Starting phenix.real_space_refine on Sun Aug 24 07:17:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ori_13038/08_2025/7ori_13038.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ori_13038/08_2025/7ori_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 { model { file = "/net/cci-nas-00/data/ceres_data/7ori_13038/08_2025/7ori_13038.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ori_13038/08_2025/7ori_13038.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ori_13038/08_2025/7ori_13038.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ori_13038/08_2025/7ori_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 3.70, 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: 1.37 Conformation dependent library (CDL) restraints added in 678.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 2.29 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: 4.33 Time building geometry restraints manager: 1.89 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 - 1.69: 23630 1.69 - 3.38: 453 3.38 - 5.07: 70 5.07 - 6.77: 10 6.77 - 8.46: 4 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=" 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 angle pdb=" CA THR A1390 " pdb=" C THR A1390 " pdb=" O THR A1390 " ideal model delta sigma weight residual 121.81 117.98 3.83 1.18e+00 7.18e-01 1.06e+01 ... (remaining 24162 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.70: 10027 22.70 - 45.40: 674 45.40 - 68.09: 133 68.09 - 90.79: 22 90.79 - 113.49: 3 Dihedral angle restraints: 10859 sinusoidal: 4896 harmonic: 5963 Sorted by residual: 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 dihedral pdb=" O4' U T 30 " pdb=" C1' U T 30 " pdb=" N1 U T 30 " pdb=" C2 U T 30 " ideal model delta sinusoidal sigma weight residual 232.00 163.89 68.11 1 1.70e+01 3.46e-03 2.08e+01 dihedral pdb=" C VAL A1239 " pdb=" N VAL A1239 " pdb=" CA VAL A1239 " pdb=" CB VAL A1239 " ideal model delta harmonic sigma weight residual -122.00 -131.71 9.71 0 2.50e+00 1.60e-01 1.51e+01 ... (remaining 10856 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: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 20.560 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 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= 0.219 Angle : 0.575 8.458 24167 Z= 0.341 Chirality : 0.043 0.314 2724 Planarity : 0.003 0.038 2898 Dihedral : 15.317 113.491 6985 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 aren 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 covalent geometry : bond 0.00315 (17767) covalent geometry : angle 0.57489 (24167) hydrogen bonds : bond 0.12072 ( 907) hydrogen bonds : angle 5.06076 ( 2629) metal coordination : bond 0.28501 ( 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 : 0.560 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: 0.8855 (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: 0.1245 time to fit residues: 35.2557 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 : 0.541 ------------------------------------------------------------------------------- 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: 3.9990 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... Flipped N/Q/H residues before XYZ refinement: ** A 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 ASN A 523 GLN A 622 ASN A 760 HIS ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1280 GLN A1334 ASN A1704 HIS A1743 GLN A2209 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.061205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.049607 restraints weight = 65799.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.051320 restraints weight = 32611.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.052502 restraints weight = 20221.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.053305 restraints weight = 14326.