Starting phenix.real_space_refine on Thu Mar 5 04:41:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ork_13040/03_2026/7ork_13040.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ork_13040/03_2026/7ork_13040.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ork_13040/03_2026/7ork_13040.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ork_13040/03_2026/7ork_13040.map" model { file = "/net/cci-nas-00/data/ceres_data/7ork_13040/03_2026/7ork_13040.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ork_13040/03_2026/7ork_13040.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 42 5.49 5 Mg 2 5.21 5 S 116 5.16 5 C 11752 2.51 5 N 3126 2.21 5 O 3660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18699 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 17799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2182, 17799 Classifications: {'peptide': 2182} Link IDs: {'PTRANS': 72, 'TRANS': 2109} Chain breaks: 6 Chain: "H" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 365 Classifications: {'RNA': 17} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 8, 'rna3p_pyr': 6} Link IDs: {'rna2p': 2, 'rna3p': 14} Chain: "T" Number of atoms: 379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 379 Classifications: {'RNA': 18} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 4, 'rna3p_pur': 6, 'rna3p_pyr': 6} Link IDs: {'rna2p': 5, 'rna3p': 12} Chain: "P" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 74 Unusual residues: {'GTG': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p_pur': 1} Link IDs: {None: 1} Chain: "A" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 75 Unusual residues: {' MG': 2, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 4, 'water': 41} Link IDs: {None: 44} Chain: "H" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "T" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16484 SG CYS A2064 49.063 99.939 50.681 1.00118.87 S Time building chain proxies: 4.24, per 1000 atoms: 0.23 Number of scatterers: 18699 At special positions: 0 Unit cell: (113.52, 119.325, 148.995, 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 116 16.00 P 42 15.00 Mg 2 11.99 O 3660 8.00 N 3126 7.00 C 11752 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.75 Conformation dependent library (CDL) restraints added in 838.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2303 " pdb="ZN ZN A2303 " - pdb=" NE2 HIS A2169 " pdb="ZN ZN A2303 " - pdb=" NE2 HIS A2182 " pdb="ZN ZN A2303 " - pdb=" SG CYS A2064 " 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4204 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 17 sheets defined 56.6% alpha, 10.7% beta 8 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 2.90 Creating SS restraints... Processing helix chain 'A' and resid 2 through 16 Processing helix chain 'A' and resid 19 through 45 Processing helix chain 'A' and resid 54 through 63 Processing helix chain 'A' and resid 98 through 121 removed outlier: 4.588A pdb=" N SER A 102 " --> pdb=" O SER A 98 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ILE A 104 " --> pdb=" O GLU A 100 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ASP A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N ILE A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 149 Processing helix chain 'A' and resid 158 through 172 Processing helix chain 'A' and resid 175 through 183 removed outlier: 3.680A pdb=" N LEU A 179 " --> pdb=" O ASP A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 203 Processing helix chain 'A' and resid 204 through 213 Processing helix chain 'A' and resid 215 through 227 removed outlier: 3.543A pdb=" N LYS A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 247 Processing helix chain 'A' and resid 247 through 260 Processing helix chain 'A' and resid 261 through 264 Processing helix chain 'A' and resid 273 through 292 Processing helix chain 'A' and resid 297 through 301 removed outlier: 3.768A pdb=" N ASP A 300 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 333 Processing helix chain 'A' and resid 340 through 350 Processing helix chain 'A' and resid 356 through 371 removed outlier: 3.646A pdb=" N LYS A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA A 371 " --> pdb=" O LEU A 367 " (cutoff:3.500A) 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: 6.742A pdb=" N SER A 483 " --> pdb=" O ASN A 479 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ARG A 484 " --> pdb=" O GLU A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 501 Processing helix chain 'A' and resid 502 through 521 removed outlier: 3.617A pdb=" N GLN A 506 " --> pdb=" O THR A 502 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL A 521 " --> pdb=" O ASN A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 620 Proline residue: A 608 - end of helix Processing helix chain 'A' and resid 626 through 639 Processing helix chain 'A' and resid 642 through 661 removed outlier: 4.211A pdb=" N LEU A 646 " --> pdb=" O THR A 642 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU A 648 " --> pdb=" O SER A 644 " (cutoff:3.500A) Proline residue: A 651 - end of helix removed outlier: 4.533A 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 702 removed outlier: 4.633A pdb=" N TYR A 698 " --> pdb=" O CYS A 694 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ASP A 699 " --> pdb=" O PHE A 695 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLN A 702 " --> pdb=" O TYR A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 747 Processing helix chain 'A' and resid 748 through 751 Processing helix chain 'A' and resid 758 through 781 removed outlier: 4.210A pdb=" N VAL A 764 " --> pdb=" O HIS A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 813 removed outlier: 3.676A pdb=" N ARG A 813 " --> pdb=" O ALA A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 830 through 838 removed outlier: 5.790A pdb=" N SER A 835 " --> pdb=" O THR A 832 " (cutoff:3.500A) removed outlier: 6.605A 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 875 through 879 removed outlier: 3.641A pdb=" N VAL A 879 " --> pdb=" O PRO A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 884 removed outlier: 3.830A pdb=" N VAL A 884 " --> pdb=" O ASP A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 900 Processing