpp) cc_final: 0.8165 (mpp) REVERT: A 400 MET cc_start: 0.8483 (tpt) cc_final: 0.8146 (tpt) REVERT: A 424 HIS cc_start: 0.5162 (OUTLIER) cc_final: 0.4657 (t-170) REVERT: A 450 MET cc_start: 0.9634 (mmt) cc_final: 0.9428 (mmm) REVERT: A 510 ASP cc_start: 0.8286 (m-30) cc_final: 0.7929 (m-30) REVERT: A 602 GLN cc_start: 0.9146 (OUTLIER) cc_final: 0.8816 (tp40) REVERT: A 900 MET cc_start: 0.8307 (tmm) cc_final: 0.7054 (tmm) REVERT: A 1056 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7476 (mm-30) REVERT: A 1169 GLU cc_start: 0.8909 (tp30) cc_final: 0.8358 (tp30) REVERT: A 1237 GLU cc_start: 0.8317 (tm-30) cc_final: 0.8053 (tm-30) REVERT: A 1415 MET cc_start: 0.9133 (ptm) cc_final: 0.8885 (ptt) REVERT: A 1457 MET cc_start: 0.7477 (mmm) cc_final: 0.7234 (mmm) REVERT: A 1496 GLU cc_start: 0.8988 (tm-30) cc_final: 0.8581 (tm-30) REVERT: A 2037 MET cc_start: 0.8962 (mpp) cc_final: 0.8685 (mpp) outliers start: 28 outliers final: 19 residues processed: 152 average time/residue: 0.1244 time to fit residues: 30.7918 Evaluate side-chains 149 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 602 GLN Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 787 THR Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1110 LEU Chi-restraints excluded: chain A residue 1260 VAL Chi-restraints excluded: chain A residue 1283 ILE Chi-restraints excluded: chain A residue 1287 CYS Chi-restraints excluded: chain A residue 1308 ASN Chi-restraints excluded: chain A residue 1350 GLU Chi-restraints excluded: chain A residue 1472 VAL Chi-restraints excluded: chain A residue 1526 ASP Chi-restraints excluded: chain A residue 1566 THR Chi-restraints excluded: chain A residue 2005 ASP Chi-restraints excluded: chain A residue 2085 THR Chi-restraints excluded: chain A residue 2090 ILE Chi-restraints excluded: chain A residue 2227 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.1953 > 50: distance: 19 - 42: 20.135 distance: 26 - 29: 23.974 distance: 29 - 30: 3.075 distance: 30 - 31: 8.648 distance: 30 - 33: 30.380 distance: 31 - 32: 38.506 distance: 31 - 35: 10.046 distance: 33 - 34: 3.457 distance: 35 - 36: 15.637 distance: 36 - 37: 20.990 distance: 36 - 39: 28.869 distance: 37 - 38: 10.784 distance: 37 - 42: 3.692 distance: 38 - 64: 21.132 distance: 39 - 40: 15.472 distance: 39 - 41: 18.341 distance: 42 - 43: 12.148 distance: 43 - 44: 7.821 distance: 43 - 46: 7.341 distance: 44 - 45: 14.242 distance: 44 - 47: 9.149 distance: 45 - 72: 24.216 distance: 47 - 48: 3.964 distance: 48 - 51: 9.485 distance: 49 - 50: 5.971 distance: 50 - 80: 12.117 distance: 51 - 52: 10.802 distance: 52 - 53: 7.237 distance: 53 - 54: 10.590 distance: 54 - 55: 25.481 distance: 56 - 57: 10.384 distance: 57 - 58: 22.672 distance: 57 - 60: 9.091 distance: 58 - 59: 4.786 distance: 58 - 64: 16.879 distance: 59 - 87: 22.210 distance: 60 - 61: 12.594 distance: 61 - 62: 8.163 distance: 61 - 63: 4.558 distance: 64 - 65: 5.894 distance: 65 - 66: 9.439 distance: 65 - 68: 7.165 distance: 66 - 67: 4.874 distance: 66 - 72: 3.663 distance: 67 - 95: 17.646 distance: 68 - 69: 3.062 distance: 68 - 70: 29.811 distance: 69 - 71: 12.590 distance: 73 - 74: 3.253 distance: 73 - 76: 7.330 distance: 74 - 75: 14.064 distance: 74 - 80: 3.612 distance: 75 - 103: 21.575 distance: 76 - 77: 4.551 distance: 77 - 78: 18.213 distance: 77 - 79: 7.557 distance: 80 - 81: 9.496 distance: 81 - 82: 11.010 distance: 81 - 84: 9.914 distance: 82 - 83: 9.157 distance: 82 - 87: 10.860 distance: 83 - 110: 17.328 distance: 84 - 85: 13.885 distance: 84 - 86: 11.461 distance: 87 - 88: 16.048 distance: 88 - 89: 10.560 distance: 89 - 90: 7.908 distance: 89 - 95: 12.083 distance: 90 - 116: 14.233 distance: 91 - 92: 4.534 distance: 92 - 93: 22.859 distance: 92 - 94: 5.576 distance: 96 - 97: 5.375 distance: 96 - 99: 4.871 distance: 97 - 98: 4.599 distance: 98 - 121: 7.603 distance: 99 - 100: 11.372 distance: 100 - 101: 7.118 distance: 100 - 102: 18.687