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.053827 restraints weight = 11222.075| |-----------------------------------------------------------------------------| r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2820 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2820 r_free = 0.2820 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 = 0.2820 r_free = 0.2820 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2820 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.0866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17770 Z= 0.112 Angle : 0.510 6.202 24167 Z= 0.270 Chirality : 0.039 0.195 2724 Planarity : 0.004 0.054 2898 Dihedral : 12.450 108.787 2850 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.65 % Allowed : 7.29 % Favored : 92.06 % 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 aren not related in a simple way. whole: 1.36 (0.19), residues: 1991 helix: 1.99 (0.16), residues: 1100 sheet: 1.19 (0.45), residues: 137 loop : -0.81 (0.22), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 813 TYR 0.019 0.001 TYR A1696 PHE 0.018 0.001 PHE A1795 TRP 0.009 0.001 TRP A1735 HIS 0.006 0.001 HIS A1156 Details of bonding type rmsd covalent geometry : bond 0.00241 (17767) covalent geometry : angle 0.51033 (24167) hydrogen bonds : bond 0.03852 ( 907) hydrogen bonds : angle 4.27318 ( 2629) metal coordination : bond 0.00363 ( 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 165 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 153 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 214 MET cc_start: 0.8325 (mpp) cc_final: 0.7926 (mpp) REVERT: A 313 ASN cc_start: 0.8897 (OUTLIER) cc_final: 0.8694 (t0) REVERT: A 365 MET cc_start: 0.8463 (tpp) cc_final: 0.8141 (tpp) REVERT: A 400 MET cc_start: 0.8693 (tpt) cc_final: 0.8291 (tpt) REVERT: A 510 ASP cc_start: 0.8289 (m-30) cc_final: 0.7905 (m-30) REVERT: A 696 ASP cc_start: 0.8606 (m-30) cc_final: 0.7863 (p0) REVERT: A 900 MET cc_start: 0.8283 (tmm) cc_final: 0.7981 (tmm) REVERT: A 1056 GLU cc_start: 0.8294 (mm-30) cc_final: 0.7559 (mm-30) REVERT: A 1457 MET cc_start: 0.7434 (mmm) cc_final: 0.7138 (mmm) REVERT: A 2037 MET cc_start: 0.8791 (mpp) cc_final: 0.8540 (mpp) outliers start: 12 outliers final: 6 residues processed: 162 average time/residue: 0.1136 time to fit residues: 29.6683 Evaluate side-chains 138 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 131 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 HIS Chi-restraints excluded: chain A residue 313 ASN 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: 2.9990 chunk 203 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 147 optimal weight: 5.9990 chunk 129 optimal weight: 6.9990 chunk 62 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 181 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 940 HIS ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1505 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.058524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.046900 restraints weight = 68256.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.048540 restraints weight = 34372.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.049690 restraints weight = 21528.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.050429 restraints weight = 15356.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.050948 restraints weight = 12190.679| |-----------------------------------------------------------------------------| r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2743 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2743 r_free = 0.2743 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2743 r_free = 0.2743 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2743 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 17770 Z= 0.234 Angle : 0.565 7.030 24167 Z= 0.295 Chirality : 0.041 0.169 2724 Planarity : 0.004 0.054 2898 Dihedral : 12.291 108.977 2837 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.24 % Allowed : 10.21 % Favored : 88.55 % 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 aren not related in a simple way. whole: 1.34 (0.19), residues: 1991 helix: 1.98 (0.16), residues: 1101 sheet: 1.06 (0.45), residues: 138 loop : -0.82 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1602 TYR 0.018 0.001 TYR A1696 PHE 0.017 0.001 PHE A1768 TRP 0.010 0.001 TRP A1293 HIS 0.009 0.001 HIS A 940 Details of bonding type rmsd covalent geometry : bond 0.00514 (17767) covalent geometry : angle 0.56515 (24167) hydrogen bonds : bond 0.04014 ( 907) hydrogen bonds : angle 4.30981 ( 2629) metal coordination : bond 0.00506 ( 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 154 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 0.708 Fit side-chains revert: symmetry clash REVERT: A 7 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.8085 (pm20) REVERT: A 214 MET cc_start: 0.8418 (mpp) cc_final: 0.7979 (mpp) REVERT: A 400 MET cc_start: 0.8657 (tpt) cc_final: 0.8276 (tpt) REVERT: A 510 ASP cc_start: 0.8355 (m-30) cc_final: 0.7971 (m-30) REVERT: A 696 ASP cc_start: 