Starting phenix.real_space_refine on Fri Mar 6 05:02:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7el9_31177/03_2026/7el9_31177.cif Found real_map, /net/cci-nas-00/data/ceres_data/7el9_31177/03_2026/7el9_31177.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7el9_31177/03_2026/7el9_31177.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7el9_31177/03_2026/7el9_31177.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7el9_31177/03_2026/7el9_31177.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7el9_31177/03_2026/7el9_31177.map" } resolution = 3.2 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= 0.004 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 Mn 2 7.51 5 Zn 8 6.06 5 P 14 5.49 5 S 182 5.16 5 C 17856 2.51 5 N 4736 2.21 5 O 5330 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 290 residue(s): 0.04s 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: 28128 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 13503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1731, 13503 Classifications: {'peptide': 1731} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 46, 'TRANS': 1684} Chain breaks: 16 Unresolved non-hydrogen bonds: 312 Unresolved non-hydrogen angles: 384 Unresolved non-hydrogen dihedrals: 272 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 10, 'HIS:plan': 2, 'GLU:plan': 12, 'GLN:plan1': 8, 'TRP:plan': 1, 'ASP:plan': 3, 'TYR:plan': 3, 'PHE:plan': 6, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 219 Chain: "B" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "C" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 149 Classifications: {'RNA': 7} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 3, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 4} Chain: "D" Number of atoms: 13503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1731, 13503 Classifications: {'peptide': 1731} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 46, 'TRANS': 1684} Chain breaks: 16 Unresolved non-hydrogen bonds: 312 Unresolved non-hydrogen angles: 384 Unresolved non-hydrogen dihedrals: 272 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 10, 'HIS:plan': 2, 'GLU:plan': 12, 'GLN:plan1': 8, 'TRP:plan': 1, 'ASP:plan': 3, 'TYR:plan': 3, 'PHE:plan': 6, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 219 Chain: "E" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "F" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 149 Classifications: {'RNA': 7} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 3, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 4} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MN': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MN': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1875 SG CYS A 284 35.729 33.354 67.843 1.00 61.94 S ATOM 1899 SG CYS A 287 34.333 31.102 64.822 1.00 59.21 S ATOM 3239 SG CYS A 470 33.068 30.588 68.474 1.00 73.81 S ATOM 9797 SG CYS A1650 89.122 41.313 75.762 1.00 91.26 S ATOM 9810 SG CYS A1652 89.365 41.871 79.157 1.00 89.97 S ATOM 9829 SG CYS A1655 86.187 43.199 75.829 1.00 72.73 S ATOM 9901 SG CYS A1664 88.952 44.493 77.184 1.00 68.67 S ATOM 13564 SG CYS B 39 30.423 64.423 92.321 1.00 81.52 S ATOM 13585 SG CYS B 42 28.292 63.007 89.412 1.00 71.41 S ATOM 13719 SG CYS B 58 27.710 63.091 93.927 1.00 94.45 S ATOM 13744 SG CYS B 61 29.997 60.964 92.428 1.00 99.69 S ATOM 13667 SG CYS B 52 38.069 66.220 98.466 1.00104.91 S ATOM 13834 SG CYS B 72 38.709 63.943 96.025 1.00 92.56 S ATOM 13858 SG CYS B 75 40.828 66.570 96.387 1.00 88.59 S ATOM 15934 SG CYS D 284 140.290 134.640 67.846 1.00 61.74 S ATOM 15958 SG CYS D 287 141.685 136.893 64.826 1.00 59.06 S ATOM 17298 SG CYS D 470 142.950 137.407 68.478 1.00 74.13 S ATOM 23856 SG CYS D1650 86.899 126.658 75.757 1.00 90.95 S ATOM 23869 SG CYS D1652 86.656 126.099 79.151 1.00 90.00 S ATOM 23888 SG CYS D1655 89.835 124.773 75.823 1.00 72.84 S ATOM 23960 SG CYS D1664 87.070 123.478 77.178 1.00 68.06 S ATOM 27623 SG CYS E 39 145.605 103.565 92.315 1.00 81.76 S ATOM 27644 SG CYS E 42 147.736 104.983 89.406 