helix chain 'A' and resid 911 through 921 Processing helix chain 'A' and resid 928 through 940 removed outlier: 3.901A pdb=" N ILE A 938 " --> pdb=" O MET A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 980 removed outlier: 3.547A pdb=" N VAL A 974 " --> pdb=" O CYS A 970 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU A 980 " --> pdb=" O ARG A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1030 removed outlier: 3.717A pdb=" N LYS A 999 " --> pdb=" O ASP A 995 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU A1002 " --> pdb=" O LEU A 998 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG A1017 " --> pdb=" O VAL A1013 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N GLU A1022 " --> pdb=" O GLN A1018 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ILE A1023 " --> pdb=" O LYS A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1040 through 1047 Processing helix chain 'A' and resid 1070 through 1079 removed outlier: 3.896A pdb=" N PHE A1074 " --> pdb=" O PHE A1070 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TRP A1075 " --> pdb=" O TYR A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1099 Processing helix chain 'A' and resid 1106 through 1115 Processing helix chain 'A' and resid 1123 through 1129 Processing helix chain 'A' and resid 1148 through 1174 removed outlier: 3.595A pdb=" N LEU A1174 " --> pdb=" O ALA A1170 " (cutoff:3.500A) Processing helix chain 'A' and resid 1201 through 1220 removed outlier: 3.666A pdb=" N ILE A1205 " --> pdb=" O GLU A1201 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE A1220 " --> pdb=" O ALA A1216 " (cutoff:3.500A) Processing helix chain 'A' and resid 1252 through 1262 removed outlier: 3.543A pdb=" N LEU A1256 " --> pdb=" O TYR A1252 " (cutoff:3.500A) Processing helix chain 'A' and resid 1267 through 1285 Processing helix chain 'A' and resid 1288 through 1307 Processing helix chain 'A' and resid 1317 through 1321 removed outlier: 3.841A pdb=" N PHE A1321 " --> pdb=" O ILE A1318 " (cutoff:3.500A) Processing helix chain 'A' and resid 1325 through 1329 Processing helix chain 'A' and resid 1330 through 1334 Processing helix chain 'A' and resid 1340 through 1347 Processing helix chain 'A' and resid 1350 through 1364 Processing helix chain 'A' and resid 1366 through 1370 removed outlier: 3.643A pdb=" N LYS A1370 " --> pdb=" O VAL A1367 " (cutoff:3.500A) Processing helix chain 'A' and resid 1373 through 1379 Processing helix chain 'A' and resid 1380 through 1384 Processing helix chain 'A' and resid 1390 through 1403 Processing helix chain 'A' and resid 1434 through 1440 removed outlier: 3.869A pdb=" N LYS A1440 " --> pdb=" O GLY A1436 " (cutoff:3.500A) Processing helix chain 'A' and resid 1441 through 1452 removed outlier: 3.609A pdb=" N SER A1445 " --> pdb=" O LEU A1441 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS A1446 " --> pdb=" O TYR A1442 " (cutoff:3.500A) Processing helix chain 'A' and resid 1455 through 1467 removed outlier: 3.513A pdb=" N GLU A1459 " --> pdb=" O GLY A1455 " (cutoff:3.500A) Processing helix chain 'A' and resid 1468 through 1472 Processing helix chain 'A' and resid 1477 through 1489 Processing helix chain 'A' and resid 1493 through 1498 Processing helix chain 'A' and resid 1502 through 1513 removed outlier: 3.637A pdb=" N GLN A1510 " --> pdb=" O LEU A1506 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE A1511 " --> pdb=" O PHE A1507 " (cutoff:3.500A) Processing helix chain 'A' and resid 1548 through 1562 removed outlier: 3.732A pdb=" N SER A1562 " --> pdb=" O ARG A1558 " (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 1612 through 1617 removed outlier: 3.680A pdb=" N LYS A1617 " --> pdb=" O ARG A1614 " (cutoff:3.500A) Processing helix chain 'A' and resid 1622 through 1633 Processing helix chain 'A' and resid 1641 through 1659 removed outlier: 3.791A pdb=" N ARG A1647 " --> pdb=" O THR A1643 " (cutoff:3.500A) Processing helix chain 'A' and resid 1660 through 1677 Processing helix chain 'A' and resid 1680 through 1703 removed outlier: 3.568A pdb=" N THR A1702 " --> pdb=" O TYR A1698 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLU A1703 " --> pdb=" O VAL A1699 " (cutoff:3.500A) Processing helix chain 'A' and resid 1717 through 1728 Processing helix chain 'A' and resid 1756 through 1779 removed outlier: 3.671A pdb=" N HIS A1773 " --> pdb=" O LYS A1769 " (cutoff:3.500A) Processing helix chain 'A' and resid 1780 through 1782 No H-bonds generated for 'chain 'A' and resid 1780 through 1782' Processing helix chain 'A' and resid 1783 through 1795 Processing helix chain 'A' and resid 1802 through 1811 Processing helix chain 'A' and resid 1814 through 1817 Processing helix chain 'A' and resid 1818 through 1826 Processing helix chain 'A' and resid 1829 through 1838 Processing helix chain 'A' and resid 1839 through 1842 removed outlier: 3.520A pdb=" N HIS A1842 " --> pdb=" O MET A1839 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1839 through 1842' Processing helix chain 'A' and resid 1892 through 1905 Processing helix chain 'A' and resid 1944 through 1956 removed outlier: 3.686A pdb=" N ALA A1956 " --> pdb=" O GLU A1952 " (cutoff:3.500A) Processing helix chain 'A' and resid 1983 through 1991 removed outlier: 3.725A pdb=" N LEU A1987 " --> pdb=" O LEU A1983 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASP A1988 " --> pdb=" O ILE A1984 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N TYR A1989 " --> pdb=" O ARG A1985 " (cutoff:3.500A) Processing helix chain 'A' and resid 2014 through 2019 removed outlier: 3.977A pdb=" N VAL A2019 " --> pdb=" O SER A2016 " (cutoff:3.500A) Processing helix chain 'A' and resid 2033 through 2038 removed outlier: 3.678A pdb=" N LYS A2038 " --> pdb=" O THR A2034 " (cutoff:3.500A) Processing helix chain 'A' and resid 2039 through 2043 Processing helix chain 'A' and resid 2046 through 2052 Processing helix chain 'A' and resid 2054 through 2060 removed outlier: 3.683A pdb=" N PHE A2058 " --> pdb=" O ASN A2054 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS A2060 " --> pdb=" O ILE A2056 " (cutoff:3.500A) Processing helix chain 'A' and resid 2072 through 2077 Processing helix chain 'A' and resid 2109 through 2129 removed outlier: 3.696A pdb=" N LYS A2123 " --> pdb=" O GLU A2119 " (cutoff:3.500A) Processing helix chain 'A' and resid 2138 through 2155 removed outlier: 3.620A pdb=" N ILE A2152 " --> pdb=" O VAL A2148 " (cutoff:3.500A) Processing helix chain 'A' and resid 2161 through 2175 Processing helix chain 'A' and resid 2178 through 2183 removed outlier: 3.986A pdb=" N HIS A2182 " --> pdb=" O ASP A2178 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER A2183 " --> pdb=" O HIS A2179 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2178 through 2183' Processing helix chain 'A' and resid 2200 through 2210 removed outlier: 4.229A pdb=" N PHE A2204 " --> pdb=" O ASN A2200 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ARG A2205 " --> pdb=" O TRP A2201 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU A2206 " --> pdb=" O VAL A2202 " (cutoff:3.500A) Processing helix chain 'A' and resid 2218 through 2237 removed outlier: 3.771A pdb=" N MET A2222 " --> pdb=" O PRO A2218 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N GLU A2224 " --> pdb=" O ASN A2220 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 84 removed outlier: 6.133A pdb=" N LEU A 88 " --> pdb=" O GLU A 125 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL A 127 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N ILE A 90 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ILE A 129 " --> pdb=" O ILE A 90 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ASP A 92 " --> pdb=" O ILE A 129 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N ILE A 131 " --> pdb=" O ASP A 92 " (cutoff:3.500A) removed outlier: 6.728A 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 Processing sheet with id=AA3, first strand: chain 'A' and resid 386 through 387 removed outlier: 4.648A pdb=" N LEU A 392 " --> pdb=" O MET A 400 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLN A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N VAL A 558 " --> pdb=" O PHE A 545 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ILE A 561 " --> pdb=" O SER A 591 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY A 586 " --> pdb=" O CYS A 583 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 386 through 387 removed outlier: 4.648A pdb=" N LEU A 392 " --> pdb=" O MET A 400 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLN A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N VAL A 558 " --> pdb=" O PHE A 545 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 663 through 664 Processing sheet with id=AA6, first strand: chain 'A' and resid 716 through 718 removed outlier: 6.264A pdb=" N TYR A 710 " --> pdb=" O THR A 717 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE A 709 " --> pdb=" O TYR A2099 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N SER A2101 " --> pdb=" O ILE A 709 " (cutoff:3.500A) removed outlier: 9.487A pdb=" N LEU A 711 " --> pdb=" O SER A2101 " (cutoff:3.500A) removed outlier: 11.728A pdb=" N ARG A2103 " --> pdb=" O LEU A 711 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N PHE A2096 " --> pdb=" O ILE A2090 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 727 through 728 Processing sheet with id=AA8, first strand: chain 'A' and resid 842 through 847 removed outlier: 4.098A pdb=" N ASP A 905 " --> pdb=" O GLY A 847 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 871 through 872 Processing sheet with id=AB1, first strand: chain 'A' and resid 959 through 962 removed outlier: 6.426A pdb=" N PHE A 945 " --> pdb=" O ILE A1104 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1236 through 1238 removed outlier: 3.644A pdb=" N GLU A1247 " --> pdb=" O LEU A1244 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1594 through 1600 removed outlier: 4.729A pdb=" N THR A1737 " --> pdb=" O GLY A1597 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N TRP A1735 " --> pdb=" O PRO A1599 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1606 through 1608 Processing sheet with id=AB5, first strand: chain 'A' and resid 1800 through 1801 Processing sheet with id=AB6, first strand: chain 'A' and resid 1844 through 1847 removed outlier: 3.784A pdb=" N ARG A1870 " --> pdb=" O GLY A1867 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLU A1877 " --> pdb=" O LEU A1881 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N LEU A1881 " --> pdb=" O GLU A1877 " (cutoff:3.500A) removed outlier: 12.778A pdb=" N LYS A1880 " --> pdb=" O THR A1966 " (cutoff:3.500A) removed outlier: 10.379A pdb=" N VAL A1968 " --> pdb=" O LYS A1880 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N THR A1882 " --> pdb=" O VAL A1968 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N VAL A1970 " --> pdb=" O THR A1882 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE A1927 " --> pdb=" O VAL A1968 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N VAL A1970 " --> pdb=" O TYR A1925 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N TYR A1925 " --> pdb=" O VAL A1970 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1999 through 2000 Processing sheet with id=AB8, first strand: chain 'A' and resid 2027 through 2028 removed outlier: 3.571A pdb=" N LEU A2031 " --> pdb=" O THR A2028 " (cutoff:3.500A) 930 hydrogen bonds defined for protein. 2640 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 21 hydrogen bonds 42 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 15 stacking parallelities Total time for adding SS restraints: 5.07 Time building geometry restraints manager: 2.