0.8580 (m-30) cc_final: 0.7937 (p0) REVERT: A 900 MET cc_start: 0.8380 (tmm) cc_final: 0.8000 (tmm) REVERT: A 1056 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7537 (mm-30) REVERT: A 1271 ASP cc_start: 0.8557 (m-30) cc_final: 0.8278 (m-30) REVERT: A 1496 GLU cc_start: 0.8947 (tm-30) cc_final: 0.8688 (tm-30) REVERT: A 2037 MET cc_start: 0.8989 (mpp) cc_final: 0.8716 (mpp) REVERT: A 2177 MET cc_start: 0.8012 (tpp) cc_final: 0.7780 (tpp) outliers start: 23 outliers final: 17 residues processed: 142 average time/residue: 0.1170 time to fit residues: 27.2505 Evaluate side-chains 145 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 312 HIS Chi-restraints excluded: chain A residue 525 ASN 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 1287 CYS Chi-restraints excluded: chain A residue 1350 GLU Chi-restraints excluded: chain A residue 1390 THR Chi-restraints excluded: chain A residue 1472 VAL Chi-restraints excluded: chain A residue 1566 THR Chi-restraints excluded: chain A residue 1609 THR Chi-restraints excluded: chain A residue 1665 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 45 optimal weight: 0.0050 chunk 80 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 chunk 194 optimal weight: 8.9990 chunk 102 optimal weight: 6.9990 chunk 65 optimal weight: 0.9980 chunk 120 optimal weight: 4.9990 chunk 11 optimal weight: 0.0980 chunk 175 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 172 optimal weight: 0.8980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 952 GLN ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1190 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.060500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.048803 restraints weight = 66667.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.050537 restraints weight = 32780.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.051749 restraints weight = 20141.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.052551 restraints weight = 14192.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.053062 restraints weight = 11090.248| |-----------------------------------------------------------------------------| r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2803 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2803 r_free = 0.2803 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2803 r_free = 0.2803 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2803 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 17770 Z= 0.102 Angle : 0.477 8.495 24167 Z= 0.251 Chirality : 0.038 0.149 2724 Planarity : 0.003 0.056 2898 Dihedral : 12.194 110.566 2835 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.35 % Allowed : 11.18 % Favored : 87.47 % 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 aren not related in a simple way. whole: 1.44 (0.19), residues: 1991 helix: 2.06 (0.16), residues: 1102 sheet: 1.14 (0.45), residues: 137 loop : -0.79 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 39 TYR 0.018 0.001 TYR A1696 PHE 0.013 0.001 PHE A1795 TRP 0.010 0.001 TRP A2219 HIS 0.008 0.001 HIS A 760 Details of bonding type rmsd covalent geometry : bond 0.00217 (17767) covalent geometry : angle 0.47670 (24167) hydrogen bonds : bond 0.03394 ( 907) hydrogen bonds : angle 4.05018 ( 2629) metal coordination : bond 0.00300 ( 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 172 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 147 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.8099 (pm20) REVERT: A 214 MET cc_start: 0.8458 (mpp) cc_final: 0.8148 (mpp) REVERT: A 365 MET cc_start: 0.8449 (tpp) cc_final: 0.8150 (tpp) REVERT: A 400 MET cc_start: 0.8513 (tpt) cc_final: 0.8161 (tpt) REVERT: A 450 MET cc_start: 0.9619 (mmt) cc_final: 0.9408 (mmm) REVERT: A 510 ASP cc_start: 0.8310 (m-30) cc_final: 0.7939 (m-30) REVERT: A 900 MET cc_start: 0.8368 (tmm) cc_final: 0.7804 (tmm) REVERT: A 934 MET cc_start: 0.9493 (mmp) cc_final: 0.9257 (mmp) REVERT: A 1006 GLU cc_start: 0.8240 (pt0) cc_final: 0.7903 (pt0) REVERT: A 1056 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7669 (mm-30) REVERT: A 1160 MET cc_start: 0.9247 (mmp) cc_final: 0.8901 (mmp) REVERT: A 1271 ASP cc_start: 0.8565 (m-30) cc_final: 0.8283 (m-30) REVERT: A 1457 MET cc_start: 0.7470 (mmm) cc_final: 0.6987 (mpp) REVERT: A 1496 GLU cc_start: 0.8969 (tm-30) cc_final: 0.8705 (tm-30) REVERT: A 2037 MET cc_start: 0.9031 (mpp) cc_final: 0.8707 (mpp) REVERT: A 2177 MET