1.00 71.52 S ATOM 27778 SG CYS E 58 148.317 104.897 93.921 1.00 95.83 S ATOM 27803 SG CYS E 61 146.030 107.024 92.423 1.00 99.71 S ATOM 27726 SG CYS E 52 137.959 101.763 98.458 1.00105.38 S ATOM 27893 SG CYS E 72 137.318 104.041 96.018 1.00 92.74 S ATOM 27917 SG CYS E 75 135.200 101.413 96.379 1.00 88.75 S Time building chain proxies: 6.27, per 1000 atoms: 0.22 Number of scatterers: 28128 At special positions: 0 Unit cell: (177, 169, 134, 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 8 29.99 Mn 2 24.99 S 182 16.00 P 14 15.00 O 5330 8.00 N 4736 7.00 C 17856 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 60 " distance=2.03 Simple disulfide: pdb=" SG CYS A1691 " - pdb=" SG CYS A1776 " distance=2.03 Simple disulfide: pdb=" SG CYS D 55 " - pdb=" SG CYS D 60 " distance=2.03 Simple disulfide: pdb=" SG CYS D1691 " - pdb=" SG CYS D1776 " distance=2.03 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: 2.54 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2302 " pdb="ZN ZN A2302 " - pdb=" ND1 HIS A 472 " pdb="ZN ZN A2302 " - pdb=" SG CYS A 284 " pdb="ZN ZN A2302 " - pdb=" SG CYS A 287 " pdb="ZN ZN A2302 " - pdb=" SG CYS A 470 " pdb=" ZN A2303 " pdb="ZN ZN A2303 " - pdb=" SG CYS A1650 " pdb="ZN ZN A2303 " - pdb=" SG CYS A1664 " pdb="ZN ZN A2303 " - pdb=" SG CYS A1652 " pdb="ZN ZN A2303 " - pdb=" SG CYS A1655 " pdb=" ZN B 101 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 61 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 58 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 39 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 42 " pdb=" ZN B 102 " pdb="ZN ZN B 102 " - pdb=" NE2 HIS B 55 " pdb="ZN ZN B 102 " - pdb=" SG CYS B 75 " pdb="ZN ZN B 102 " - pdb=" SG CYS B 72 " pdb="ZN ZN B 102 " - pdb=" SG CYS B 52 " pdb=" ZN D2302 " pdb="ZN ZN D2302 " - pdb=" ND1 HIS D 472 " pdb="ZN ZN D2302 " - pdb=" SG CYS D 284 " pdb="ZN ZN D2302 " - pdb=" SG CYS D 287 " pdb="ZN ZN D2302 " - pdb=" SG CYS D 470 " pdb=" ZN D2303 " pdb="ZN ZN D2303 " - pdb=" SG CYS D1650 " pdb="ZN ZN D2303 " - pdb=" SG CYS D1664 " pdb="ZN ZN D2303 " - pdb=" SG CYS D1652 " pdb="ZN ZN D2303 " - pdb=" SG CYS D1655 " pdb=" ZN E 101 " pdb="ZN ZN E 101 " - pdb=" SG CYS E 61 " pdb="ZN ZN E 101 " - pdb=" SG CYS E 58 " pdb="ZN ZN E 101 " - pdb=" SG CYS E 39 " pdb="ZN ZN E 101 " - pdb=" SG CYS E 42 " pdb=" ZN E 102 " pdb="ZN ZN E 102 " - pdb=" NE2 HIS E 55 " pdb="ZN ZN E 102 " - pdb=" SG CYS E 75 " pdb="ZN ZN E 102 " - pdb=" SG CYS E 72 " pdb="ZN ZN E 102 " - pdb=" SG CYS E 52 " Number of angles added : 36 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6744 Finding SS restraints... Secondary structure from input PDB file: 148 helices and 24 sheets defined 49.7% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'A' and resid 7 through 12 Processing helix chain 'A' and resid 22 through 31 Processing helix chain 'A' and resid 37 through 56 Processing helix chain 'A' and resid 57 through 59 No H-bonds generated for 'chain 'A' and resid 57 through 59' Processing helix chain 'A' and resid 108 through 131 removed outlier: 4.472A pdb=" N LEU A 126 " --> pdb=" O LYS A 122 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS A 127 " --> pdb=" O LEU A 123 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N HIS A 128 " --> pdb=" O LEU A 124 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ASP A 129 " --> pdb=" O ASN A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 171 removed outlier: 3.823A pdb=" N ARG A 161 " --> pdb=" O ILE A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 190 removed outlier: 4.135A pdb=" N ILE A 188 " --> pdb=" O TYR A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 221 Processing helix chain 'A' and resid 231 through 250 removed outlier: 3.753A pdb=" N VAL A 235 " --> pdb=" O ARG A 231 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 274 Processing helix chain 'A' and resid 284 through 289 Processing helix chain 'A' and resid 289 through 303 Processing helix chain 'A' and resid 322 through 337 Processing helix chain 'A' and resid 345 through 366 removed