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3457 1.33 - 1.45: 4812 1.45 - 1.57: 10565 1.57 - 1.69: 80 1.69 - 1.81: 192 Bond restraints: 19106 Sorted by residual: bond pdb=" C5B GTG P 1 " pdb=" C6B GTG P 1 " ideal model delta sigma weight residual 1.424 1.330 0.094 2.00e-02 2.50e+03 2.19e+01 bond pdb=" C5A GTG P 1 " pdb=" C6A GTG P 1 " ideal model delta sigma weight residual 1.427 1.335 0.092 2.00e-02 2.50e+03 2.11e+01 bond pdb=" C1D GTG P 1 " pdb=" O4D GTG P 1 " ideal model delta sigma weight residual 1.383 1.449 -0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" N VAL A2221 " pdb=" CA VAL A2221 " ideal model delta sigma weight residual 1.452 1.490 -0.038 1.18e-02 7.18e+03 1.04e+01 bond pdb=" C PRO A2217 " pdb=" O PRO A2217 " ideal model delta sigma weight residual 1.240 1.204 0.036 1.12e-02 7.97e+03 1.04e+01 ... (remaining 19101 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 25373 2.17 - 4.34: 535 4.34 - 6.51: 31 6.51 - 8.68: 17 8.68 - 10.85: 4 Bond angle restraints: 25960 Sorted by residual: angle pdb=" C PHE A2131 " pdb=" CA PHE A2131 " pdb=" CB PHE A2131 " ideal model delta sigma weight residual 111.36 101.01 10.35 1.63e+00 3.76e-01 4.03e+01 angle pdb=" N PRO A2217 " pdb=" CA PRO A2217 " pdb=" C PRO A2217 " ideal model delta sigma weight residual 110.70 118.05 -7.35 1.22e+00 6.72e-01 3.63e+01 angle pdb=" N GLU A2133 " pdb=" CA GLU A2133 " pdb=" C GLU A2133 " ideal model delta sigma weight residual 113.28 106.53 6.75 1.22e+00 6.72e-01 3.06e+01 angle pdb=" N PRO A2094 " pdb=" CA PRO A2094 " pdb=" C PRO A2094 " ideal model delta sigma weight residual 112.47 101.62 10.85 2.06e+00 2.36e-01 2.77e+01 angle pdb=" N VAL A 95 " pdb=" CA VAL A 95 " pdb=" C VAL A 95 " ideal model delta sigma weight residual 111.77 106.37 5.40 1.04e+00 9.25e-01 2.70e+01 ... (remaining 25955 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.61: 10741 19.61 - 39.22: 736 39.22 - 58.83: 183 58.83 - 78.44: 54 78.44 - 98.05: 13 Dihedral angle restraints: 11727 sinusoidal: 5251 harmonic: 6476 Sorted by residual: dihedral pdb=" O4' C T 21 " pdb=" C1' C T 21 " pdb=" N1 C T 21 " pdb=" C2 C T 21 " ideal model delta sinusoidal sigma weight residual -128.00 -57.57 -70.43 1 1.70e+01 3.46e-03 2.21e+01 dihedral pdb=" C PHE A2131 " pdb=" N PHE A2131 " pdb=" CA PHE A2131 " pdb=" CB PHE A2131 " ideal model delta harmonic sigma weight residual -122.60 -111.47 -11.13 0 2.50e+00 1.60e-01 1.98e+01 dihedral pdb=" C THR A2093 " pdb=" N THR A2093 " pdb=" CA THR A2093 " pdb=" CB THR A2093 " ideal model delta harmonic sigma weight residual -122.00 -132.22 10.22 0 2.50e+00 1.60e-01 1.67e+01 ... (remaining 11724 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2463 0.064 - 0.128: 389 0.128 - 0.192: 52 0.192 - 0.256: 8 0.256 - 0.320: 4 Chirality restraints: 2916 Sorted by residual: chirality pdb=" CA PHE A2131 " pdb=" N PHE A2131 " pdb=" C PHE A2131 " pdb=" CB PHE A2131 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CA THR A2093 " pdb=" N THR A2093 " pdb=" C THR A2093 " pdb=" CB THR A2093 " both_signs ideal model delta sigma weight residual False 2.53 2.23 0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" C4D GTG P 1 " pdb=" C3D GTG P 1 " pdb=" C5D GTG P 1 " pdb=" O4D GTG P 1 " both_signs ideal model delta sigma weight residual False -2.52 -2.81 0.29 2.00e-01 2.50e+01 2.07e+00 ... (remaining 2913 not shown) Planarity restraints: 3146 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A2199 " 0.019 2.00e-02 2.50e+03 3.68e-02 1.36e+01 pdb=" C ILE A2199 " -0.064 2.00e-02 2.50e+03 pdb=" O ILE A2199 " 0.024 2.00e-02 2.50e+03 pdb=" N ASN A2200 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A1892 " 0.044 5.00e-02 4.00e+02 6.68e-02 7.13e+00 pdb=" N PRO A1893 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO A1893 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A1893 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A2130 " -0.011 2.00e-02 2.50e+03 2.33e-02 5.45e+00 pdb=" C THR A2130 " 0.040 2.00e-02 2.50e+03 pdb=" O THR A2130 " -0.015 2.00e-02 2.50e+03 pdb=" N PHE A2131 " -0.014 2.00e-02 2.50e+03 ... (remaining 3143 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 101 2.58 - 3.16: 15133 3.16 - 3.74: 29522 3.74 - 4.32: 43414 4.32 - 4.90: 70737 Nonbonded interactions: 158907 Sorted by model distance: nonbonded pdb=" OD2 ASP A1060 " pdb="MG MG A2302 " model vdw 1.996 2.170 nonbonded pdb=" OD1 ASP A2178 " pdb="ZN ZN A2303 " model vdw 2.074 2.230 nonbonded pdb=" OD2 ASP A1187 " pdb="MG MG A2302 " model vdw 2.145 2.170 nonbonded pdb=" O MET A1061 " pdb="MG MG A2302 " model vdw 2.166 2.170 nonbonded pdb=" OE1 GLN A 301 " pdb=" O HOH A2401 " model vdw 2.245 3.040 ... (remaining 158902 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.580 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 23.520 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 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 0.094 19110 Z= 0.320 Angle : 0.706 10.847 25960 Z= 0.455 Chirality : 0.050 0.320 2916 Planarity : 0.004 0.067 3146 Dihedral : 14.880 98.048 7523 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.04 % Allowed : 0.94 % Favored : 98.01 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.18), residues: 2168 helix: 1.24 (0.16), residues: 1094 sheet: -0.38 (0.37), residues: 199 loop : -0.93 (0.20), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1949 TYR 0.019 0.001 TYR A 677 PHE 0.031 0.001 PHE A1795 TRP 0.013 0.001 TRP A2160 HIS 0.004 0.001 HIS A1855 Details of bonding type rmsd covalent geometry : bond 0.00530 (19106) covalent geometry : angle 0.70601 (25960) hydrogen bonds : bond 0.14302 ( 936) hydrogen bonds : angle 5.80841 ( 2682) metal coordination : bond 0.05169 ( 3) Misc. bond : bond 0.04317 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 224 time to evaluate : 0.630 Fit side-chains REVERT: A 10 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8283 (mt) REVERT: A 1963 ASN cc_start: 0.8400 (t0) cc_final: 0.7881 (t0) REVERT: A 2035 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7355 (mm-30) outliers start: 21 outliers final: 4 residues processed: 240 average time/residue: 0.1465 time to fit residues: 52.5436 Evaluate side-chains 196 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 191 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 1988 ASP Chi-restraints excluded: chain A residue 2162 THR Chi-restraints excluded: chain A residue 2163 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 216 optimal weight: 0.0870 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.0980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 6.9990 chunk 212 optimal weight: 1.9990 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN A 316 ASN A 469 ASN A 752 ASN A1202 ASN ** A1243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1334 ASN A2054 ASN A2134 ASN A2169 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.113199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.080099 restraints weight = 27575.184| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 1.85 r_work: 0.2726 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2590 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.0874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.336 19110 Z= 0.154 Angle : 0.486 7.196 25960 Z= 0.263 Chirality : 0.041 0.207 2916 Planarity : 0.004 0.060 3146 Dihedral : 11.596 94.653 3011 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.80 % Allowed : 4.77 % Favored : 94.