cc_start: 0.8060 (tpp) cc_final: 0.7842 (tpp) REVERT: A 2180 MET cc_start: 0.8886 (ttt) cc_final: 0.8503 (tpp) outliers start: 25 outliers final: 15 residues processed: 160 average time/residue: 0.1183 time to fit residues: 30.1368 Evaluate side-chains 144 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 0.631 ------------------------------------------------------------------------------- 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 312 HIS Chi-restraints excluded: chain A residue 525 ASN 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 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 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: 0.8980 chunk 41 optimal weight: 3.9990 chunk 193 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 1 optimal weight: 7.9990 chunk 50 optimal weight: 0.4980 chunk 112 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 109 optimal weight: 3.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.059543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.047889 restraints weight = 66629.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.049578 restraints weight = 32972.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.050753 restraints weight = 20413.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.051539 restraints weight = 14457.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.052058 restraints weight = 11359.636| |-----------------------------------------------------------------------------| r_work (final): 0.2775 ------------------------------------------------------------------------------- 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 = 0.66 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 | |-----------------------------------------------------------------------------| r_final: 0.2775 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17770 Z= 0.150 Angle : 0.493 7.032 24167 Z= 0.258 Chirality : 0.039 0.145 2724 Planarity : 0.003 0.052 2898 Dihedral : 12.144 110.599 2835 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.67 % Allowed : 11.99 % Favored : 86.34 % 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 aren not related in a simple way. whole: 1.45 (0.19), residues: 1991 helix: 2.08 (0.16), residues: 1101 sheet: 1.17 (0.45), residues: 137 loop : -0.80 (0.22), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1439 TYR 0.018 0.001 TYR A1528 PHE 0.013 0.001 PHE A1795 TRP 0.007 0.001 TRP A1143 HIS 0.005 0.001 HIS A 760 Details of bonding type rmsd covalent geometry : bond 0.00335 (17767) covalent geometry : angle 0.49329 (24167) hydrogen bonds : bond 0.03502 ( 907) hydrogen bonds : angle 4.05215 ( 2629) metal coordination : bond 0.00280 ( 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 164 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 133 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.8088 (pm20) REVERT: A 214 MET cc_start: 0.8471 (mpp) cc_final: 0.8144 (mpp) REVERT: A 365 MET cc_start: 0.8526 (tpp) cc_final: 0.8202 (tpp) REVERT: A 400 MET cc_start: 0.8504 (tpt) cc_final: 0.8160 (tpt) REVERT: A 424 HIS cc_start: 0.4897 (OUTLIER) cc_final: 0.4275 (t-170) REVERT: A 510 ASP cc_start: 0.8295 (m-30) cc_final: 0.7911 (m-30) REVERT: A 900 MET cc_start: 0.8392 (tmm) cc_final: 0.7090 (tmm) REVERT: A 940 HIS cc_start: 0.8198 (OUTLIER) cc_final: 0.7907 (t70) REVERT: A 1056 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7637 (mm-30) REVERT: A 1169 GLU cc_start: 0.8875 (tp30) cc_final: 0.8394 (tp30) REVERT: A 1271 ASP cc_start: 0.8576 (m-30) cc_final: 0.8282 (m-30) REVERT: A 1457 MET cc_start: 0.7480 (mmm) cc_final: 0.7070 (mpp) REVERT: A 1496 GLU cc_start: 0.8976 (tm-30) cc_final: 0.8540 (tm-30) REVERT: A 2037 MET cc_start: 0.9047 (mpp) cc_final: 0.8655 (mpp) REVERT: A 2177 MET cc_start: 0.8008 (tpp) cc_final: 0.7746 (tpp) REVERT: A 2180 MET cc_start: 0.8885 (ttt) cc_final: 0.8325 (tpp) outliers start: 31 outliers final: 16 residues processed: 152 average time/residue: 0.1124 time to fit residues: 27.9810 Evaluate side-chains 149 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 312 HIS Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 940 HIS 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 1472 VAL Chi-restraints excluded: chain A residue 1526 ASP Chi-restraints excluded: chain A residue 1566 THR Chi-restraints excluded: chain A residue 1665 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 44 optimal weight: 6.9990 chunk 100 optimal weight: 0.9990 chunk 115 optimal weight: 5.9990 chunk 109 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 176 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 193 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 154 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.059866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.048288 restraints weight = 66118.