outlier: 3.768A pdb=" N ASP A 366 " --> pdb=" O VAL A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 405 Processing helix chain 'A' and resid 412 through 423 removed outlier: 4.007A pdb=" N ASN A 416 " --> pdb=" O ASN A 412 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU A 421 " --> pdb=" O CYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 451 Processing helix chain 'A' and resid 474 through 478 Processing helix chain 'A' and resid 479 through 502 removed outlier: 3.668A pdb=" N GLN A 483 " --> pdb=" O SER A 479 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N MET A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 578 removed outlier: 3.504A pdb=" N ARG A 577 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 598 Processing helix chain 'A' and resid 604 through 623 Proline residue: A 611 - end of helix Processing helix chain 'A' and resid 625 through 644 removed outlier: 3.564A pdb=" N ASN A 644 " --> pdb=" O MET A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 656 removed outlier: 3.872A pdb=" N VAL A 656 " --> pdb=" O THR A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 680 removed outlier: 3.912A pdb=" N VAL A 667 " --> pdb=" O SER A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 702 Processing helix chain 'A' and resid 703 through 706 Processing helix chain 'A' and resid 712 through 732 Proline residue: A 727 - end of helix Processing helix chain 'A' and resid 745 through 760 Processing helix chain 'A' and resid 776 through 789 Processing helix chain 'A' and resid 1135 through 1156 Processing helix chain 'A' and resid 1163 through 1181 Processing helix chain 'A' and resid 1191 through 1196 Processing helix chain 'A' and resid 1197 through 1207 removed outlier: 4.344A pdb=" N MET A1207 " --> pdb=" O ALA A1203 " (cutoff:3.500A) Processing helix chain 'A' and resid 1221 through 1233 Processing helix chain 'A' and resid 1239 through 1248 removed outlier: 3.542A pdb=" N ILE A1248 " --> pdb=" O GLU A1244 " (cutoff:3.500A) Processing helix chain 'A' and resid 1264 through 1276 removed outlier: 4.562A pdb=" N GLN A1275 " --> pdb=" O HIS A1271 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU A1276 " --> pdb=" O GLN A1272 " (cutoff:3.500A) Processing helix chain 'A' and resid 1295 through 1319 Processing helix chain 'A' and resid 1351 through 1365 Processing helix chain 'A' and resid 1395 through 1405 Processing helix chain 'A' and resid 1411 through 1429 removed outlier: 3.563A pdb=" N ASN A1429 " --> pdb=" O GLN A1425 " (cutoff:3.500A) Processing helix chain 'A' and resid 1433 through 1450 removed outlier: 3.699A pdb=" N THR A1437 " --> pdb=" O THR A1433 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG A1438 " --> pdb=" O LYS A1434 " (cutoff:3.500A) Processing helix chain 'A' and resid 1464 through 1468 Processing helix chain 'A' and resid 1472 through 1485 Processing helix chain 'A' and resid 1490 through 1507 Processing helix chain 'A' and resid 1513 through 1520 Processing helix chain 'A' and resid 1523 through 1534 removed outlier: 3.508A pdb=" N TYR A1533 " --> pdb=" O GLY A1529 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA A1534 " --> pdb=" O PHE A1530 " (cutoff:3.500A) Processing helix chain 'A' and resid 1539 through 1545 Processing helix chain 'A' and resid 1579 through 1590 removed outlier: 3.625A pdb=" N LYS A1583 " --> pdb=" O PRO A1579 " (cutoff:3.500A) Processing helix chain 'A' and resid 1613 through 1625 Processing helix chain 'A' and resid 1639 through 1645 Processing helix chain 'A' and resid 1665 through 1669 removed outlier: 3.683A pdb=" N LEU A1668 " --> pdb=" O ASN A1665 " (cutoff:3.500A) Processing helix chain 'A' and resid 1678 through 1694 removed outlier: 3.517A pdb=" N GLY A1694 " --> pdb=" O ALA A1690 " (cutoff:3.500A) Processing helix chain 'A' and resid 1695 through 1698 Processing helix chain 'A' and resid 1732 through 1744 Processing helix chain 'A' and resid 1744 through 1750 removed outlier: 3.548A pdb=" N GLU A1750 " --> pdb=" O VAL A1746 " (cutoff:3.500A) Processing helix