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.18), residues: 2168 helix: 1.61 (0.16), residues: 1110 sheet: -0.29 (0.38), residues: 192 loop : -0.95 (0.20), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 595 TYR 0.016 0.001 TYR A 677 PHE 0.021 0.001 PHE A1795 TRP 0.013 0.001 TRP A2219 HIS 0.004 0.001 HIS A1855 Details of bonding type rmsd covalent geometry : bond 0.00299 (19106) covalent geometry : angle 0.48595 (25960) hydrogen bonds : bond 0.04084 ( 936) hydrogen bonds : angle 4.19349 ( 2682) metal coordination : bond 0.19375 ( 3) Misc. bond : bond 0.00055 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 197 time to evaluate : 0.559 Fit side-chains REVERT: A 10 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8265 (mt) REVERT: A 365 MET cc_start: 0.8204 (tpp) cc_final: 0.7938 (tmm) REVERT: A 2005 ASP cc_start: 0.7857 (OUTLIER) cc_final: 0.7624 (t0) REVERT: A 2035 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7870 (mm-30) outliers start: 16 outliers final: 8 residues processed: 211 average time/residue: 0.1368 time to fit residues: 43.7160 Evaluate side-chains 195 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 185 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 819 ASN Chi-restraints excluded: chain A residue 1791 ILE Chi-restraints excluded: chain A residue 2002 VAL Chi-restraints excluded: chain A residue 2005 ASP Chi-restraints excluded: chain A residue 2137 ILE Chi-restraints excluded: chain A residue 2162 THR Chi-restraints excluded: chain A residue 2214 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 178 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 197 optimal weight: 0.2980 chunk 203 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 chunk 199 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 183 optimal weight: 0.9990 chunk 84 optimal weight: 8.9990 overall best weight: 1.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN A 469 ASN A1185 HIS ** A1243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2225 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.112195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.079109 restraints weight = 27805.577| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 1.89 r_work: 0.2695 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2560 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 moved from start: 0.1016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 19110 Z= 0.164 Angle : 0.480 7.704 25960 Z= 0.259 Chirality : 0.041 0.176 2916 Planarity : 0.004 0.059 3146 Dihedral : 11.504 86.900 3008 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.94 % Allowed : 6.07 % Favored : 92.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.18), residues: 2168 helix: 1.78 (0.16), residues: 1110 sheet: -0.23 (0.38), residues: 193 loop : -0.96 (0.20), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 12 TYR 0.018 0.001 TYR A 677 PHE 0.021 0.001 PHE A1795 TRP 0.015 0.001 TRP A2219 HIS 0.003 0.001 HIS A1855 Details of bonding type rmsd covalent geometry : bond 0.00387 (19106) covalent geometry : angle 0.47986 (25960) hydrogen bonds : bond 0.04197 ( 936) hydrogen bonds : angle 4.09086 ( 2682) metal coordination : bond 0.00623 ( 3) Misc. bond : bond 0.00010 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 199 time to evaluate : 0.454 Fit side-chains REVERT: A 89 TYR cc_start: 0.8034 (m-10) cc_final: 0.7796 (m-10) REVERT: A 365 MET cc_start: 0.8287 (tpp) cc_final: 0.7957 (ttp) REVERT: A 2005 ASP cc_start: 0.7939 (OUTLIER) cc_final: 0.7727 (t0) REVERT: A 2035 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7929 (mm-30) outliers start: 19 outliers final: 12 residues processed: 211 average time/residue: 0.1370 time to fit residues: 44.2261 Evaluate side-chains 204 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 191 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 472 LYS Chi-restraints excluded: chain A residue 819 ASN Chi-restraints excluded: chain A residue 1160 MET Chi-restraints excluded: chain A residue 1871 SER Chi-restraints excluded: chain A residue 2002 VAL Chi-restraints excluded: chain A residue 2005 ASP Chi-restraints excluded: chain A residue 2054 ASN Chi-restraints excluded: chain A residue 2162 THR Chi-restraints excluded: chain A residue 2211 LEU Chi-restraints excluded: chain A residue 2214 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 14 optimal weight: 8.9990 chunk 72 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 37 optimal weight: 0.0970 chunk 187 optimal weight: 5.9990 chunk 160 optimal weight: 0.7980 chunk 10 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 163 optimal weight: 5.9990 chunk 73 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN A2225 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.112534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.079483 restraints weight = 28042.627| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 1.90 r_work: 0.2712 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2577 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19110 Z= 0.137 Angle : 0.462 7.231 25960 Z= 0.249 Chirality : 0.040 0.202 2916 Planarity : 0.003 0.055 3146 Dihedral : 11.427 81.612 3008 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.99 % Allowed : 7.51 % Favored : 91.