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.049956 restraints weight = 33183.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.051112 restraints weight = 20679.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.051886 restraints weight = 14738.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.052371 restraints weight = 11600.522| |-----------------------------------------------------------------------------| r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2784 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2784 r_free = 0.2784 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 = 0.2784 r_free = 0.2784 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2784 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17770 Z= 0.124 Angle : 0.490 7.510 24167 Z= 0.256 Chirality : 0.038 0.171 2724 Planarity : 0.003 0.055 2898 Dihedral : 12.132 111.044 2835 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.73 % Allowed : 12.69 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.46 (0.19), residues: 1991 helix: 2.09 (0.16), residues: 1104 sheet: 1.24 (0.45), residues: 136 loop : -0.81 (0.22), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 39 TYR 0.016 0.001 TYR A1696 PHE 0.020 0.001 PHE A1507 TRP 0.007 0.001 TRP A1143 HIS 0.005 0.001 HIS A 760 Details of bonding type rmsd covalent geometry : bond 0.00276 (17767) covalent geometry : angle 0.48950 (24167) hydrogen bonds : bond 0.03388 ( 907) hydrogen bonds : angle 3.98702 ( 2629) metal coordination : bond 0.00104 ( 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 168 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 136 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.8082 (pm20) REVERT: A 214 MET cc_start: 0.8513 (mpp) cc_final: 0.8207 (mpp) REVERT: A 365 MET cc_start: 0.8567 (tpp) cc_final: 0.8230 (tpp) REVERT: A 400 MET cc_start: 0.8488 (tpt) cc_final: 0.8116 (tpt) REVERT: A 510 ASP cc_start: 0.8292 (m-30) cc_final: 0.7924 (m-30) REVERT: A 900 MET cc_start: 0.8302 (tmm) cc_final: 0.6938 (tmm) REVERT: A 1056 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7612 (mm-30) REVERT: A 1169 GLU cc_start: 0.8897 (tp30) cc_final: 0.8407 (tp30) REVERT: A 1271 ASP cc_start: 0.8553 (m-30) cc_final: 0.8286 (m-30) REVERT: A 1343 MET cc_start: 0.9221 (mmm) cc_final: 0.8947 (tpp) REVERT: A 1496 GLU cc_start: 0.8992 (tm-30) cc_final: 0.8566 (tm-30) REVERT: A 2037 MET cc_start: 0.8972 (mpp) cc_final: 0.8692 (mpp) REVERT: A 2177 MET cc_start: 0.7942 (tpp) cc_final: 0.7701 (tpp) REVERT: A 2180 MET cc_start: 0.8796 (ttt) cc_final: 0.8282 (tpp) outliers start: 32 outliers final: 18 residues processed: 156 average time/residue: 0.1054 time to fit residues: 27.3485 Evaluate side-chains 149 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 0.541 ------------------------------------------------------------------------------- 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 312 HIS Chi-restraints excluded: chain A residue 525 ASN 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 1472 VAL Chi-restraints excluded: chain A residue 1526 ASP Chi-restraints excluded: chain A residue 1566 THR 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 2222 MET 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: 0.7980 chunk 155 optimal weight: 8.9990 chunk 79 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 65 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 102 optimal weight: 0.2980 chunk 107 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.2989 r_free = 0.2989 target = 0.059604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.048032 restraints weight = 66117.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.049700 restraints weight = 33262.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.050852 restraints weight = 20791.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.051630 restraints weight = 14839.