chain 'A' and resid 1758 through 1764 removed outlier: 3.662A pdb=" N SER A1762 " --> pdb=" O ASP A1758 " (cutoff:3.500A) Processing helix chain 'A' and resid 1774 through 1783 removed outlier: 4.220A pdb=" N ASP A1780 " --> pdb=" O CYS A1776 " (cutoff:3.500A) Processing helix chain 'A' and resid 1788 through 1793 Processing helix chain 'A' and resid 1805 through 1809 Processing helix chain 'A' and resid 1826 through 1843 removed outlier: 3.669A pdb=" N ILE A1830 " --> pdb=" O SER A1826 " (cutoff:3.500A) Processing helix chain 'A' and resid 1851 through 1856 Processing helix chain 'A' and resid 1860 through 1864 removed outlier: 4.168A pdb=" N VAL A1863 " --> pdb=" O PHE A1860 " (cutoff:3.500A) Processing helix chain 'A' and resid 1875 through 1884 Processing helix chain 'A' and resid 1919 through 1924 removed outlier: 4.384A pdb=" N LEU A1924 " --> pdb=" O ASP A1920 " (cutoff:3.500A) Processing helix chain 'A' and resid 1933 through 1940 Processing helix chain 'A' and resid 2003 through 2015 Processing helix chain 'A' and resid 2031 through 2037 Processing helix chain 'A' and resid 2101 through 2110 removed outlier: 3.788A pdb=" N ALA A2110 " --> pdb=" O LYS A2106 " (cutoff:3.500A) Processing helix chain 'A' and resid 2113 through 2123 removed outlier: 3.590A pdb=" N VAL A2117 " --> pdb=" O ASP A2113 " (cutoff:3.500A) Processing helix chain 'A' and resid 2123 through 2129 removed outlier: 3.603A pdb=" N TYR A2127 " --> pdb=" O GLN A2123 " (cutoff:3.500A) Processing helix chain 'A' and resid 2139 through 2146 Processing helix chain 'A' and resid 2150 through 2155 Processing helix chain 'B' and resid 58 through 69 removed outlier: 3.723A pdb=" N ASN B 68 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER B 69 " --> pdb=" O MET B 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 12 Processing helix chain 'D' and resid 22 through 31 Processing helix chain 'D' and resid 37 through 56 Processing helix chain 'D' and resid 57 through 59 No H-bonds generated for 'chain 'D' and resid 57 through 59' Processing helix chain 'D' and resid 108 through 131 removed outlier: 4.473A pdb=" N LEU D 126 " --> pdb=" O LYS D 122 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS D 127 " --> pdb=" O LEU D 123 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N HIS D 128 " --> pdb=" O LEU D 124 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ASP D 129 " --> pdb=" O ASN D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 171 removed outlier: 3.823A pdb=" N ARG D 161 " --> pdb=" O ILE D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 190 removed outlier: 4.135A pdb=" N ILE D 188 " --> pdb=" O TYR D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 221 Processing helix chain 'D' and resid 231 through 250 removed outlier: 3.753A pdb=" N VAL D 235 " --> pdb=" O ARG D 231 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP D 248 " --> pdb=" O LEU D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 274 Processing helix chain 'D' and resid 284 through 289 Processing helix chain 'D' and resid 289 through 303 Processing helix chain 'D' and resid 322 through 337 Processing helix chain 'D' and resid 345 through 366 removed outlier: 3.769A pdb=" N ASP D 366 " --> pdb=" O VAL D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 405 Processing helix chain 'D' and resid 412 through 423 removed outlier: 4.006A pdb=" N ASN D 416 " --> pdb=" O ASN D 412 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU D 421 " --> pdb=" O CYS D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 440 through 451 Processing helix chain 'D' and resid 474 through 478 Processing helix chain 'D' and resid 479 through 502 removed outlier: 3.668A pdb=" N GLN D 483 " --> pdb=" O SER D 479 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N MET D 484 " --> pdb=" O SER D 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 578 removed outlier: 3.504A pdb=" N ARG D 577 " --> pdb=" O ASP D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 598 Processing helix chain 'D' and resid 604 through 623 Proline