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.18), residues: 2168 helix: 1.89 (0.16), residues: 1110 sheet: -0.11 (0.39), residues: 190 loop : -0.89 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 12 TYR 0.015 0.001 TYR A 106 PHE 0.017 0.001 PHE A1768 TRP 0.013 0.001 TRP A1143 HIS 0.003 0.001 HIS A1855 Details of bonding type rmsd covalent geometry : bond 0.00320 (19106) covalent geometry : angle 0.46171 (25960) hydrogen bonds : bond 0.03860 ( 936) hydrogen bonds : angle 4.01295 ( 2682) metal coordination : bond 0.00354 ( 3) Misc. bond : bond 0.00006 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 197 time to evaluate : 0.691 Fit side-chains REVERT: A 365 MET cc_start: 0.8256 (tpp) cc_final: 0.7926 (ttp) REVERT: A 2005 ASP cc_start: 0.7920 (OUTLIER) cc_final: 0.7706 (t0) REVERT: A 2035 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7906 (mm-30) outliers start: 20 outliers final: 15 residues processed: 209 average time/residue: 0.1430 time to fit residues: 45.1993 Evaluate side-chains 200 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 184 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 819 ASN Chi-restraints excluded: chain A residue 1160 MET Chi-restraints excluded: chain A residue 1871 SER Chi-restraints excluded: chain A residue 1873 THR Chi-restraints excluded: chain A residue 1988 ASP Chi-restraints excluded: chain A residue 2002 VAL Chi-restraints excluded: chain A residue 2005 ASP Chi-restraints excluded: chain A residue 2054 ASN Chi-restraints excluded: chain A residue 2162 THR Chi-restraints excluded: chain A residue 2211 LEU Chi-restraints excluded: chain A residue 2214 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 142 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 181 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 128 optimal weight: 7.9990 chunk 54 optimal weight: 0.0060 chunk 89 optimal weight: 0.8980 chunk 217 optimal weight: 5.9990 chunk 111 optimal weight: 0.9980 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.113606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.080755 restraints weight = 27769.680| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 1.83 r_work: 0.2726 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2589 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 19110 Z= 0.105 Angle : 0.439 6.716 25960 Z= 0.238 Chirality : 0.039 0.184 2916 Planarity : 0.003 0.055 3146 Dihedral : 11.328 82.721 3008 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.09 % Allowed : 8.11 % Favored : 90.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.18), residues: 2168 helix: 1.95 (0.16), residues: 1119 sheet: -0.06 (0.38), residues: 195 loop : -0.81 (0.21), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1949 TYR 0.016 0.001 TYR A 106 PHE 0.014 0.001 PHE A1768 TRP 0.013 0.001 TRP A1143 HIS 0.003 0.001 HIS A1855 Details of bonding type rmsd covalent geometry : bond 0.00234 (19106) covalent geometry : angle 0.43937 (25960) hydrogen bonds : bond 0.03506 ( 936) hydrogen bonds : angle 3.92607 ( 2682) metal coordination : bond 0.00094 ( 3) Misc. bond : bond 0.00004 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 194 time to evaluate : 0.685 Fit side-chains REVERT: A 365 MET cc_start: 0.8268 (tpp) cc_final: 0.7918 (ttp) REVERT: A 2005 ASP cc_start: 0.7897 (OUTLIER) cc_final: 0.7684 (t0) outliers start: 22 outliers final: 17 residues processed: 207 average time/residue: 0.1413 time to fit residues: 44.3476 Evaluate side-chains 208 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 190 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 819 ASN Chi-restraints excluded: chain A residue 1160 MET Chi-restraints excluded: chain A residue 1873 THR Chi-restraints excluded: chain A residue 1988 ASP Chi-restraints excluded: chain A residue 2002 VAL Chi-restraints excluded: chain A residue 2005 ASP Chi-restraints excluded: chain A residue 2054 ASN Chi-restraints excluded: chain A residue 2162 THR Chi-restraints excluded: chain A residue 2211 LEU Chi-restraints excluded: chain A residue 2214 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 76 optimal weight: 2.9990 chunk 208 optimal weight: 10.0000 chunk 108 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 169 optimal weight: 0.9980 chunk 147 optimal weight: 1.9990 chunk 189 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 121 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.112992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.079938 restraints weight = 27365.955| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 1.86 r_work: 0.2722 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2584 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 19110 Z= 0.129 Angle : 0.451 7.096 25960 Z= 0.243 Chirality : 0.040 0.207 2916 Planarity : 0.003 0.056 3146 Dihedral : 11.298 83.323 3008 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.49 % Allowed : 8.20 % Favored : 90.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.18), residues: 2168 helix: 1.98 (0.16), residues: 1119 sheet: 0.01 (0.39), residues: 190 loop : -0.77 (0.21), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1949 TYR 0.017 0.001 TYR A 106 PHE 0.016 0.001 PHE A1768 TRP 0.014 0.001 TRP A2219 HIS 0.003 0.001 HIS A1855 Details of bonding type rmsd covalent geometry : bond 0.00299 (19106) covalent geometry : angle 0.45053 (25960) hydrogen bonds : bond 0.03685 ( 936) hydrogen bonds : angle 3.91120 ( 2682) metal coordination : bond 0.00184 ( 3) Misc. bond : bond 0.00001 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 192 time to evaluate : 0.459 Fit side-chains REVERT: A 2005 ASP cc_start: 0.7949 (OUTLIER) cc_final: 0.7740 (t0) REVERT: A 2037 MET cc_start: 0.9258 (OUTLIER) cc_final: 0.8757 (mtm) outliers start: 30 outliers final: 19 residues processed: 211 average time/residue: 0.1417 time to fit residues: 45.0983 Evaluate side-chains 206 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 185 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 732 PHE Chi-restraints excluded: chain A residue 819 ASN Chi-restraints excluded: chain A residue 1160 MET Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1238 PHE Chi-restraints excluded: chain A residue 1871 SER Chi-restraints excluded: chain A residue 1873 THR Chi-restraints excluded: chain A residue 1988 ASP Chi-restraints excluded: chain A residue 2002 VAL Chi-restraints excluded: chain A residue 2005 ASP Chi-restraints excluded: chain A residue 2037 MET Chi-restraints excluded: chain A residue 2054 ASN Chi-restraints excluded: chain A residue 2162 THR Chi-restraints excluded: chain A residue 2211 LEU Chi-restraints excluded: chain A residue 2214 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 188 optimal weight: 0.7980 chunk 175 optimal weight: 0.7980 chunk 173 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 178 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 190 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 182 optimal weight: 1.9990 chunk 201 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN A2225 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.113041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.079789 restraints weight = 27593.776| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 1.83 r_work: 0.2705 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2563 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19110 Z= 0.130 Angle : 0.452 7.057 25960 Z= 0.244 Chirality : 0.040 0.199 2916 Planarity : 0.003 0.056 3146 Dihedral : 11.280 83.488 3008 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.29 % Allowed : 8.40 % Favored : 90.