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.052087 restraints weight = 11706.984| |-----------------------------------------------------------------------------| r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2779 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2779 r_free = 0.2779 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2779 r_free = 0.2779 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2779 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17770 Z= 0.136 Angle : 0.501 8.272 24167 Z= 0.259 Chirality : 0.039 0.168 2724 Planarity : 0.003 0.052 2898 Dihedral : 12.132 110.984 2835 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.30 % Allowed : 13.55 % Favored : 85.15 % 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 aren not related in a simple way. whole: 1.48 (0.19), residues: 1991 helix: 2.11 (0.16), residues: 1105 sheet: 1.23 (0.45), residues: 137 loop : -0.83 (0.23), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 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 0.004 0.001 HIS A 760 Details of bonding type rmsd covalent geometry : bond 0.00307 (17767) covalent geometry : angle 0.50127 (24167) hydrogen bonds : bond 0.03395 ( 907) hydrogen bonds : angle 3.98110 ( 2629) metal coordination : bond 0.00255 ( 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 154 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.8042 (pm20) REVERT: A 214 MET cc_start: 0.8530 (mpp) cc_final: 0.8183 (mpp) REVERT: A 400 MET cc_start: 0.8468 (tpt) cc_final: 0.8101 (tpt) REVERT: A 424 HIS cc_start: 0.5094 (OUTLIER) cc_final: 0.4636 (t-170) REVERT: A 450 MET cc_start: 0.9621 (mmt) cc_final: 0.9393 (mmm) REVERT: A 510 ASP cc_start: 0.8290 (m-30) cc_final: 0.7920 (m-30) REVERT: A 900 MET cc_start: 0.8299 (tmm) cc_final: 0.7808 (tmm) REVERT: A 1056 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7600 (mm-30) REVERT: A 1169 GLU cc_start: 0.8933 (tp30) cc_final: 0.8430 (tp30) REVERT: A 1237 GLU cc_start: 0.8365 (tm-30) cc_final: 0.8100 (tm-30) REVERT: A 1271 ASP cc_start: 0.8569 (m-30) cc_final: 0.8362 (m-30) REVERT: A 1457 MET cc_start: 0.7510 (mmm) cc_final: 0.7242 (mmm) REVERT: A 1496 GLU cc_start: 0.8998 (tm-30) cc_final: 0.8586 (tm-30) REVERT: A 2037 MET cc_start: 0.9035 (mpp) cc_final: 0.8721 (mpp) REVERT: A 2177 MET cc_start: 0.7962 (tpp) cc_final: 0.7719 (tpp) REVERT: A 2180 MET cc_start: 0.8783 (ttt) cc_final: 0.8301 (tpp) outliers start: 24 outliers final: 17 residues processed: 146 average time/residue: 0.1105 time to fit residues: 26.7485 Evaluate side-chains 148 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 0.512 ------------------------------------------------------------------------------- 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 312 HIS Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 525 ASN 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 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 1799 ASP Chi-restraints excluded: chain A residue 2005 ASP Chi-restraints excluded: chain A residue 2090 ILE Chi-restraints excluded: chain A residue 2222 MET Chi-restraints excluded: chain A residue 2227 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 30 optimal weight: 3.9990 chunk 68 optimal weight: 8.9990 chunk 55 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 137 optimal weight: 0.9980 chunk 140 optimal weight: 8.9990 chunk 52 optimal weight: 0.9980 chunk 143 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 11 optimal weight: 8.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** 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 = 0.2970 r_free = 0.2970 target = 0.058762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.047139 restraints weight = 67007.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.048796 restraints weight = 33906.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.049935 restraints weight = 21236.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.050720 restraints weight = 15213.