residue: D 611 - end of helix Processing helix chain 'D' and resid 625 through 644 removed outlier: 3.564A pdb=" N ASN D 644 " --> pdb=" O MET D 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 651 through 656 removed outlier: 3.872A pdb=" N VAL D 656 " --> pdb=" O THR D 652 " (cutoff:3.500A) Processing helix chain 'D' and resid 661 through 680 removed outlier: 3.911A pdb=" N VAL D 667 " --> pdb=" O SER D 663 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 702 Processing helix chain 'D' and resid 703 through 706 Processing helix chain 'D' and resid 712 through 732 Proline residue: D 727 - end of helix Processing helix chain 'D' and resid 745 through 760 Processing helix chain 'D' and resid 776 through 789 Processing helix chain 'D' and resid 1135 through 1156 Processing helix chain 'D' and resid 1163 through 1181 Processing helix chain 'D' and resid 1191 through 1196 Processing helix chain 'D' and resid 1197 through 1207 removed outlier: 4.344A pdb=" N MET D1207 " --> pdb=" O ALA D1203 " (cutoff:3.500A) Processing helix chain 'D' and resid 1221 through 1233 Processing helix chain 'D' and resid 1239 through 1248 removed outlier: 3.542A pdb=" N ILE D1248 " --> pdb=" O GLU D1244 " (cutoff:3.500A) Processing helix chain 'D' and resid 1264 through 1276 removed outlier: 4.562A pdb=" N GLN D1275 " --> pdb=" O HIS D1271 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU D1276 " --> pdb=" O GLN D1272 " (cutoff:3.500A) Processing helix chain 'D' and resid 1295 through 1319 Processing helix chain 'D' and resid 1351 through 1365 Processing helix chain 'D' and resid 1395 through 1405 Processing helix chain 'D' and resid 1411 through 1429 removed outlier: 3.563A pdb=" N ASN D1429 " --> pdb=" O GLN D1425 " (cutoff:3.500A) Processing helix chain 'D' and resid 1433 through 1450 removed outlier: 3.699A pdb=" N THR D1437 " --> pdb=" O THR D1433 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG D1438 " --> pdb=" O LYS D1434 " (cutoff:3.500A) Processing helix chain 'D' and resid 1464 through 1468 Processing helix chain 'D' and resid 1472 through 1485 Processing helix chain 'D' and resid 1490 through 1507 Processing helix chain 'D' and resid 1513 through 1520 Processing helix chain 'D' and resid 1523 through 1534 removed outlier: 3.508A pdb=" N TYR D1533 " --> pdb=" O GLY D1529 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA D1534 " --> pdb=" O PHE D1530 " (cutoff:3.500A) Processing helix chain 'D' and resid 1539 through 1545 Processing helix chain 'D' and resid 1579 through 1590 removed outlier: 3.625A pdb=" N LYS D1583 " --> pdb=" O PRO D1579 " (cutoff:3.500A) Processing helix chain 'D' and resid 1613 through 1625 Processing helix chain 'D' and resid 1639 through 1645 Processing helix chain 'D' and resid 1665 through 1669 removed outlier: 3.684A pdb=" N LEU D1668 " --> pdb=" O ASN D1665 " (cutoff:3.500A) Processing helix chain 'D' and resid 1678 through 1694 removed outlier: 3.516A pdb=" N GLY D1694 " --> pdb=" O ALA D1690 " (cutoff:3.500A) Processing helix chain 'D' and resid 1695 through 1698 Processing helix chain 'D' and resid 1732 through 1744 Processing helix chain 'D' and resid 1744 through 1750 removed outlier: 3.548A pdb=" N GLU D1750 " --> pdb=" O VAL D1746 " (cutoff:3.500A) Processing helix chain 'D' and resid 1758 through 1764 removed outlier: 3.662A pdb=" N SER D1762 " --> pdb=" O ASP D1758 " (cutoff:3.500A) Processing helix chain 'D' and resid 1774 through 1783 removed outlier: 4.221A pdb=" N ASP D1780 " --> pdb=" O CYS D1776 " (cutoff:3.500A) Processing helix chain 'D' and resid 1788 through 1793 Processing helix chain 'D' and resid 1805 through 1809 Processing helix chain 'D' and resid 1826 through 1843 removed outlier: 3.669A pdb=" N ILE D1830 " --> pdb=" O SER D1826 " (cutoff:3.500A) Processing helix chain 'D' and resid 1851 through 1856 Processing helix chain 'D' and resid 1860 through 1864 removed outlier: 4.168A pdb=" N VAL D1863 " --> pdb=" O PHE D1860 " (cutoff:3.500A) Processing helix chain 'D' and resid 1875 through 1884 Processing helix chain 