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.18), residues: 2168 helix: 2.04 (0.16), residues: 1113 sheet: 0.03 (0.40), residues: 185 loop : -0.77 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1949 TYR 0.014 0.001 TYR A1576 PHE 0.018 0.001 PHE A1613 TRP 0.014 0.001 TRP A2219 HIS 0.003 0.001 HIS A1855 Details of bonding type rmsd covalent geometry : bond 0.00303 (19106) covalent geometry : angle 0.45169 (25960) hydrogen bonds : bond 0.03648 ( 936) hydrogen bonds : angle 3.90480 ( 2682) metal coordination : bond 0.00203 ( 3) Misc. bond : bond 0.00002 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 190 time to evaluate : 0.793 Fit side-chains REVERT: A 87 VAL cc_start: 0.7462 (OUTLIER) cc_final: 0.7261 (p) REVERT: A 365 MET cc_start: 0.8318 (tpp) cc_final: 0.7985 (tmm) REVERT: A 2005 ASP cc_start: 0.7957 (OUTLIER) cc_final: 0.7743 (t0) REVERT: A 2035 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7767 (mm-30) REVERT: A 2037 MET cc_start: 0.9156 (OUTLIER) cc_final: 0.8591 (mtm) outliers start: 26 outliers final: 20 residues processed: 206 average time/residue: 0.1455 time to fit residues: 45.6640 Evaluate side-chains 207 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 184 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 732 PHE Chi-restraints excluded: chain A residue 819 ASN Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 1160 MET Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1238 PHE Chi-restraints excluded: chain A residue 1871 SER Chi-restraints excluded: chain A residue 1873 THR Chi-restraints excluded: chain A residue 1988 ASP Chi-restraints excluded: chain A residue 2002 VAL Chi-restraints excluded: chain A residue 2005 ASP Chi-restraints excluded: chain A residue 2037 MET Chi-restraints excluded: chain A residue 2054 ASN Chi-restraints excluded: chain A residue 2162 THR Chi-restraints excluded: chain A residue 2211 LEU Chi-restraints excluded: chain A residue 2214 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 166 optimal weight: 1.9990 chunk 185 optimal weight: 0.0770 chunk 5 optimal weight: 9.9990 chunk 146 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 188 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.7142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.113996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.081590 restraints weight = 27650.040| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 1.79 r_work: 0.2742 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2603 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 19110 Z= 0.104 Angle : 0.437 6.899 25960 Z= 0.236 Chirality : 0.039 0.191 2916 Planarity : 0.003 0.056 3146 Dihedral : 11.219 83.611 3008 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.19 % Allowed : 9.10 % Favored : 89.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.18), residues: 2168 helix: 2.12 (0.16), residues: 1109 sheet: 0.08 (0.40), residues: 185 loop : -0.70 (0.21), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1949 TYR 0.014 0.001 TYR A 106 PHE 0.027 0.001 PHE A1613 TRP 0.013 0.001 TRP A1143 HIS 0.002 0.001 HIS A1855 Details of bonding type rmsd covalent geometry : bond 0.00233 (19106) covalent geometry : angle 0.43650 (25960) hydrogen bonds : bond 0.03387 ( 936) hydrogen bonds : angle 3.84818 ( 2682) metal coordination : bond 0.00214 ( 3) Misc. bond : bond 0.00009 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 196 time to evaluate : 0.572 Fit side-chains REVERT: A 365 MET cc_start: 0.8290 (tpp) cc_final: 0.7968 (tmm) REVERT: A 2005 ASP cc_start: 0.7932 (OUTLIER) cc_final: 0.7725 (t0) REVERT: A 2035 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7803 (mm-30) REVERT: A 2037 MET cc_start: 0.9133 (OUTLIER) cc_final: 0.8590 (mtm) outliers start: 24 outliers final: 20 residues processed: 210 average time/residue: 0.1331 time to fit residues: 42.4386 Evaluate side-chains 208 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 186 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 732 PHE Chi-restraints excluded: chain A residue 819 ASN Chi-restraints excluded: chain A residue 1160 MET Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1238 PHE Chi-restraints excluded: chain A residue 1871 SER Chi-restraints excluded: chain A residue 1873 THR Chi-restraints excluded: chain A residue 1988 ASP Chi-restraints excluded: chain A residue 2002 VAL Chi-restraints excluded: chain A residue 2005 ASP Chi-restraints excluded: chain A residue 2037 MET Chi-restraints excluded: chain A residue 2054 ASN Chi-restraints excluded: chain A residue 2162 THR Chi-restraints excluded: chain A residue 2211 LEU Chi-restraints excluded: chain A residue 2214 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 198 optimal weight: 7.9990 chunk 215 optimal weight: 4.9990 chunk 206 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 29 optimal weight: 0.0980 chunk 37 optimal weight: 0.0040 chunk 127 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 189 optimal weight: 0.0670 chunk 59 optimal weight: 0.4980 chunk 49 optimal weight: 2.9990 overall best weight: 0.3130 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN A 622 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.115920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.083500 restraints weight = 27847.263| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 1.82 r_work: 0.2780 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 19110 Z= 0.085 Angle : 0.423 6.838 25960 Z= 0.228 Chirality : 0.038 0.183 2916 Planarity : 0.003 0.055 3146 Dihedral : 11.058 