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.051207 restraints weight = 11991.705| |-----------------------------------------------------------------------------| r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2754 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2754 r_free = 0.2754 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2754 r_free = 0.2754 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2754 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 17770 Z= 0.190 Angle : 0.535 7.956 24167 Z= 0.279 Chirality : 0.040 0.184 2724 Planarity : 0.003 0.048 2898 Dihedral : 12.137 110.593 2835 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.24 % Allowed : 13.88 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.42 (0.19), residues: 1991 helix: 2.06 (0.16), residues: 1106 sheet: 1.18 (0.44), residues: 137 loop : -0.86 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1439 TYR 0.014 0.001 TYR A1696 PHE 0.020 0.001 PHE A1507 TRP 0.008 0.001 TRP A 281 HIS 0.005 0.001 HIS A 760 Details of bonding type rmsd covalent geometry : bond 0.00425 (17767) covalent geometry : angle 0.53499 (24167) hydrogen bonds : bond 0.03678 ( 907) hydrogen bonds : angle 4.07071 ( 2629) metal coordination : bond 0.00607 ( 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 151 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 0.699 Fit side-chains revert: symmetry clash REVERT: A 7 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.8033 (pm20) REVERT: A 214 MET cc_start: 0.8529 (mpp) cc_final: 0.8173 (mpp) REVERT: A 351 MET cc_start: 0.8924 (ptt) cc_final: 0.8655 (ptt) REVERT: A 365 MET cc_start: 0.8460 (tpp) cc_final: 0.8220 (tpp) REVERT: A 400 MET cc_start: 0.8419 (tpt) cc_final: 0.8039 (tpp) REVERT: A 424 HIS cc_start: 0.5144 (OUTLIER) cc_final: 0.4569 (t-170) REVERT: A 510 ASP cc_start: 0.8367 (m-30) cc_final: 0.7986 (m-30) REVERT: A 900 MET cc_start: 0.8274 (tmm) cc_final: 0.6906 (tmm) REVERT: A 1056 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7614 (mm-30) REVERT: A 1237 GLU cc_start: 0.8345 (tm-30) cc_final: 0.8089 (tm-30) REVERT: A 1271 ASP cc_start: 0.8553 (m-30) cc_final: 0.8295 (m-30) REVERT: A 1415 MET cc_start: 0.8705 (ptt) cc_final: 0.7897 (ppp) REVERT: A 1457 MET cc_start: 0.7383 (mmm) cc_final: 0.7091 (mmm) REVERT: A 1496 GLU cc_start: 0.9022 (tm-30) cc_final: 0.8617 (tm-30) REVERT: A 2037 MET cc_start: 0.8857 (mpp) cc_final: 0.8547 (mpp) REVERT: A 2177 MET cc_start: 0.8021 (tpp) cc_final: 0.7807 (tpp) REVERT: A 2180 MET cc_start: 0.8792 (ttt) cc_final: 0.8331 (tpp) outliers start: 23 outliers final: 18 residues processed: 143 average time/residue: 0.1161 time to fit residues: 27.5079 Evaluate side-chains 144 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.856 ------------------------------------------------------------------------------- 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 312 HIS Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 525 ASN 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 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 2222 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 171 optimal weight: 5.9990 chunk 156 optimal weight: 4.9990 chunk 151 optimal weight: 2.9990 chunk 66 optimal weight: 0.4980 chunk 70 optimal weight: 0.6980 chunk 115 optimal weight: 7.9990 chunk 68 optimal weight: 8.9990 chunk 53 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 163 optimal weight: 0.9980 chunk 167 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 ASN ** 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 = 0.3005 r_free = 0.3005 target = 0.060281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.048694 restraints weight = 65850.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.050388 restraints weight = 33034.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.051551 restraints weight = 20506.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.052295 restraints weight = 14621.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.052837 restraints weight = 11601.681| |-----------------------------------------------------------------------------| r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2798 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2798 r_free = 0.2798 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2798 r_free = 0.2798 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2798 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17770 Z= 0.106 Angle : 0.508 8.898 24167 Z= 0.262 Chirality : 0.038 0.159 2724 Planarity : 0.003 0.051 2898 Dihedral : 12.067 111.102 2831 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.51 % Allowed : 13.98 % 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 aren not related in a simple way. whole: 1.46 (0.19), residues: 1991 helix: 2.10 (0.16), residues: 1104 sheet: 1.30 (0.46), residues: 126 loop : -0.82 (0.23), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 39 TYR 0.015 0.001 TYR A1696 PHE 0.022 0.001 PHE A1507 TRP 0.006 0.001 TRP