'D' and resid 1919 through 1924 removed outlier: 4.384A pdb=" N LEU D1924 " --> pdb=" O ASP D1920 " (cutoff:3.500A) Processing helix chain 'D' and resid 1933 through 1940 Processing helix chain 'D' and resid 2003 through 2015 Processing helix chain 'D' and resid 2031 through 2037 Processing helix chain 'D' and resid 2101 through 2110 removed outlier: 3.788A pdb=" N ALA D2110 " --> pdb=" O LYS D2106 " (cutoff:3.500A) Processing helix chain 'D' and resid 2113 through 2123 removed outlier: 3.590A pdb=" N VAL D2117 " --> pdb=" O ASP D2113 " (cutoff:3.500A) Processing helix chain 'D' and resid 2123 through 2129 removed outlier: 3.603A pdb=" N TYR D2127 " --> pdb=" O GLN D2123 " (cutoff:3.500A) Processing helix chain 'D' and resid 2139 through 2146 Processing helix chain 'D' and resid 2150 through 2155 Processing helix chain 'E' and resid 58 through 69 removed outlier: 3.724A pdb=" N ASN E 68 " --> pdb=" O THR E 64 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER E 69 " --> pdb=" O MET E 65 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 94 removed outlier: 3.580A pdb=" N THR A 97 " --> pdb=" O THR A 94 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LEU A 98 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ILE A 140 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N LEU A 100 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ASP A 142 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLU A 102 " --> pdb=" O ASP A 142 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ARG A 144 " --> pdb=" O GLU A 102 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N PHE A 104 " --> pdb=" O ARG A 144 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 258 through 260 Processing sheet with id=AA3, first strand: chain 'A' and resid 385 through 387 removed outlier: 3.861A pdb=" N CYS A 528 " --> pdb=" O VAL A 393 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LEU A 559 " --> pdb=" O GLU A 567 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N GLU A 567 " --> pdb=" O LEU A 559 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 735 through 736 removed outlier: 7.098A pdb=" N PHE A1117 " --> pdb=" O GLU A1237 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1379 through 1382 Processing sheet with id=AA6, first strand: chain 'A' and resid 1548 through 1549 Processing sheet with id=AA7, first strand: chain 'A' and resid 1630 through 1631 Processing sheet with id=AA8, first strand: chain 'A' and resid 1716 through 1719 Processing sheet with id=AA9, first strand: chain 'A' and resid 1847 through 1848 removed outlier: 6.674A pdb=" N PHE A2085 " --> pdb=" O LEU A2092 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1952 through 1961 removed outlier: 7.121A pdb=" N GLY A1980 " --> pdb=" O VAL A1992 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1952 through 1961 Processing sheet with id=AB3, first strand: chain 'B' and resid 50 through 51 Processing sheet with id=AB4, first strand: chain 'D' and resid 90 through 94 removed outlier: 3.580A pdb=" N THR D 97 " --> pdb=" O THR D 94 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N LEU D 98 " --> pdb=" O VAL D 138 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N ILE D 140 " --> pdb=" O LEU D 98 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N LEU D 100 " --> pdb=" O ILE D 140 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N ASP D 142 " --> pdb=" O LEU D 100 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLU D 102 " --> pdb=" O ASP D 142 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ARG D 144 " --> pdb=" O GLU D 102 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N PHE D 104 " --> pdb=" O ARG D 144 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 258 through 260 Processing sheet with id=AB6, first strand: chain 'D' and resid 385 through 387 removed outlier: 3.862A pdb=" N CYS D 528 " --> pdb=" O VAL D 393 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LEU D 559 " --> pdb=" O GLU D 567 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N GLU D 567 " --> pdb=" O