83.562 3008 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.29 % Allowed : 9.20 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.19), residues: 2168 helix: 2.21 (0.16), residues: 1114 sheet: 0.23 (0.40), residues: 184 loop : -0.62 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1949 TYR 0.013 0.001 TYR A 106 PHE 0.022 0.001 PHE A1613 TRP 0.015 0.001 TRP A1143 HIS 0.002 0.000 HIS A 801 Details of bonding type rmsd covalent geometry : bond 0.00181 (19106) covalent geometry : angle 0.42252 (25960) hydrogen bonds : bond 0.02888 ( 936) hydrogen bonds : angle 3.72739 ( 2682) metal coordination : bond 0.00277 ( 3) Misc. bond : bond 0.00006 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 204 time to evaluate : 0.746 Fit side-chains REVERT: A 365 MET cc_start: 0.8322 (tpp) cc_final: 0.7960 (tmm) REVERT: A 1768 PHE cc_start: 0.8383 (m-80) cc_final: 0.8162 (m-80) REVERT: A 2005 ASP cc_start: 0.7913 (OUTLIER) cc_final: 0.7706 (t0) REVERT: A 2035 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7844 (mm-30) outliers start: 26 outliers final: 19 residues processed: 220 average time/residue: 0.1439 time to fit residues: 47.9310 Evaluate side-chains 208 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 188 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 732 PHE Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 1160 MET Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1238 PHE Chi-restraints excluded: chain A residue 1873 THR Chi-restraints excluded: chain A residue 1988 ASP Chi-restraints excluded: chain A residue 2002 VAL Chi-restraints excluded: chain A residue 2005 ASP Chi-restraints excluded: chain A residue 2054 ASN Chi-restraints excluded: chain A residue 2211 LEU Chi-restraints excluded: chain A residue 2214 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 129 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 213 optimal weight: 6.9990 chunk 149 optimal weight: 9.9990 chunk 151 optimal weight: 0.5980 chunk 186 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 107 optimal weight: 0.1980 chunk 65 optimal weight: 0.8980 chunk 212 optimal weight: 0.9980 chunk 178 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN A 752 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.114018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.081158 restraints weight = 27787.914| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 1.85 r_work: 0.2737 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2601 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19110 Z= 0.118 Angle : 0.443 7.089 25960 Z= 0.239 Chirality : 0.039 0.203 2916 Planarity : 0.003 0.056 3146 Dihedral : 11.093 83.306 3007 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.19 % Allowed : 9.90 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.19), residues: 2168 helix: 2.21 (0.16), residues: 1109 sheet: 0.21 (0.40), residues: 188 loop : -0.66 (0.21), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1949 TYR 0.014 0.001 TYR A 106 PHE 0.030 0.001 PHE A1613 TRP 0.011 0.001 TRP A2219 HIS 0.003 0.001 HIS A1954 Details of bonding type rmsd covalent geometry : bond 0.00270 (19106) covalent geometry : angle 0.44304 (25960) hydrogen bonds : bond 0.03387 ( 936) hydrogen bonds : angle 3.79657 ( 2682) metal coordination : bond 0.00167 ( 3) Misc. bond : bond 0.00009 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 186 time to evaluate : 0.717 Fit side-chains REVERT: A 365 MET cc_start: 0.8291 (tpp) cc_final: 0.7958 (tmm) REVERT: A 2035 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7836 (mm-30) REVERT: A 2037 MET cc_start: 0.9349 (OUTLIER) cc_final: 0.8815 (mtm) outliers start: 24 outliers final: 20 residues processed: 201 average time/residue: 0.1418 time to fit residues: 43.6935 Evaluate side-chains 205 residues out of total 2011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 184 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 732 PHE Chi-restraints excluded: chain A residue 819 ASN Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 1160 MET Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1238 PHE Chi-restraints excluded: chain A residue 1873 THR Chi-restraints excluded: chain A residue 1988 ASP Chi-restraints excluded: chain A residue 2002 VAL Chi-restraints excluded: chain A residue 2037 MET Chi-restraints excluded: chain A residue 2054 ASN Chi-restraints excluded: chain A residue 2211 LEU Chi-restraints excluded: chain A residue 2214 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 50 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 179 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 158 optimal weight: 5.9990 chunk 95 optimal weight: 0.6980 chunk 151 optimal weight: 1.9990 chunk 191 optimal weight: 0.0770 chunk 67 optimal weight: 1.9990 chunk 195 optimal weight: 6.9990 chunk 177 optimal weight: 0.0970 overall best weight: 0.7738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN A 752 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.114284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.081417 restraints weight = 27938.751| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 1.85 r_work: 0.2748 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2613 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 19110 Z= 0.107 Angle : 0.436 6.748 25960 Z= 0.235 Chirality : 0.039 0.182 2916 Planarity : 0.003 0.056 3146 Dihedral : 11.084 83.370 3007 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.04 % Allowed : 9.90 % Favored : 89.06 % 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 are not related in a simple way. whole: 1.39 (0.19), residues: 2168 helix: 2.20 (0.16), residues: 1114 sheet: 0.21 (0.40), residues: 188 loop : -0.64 (0.21), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1949 TYR 0.013 0.001 TYR A 106 PHE 0.027 0.001 PHE A1613 TRP 0.012 0.001 TRP A1143 HIS 0.002 0.001 HIS A1855 Details of bonding type rmsd covalent geometry : bond 0.00243 (19106) covalent geometry : angle 0.43550 (25960) hydrogen bonds : bond 0.03278 ( 936) hydrogen bonds : angle 3.78673 ( 2682) metal coordination : bond 0.00286 ( 3) Misc. bond : bond 0.00009 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4866.14 seconds wall clock time: 85 minutes 18.71 seconds (5118.71 seconds total)