A1143 HIS 0.004 0.001 HIS A 760 Details of bonding type rmsd covalent geometry : bond 0.00235 (17767) covalent geometry : angle 0.50760 (24167) hydrogen bonds : bond 0.03352 ( 907) hydrogen bonds : angle 3.94033 ( 2629) metal coordination : bond 0.00111 ( 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 166 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 138 time to evaluate : 0.834 Fit side-chains REVERT: A 7 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.8043 (pm20) REVERT: A 214 MET cc_start: 0.8521 (mpp) cc_final: 0.8162 (mpp) REVERT: A 284 MET cc_start: 0.9355 (tmm) cc_final: 0.9136 (ppp) REVERT: A 400 MET cc_start: 0.8466 (tpt) cc_final: 0.8090 (tpt) REVERT: A 424 HIS cc_start: 0.5061 (OUTLIER) cc_final: 0.4547 (t-170) REVERT: A 510 ASP cc_start: 0.8308 (m-30) cc_final: 0.7944 (m-30) REVERT: A 602 GLN cc_start: 0.9131 (OUTLIER) cc_final: 0.8836 (tp40) REVERT: A 900 MET cc_start: 0.8262 (tmm) cc_final: 0.6936 (tmm) REVERT: A 1056 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7594 (mm-30) REVERT: A 1237 GLU cc_start: 0.8298 (tm-30) cc_final: 0.8043 (tm-30) REVERT: A 1415 MET cc_start: 0.8628 (ptt) cc_final: 0.7946 (ppp) REVERT: A 1457 MET cc_start: 0.7458 (mmm) cc_final: 0.7185 (mmm) REVERT: A 1496 GLU cc_start: 0.8976 (tm-30) cc_final: 0.8569 (tm-30) REVERT: A 2037 MET cc_start: 0.8911 (mpp) cc_final: 0.8602 (mpp) REVERT: A 2177 MET cc_start: 0.7981 (tpp) cc_final: 0.7751 (tpp) REVERT: A 2180 MET cc_start: 0.8705 (ttt) cc_final: 0.8184 (tpt) outliers start: 28 outliers final: 20 residues processed: 156 average time/residue: 0.1186 time to fit residues: 30.8078 Evaluate side-chains 152 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 0.669 ------------------------------------------------------------------------------- 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 312 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 640 SER Chi-restraints excluded: chain A residue 787 THR Chi-restraints excluded: chain A residue 964 GLU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1260 VAL 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 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 2222 MET 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-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.3763 > 50: distance: 19 - 42: 24.119 distance: 26 - 29: 24.465 distance: 29 - 30: 9.885 distance: 30 - 31: 16.582 distance: 30 - 33: 36.612 distance: 31 - 32: 25.019 distance: 31 - 35: 20.306 distance: 33 - 34: 9.962 distance: 35 - 36: 21.240 distance: 36 - 37: 12.779 distance: 36 - 39: 9.665 distance: 37 - 38: 20.429 distance: 37 - 42: 17.551 distance: 38 - 64: 24.100 distance: 39 - 40: 39.763 distance: 39 - 41: 28.329 distance: 42 - 43: 8.192 distance: 43 - 44: 11.896 distance: 43 - 46: 12.533 distance: 44 - 45: 15.661 distance: 44 - 47: 12.462 distance: 45 - 72: 19.652 distance: 47 - 48: 5.003 distance: 48 - 49: 7.625 distance: 48 - 51: 11.142 distance: 49 - 50: 7.938 distance: 49 - 56: 6.218 distance: 50 - 80: 15.797 distance: 51 - 52: 13.763 distance: 52 - 53: 4.366 distance: 53 - 54: 10.454 distance: 54 - 55: 27.500 distance: 56 - 57: 9.146 distance: 57 - 58: 19.909 distance: 57 - 60: 6.657 distance: 58 - 59: 4.506 distance: 58 - 64: 7.949 distance: 59 - 87: 24.269 distance: 60 - 61: 19.264 distance: 61 - 62: 6.494 distance: 61 - 63: 7.075 distance: 65 - 66: 14.670 distance: 65 - 68: 16.034 distance: 66 - 67: 15.398 distance: 66 - 72: 6.401 distance: 67 - 95: 16.471 distance: 68 - 69: 4.613 distance: 68 - 70: 37.378 distance: 72 - 73: 6.108 distance: 73 - 74: 6.041 distance: 73 - 76: 9.839 distance: 74 - 75: 16.541 distance: 74 - 80: 9.056 distance: 75 - 103: 28.281 distance: 76 - 77: 8.579 distance: 77 - 78: 21.107 distance: 77 - 79: 8.627 distance: 80 - 81: 21.621 distance: 81 - 82: 18.055 distance: 81 - 84: 14.127 distance: 82 - 83: 11.785 distance: 82 - 87: 24.638 distance: 83 - 110: 21.689 distance: 84 - 85: 10.881 distance: 84 - 86: 32.964 distance: 87 - 88: 9.130 distance: 88 - 89: 11.469 distance: 88 - 91: 11.549 distance: 89 - 90: 18.196 distance: 89 - 95: 6.539 distance: 90 - 117: 17.009 distance: 91 - 92: 24.712 distance: 92 - 93: 20.442 distance: 92 - 94: 8.815 distance: 95 - 96: 5.996 distance: 96 - 97: 12.694 distance: 96 - 99: 14.557 distance: 97 - 98: 15.044 distance: 97 - 103: 9.759 distance: 98 - 122: 8.952 distance: 99 - 100: 13.603 distance: 100 - 101: 9.653 distance: 100 - 102: 14.950