LEU D 559 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 735 through 736 removed outlier: 7.098A pdb=" N PHE D1117 " --> pdb=" O GLU D1237 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 1379 through 1382 Processing sheet with id=AB9, first strand: chain 'D' and resid 1548 through 1549 Processing sheet with id=AC1, first strand: chain 'D' and resid 1630 through 1631 Processing sheet with id=AC2, first strand: chain 'D' and resid 1716 through 1719 Processing sheet with id=AC3, first strand: chain 'D' and resid 1847 through 1848 removed outlier: 6.675A pdb=" N PHE D2085 " --> pdb=" O LEU D2092 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 1952 through 1961 removed outlier: 7.121A pdb=" N GLY D1980 " --> pdb=" O VAL D1992 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 1952 through 1961 Processing sheet with id=AC6, first strand: chain 'E' and resid 50 through 51 1312 hydrogen bonds defined for protein. 3768 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.97 Time building geometry restraints manager: 3.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8991 1.34 - 1.46: 3928 1.46 - 1.57: 15423 1.57 - 1.69: 26 1.69 - 1.81: 262 Bond restraints: 28630 Sorted by residual: bond pdb=" N ARG D1509 " pdb=" CA ARG D1509 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.29e-02 6.01e+03 8.03e+00 bond pdb=" N ARG A1509 " pdb=" CA ARG A1509 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.29e-02 6.01e+03 8.03e+00 bond pdb=" N ILE A1510 " pdb=" CA ILE A1510 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.97e+00 bond pdb=" N ILE D1510 " pdb=" CA ILE D1510 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.84e+00 bond pdb=" N CYS A 55 " pdb=" CA CYS A 55 " ideal model delta sigma weight residual 1.456 1.491 -0.034 1.31e-02 5.83e+03 6.76e+00 ... (remaining 28625 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 38113 1.91 - 3.83: 516 3.83 - 5.74: 79 5.74 - 7.65: 16 7.65 - 9.56: 8 Bond angle restraints: 38732 Sorted by residual: angle pdb=" N GLU A 56 " pdb=" CA GLU A 56 " pdb=" C GLU A 56 " ideal model delta sigma weight residual 112.54 106.86 5.68 1.22e+00 6.72e-01 2.17e+01 angle pdb=" N GLU D 56 " pdb=" CA GLU D 56 " pdb=" C GLU D 56 " ideal model delta sigma weight residual 112.54 106.89 5.65 1.22e+00 6.72e-01 2.14e+01 angle pdb=" N GLU D 427 " pdb=" CA GLU D 427 " pdb=" C GLU D 427 " ideal model delta sigma weight residual 114.56 108.91 5.65 1.27e+00 6.20e-01 1.98e+01 angle pdb=" N GLU A 427 " pdb=" CA GLU A 427 " pdb=" C GLU A 427 " ideal model delta sigma weight residual 114.56 108.91 5.65 1.27e+00 6.20e-01 1.98e+01 angle pdb=" N THR D1753 " pdb=" CA THR D1753 " pdb=" C THR D1753 " ideal model delta sigma weight residual 109.81 116.46 -6.65 2.21e+00 2.05e-01 9.06e+00 ... (remaining 38727 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 15615 17.97 - 35.94: 1304 35.94 - 53.92: 312 53.92 - 71.89: 81 71.89 - 89.86: 32 Dihedral angle restraints: 17344 sinusoidal: 6982 harmonic: 10362 Sorted by residual: dihedral pdb=" CA SER A 192 " pdb=" C SER A 192 " pdb=" N ASN A 193 " pdb=" CA ASN A 193 " ideal model delta harmonic sigma weight residual 180.00 150.40 29.60 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CA SER D 192 " pdb=" C SER D 192 " pdb=" N ASN D 193 " pdb=" CA ASN D 193 " ideal model delta harmonic sigma weight residual 180.00 150.44 29.56 0 5.00e+00 4.00e-02 3.49e+01 dihedral pdb=" CB CYS A1691 " pdb=" SG CYS A1691 " pdb=" SG CYS A1776 " pdb=" CB CYS A1776 " ideal model delta sinusoidal sigma weight residual 93.00 142.20 -49.20 1 1.00e+01 1.00e-02 3.33e+01 ... (remaining 17341 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3850 0.055 - 0.111: 605 0.111 - 0.166: 40 0.166 - 0.222: 6 0.222 - 0.277: 5 Chirality restraints: 4506 Sorted by residual: chirality pdb=" CA ARG D1509 " pdb=" N ARG D1509 " pdb=" C ARG D1509 " pdb=" CB ARG D1509 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CA ARG A1509 " pdb=" N ARG A1509 " pdb=" C ARG A1509 " pdb=" CB ARG A1509 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA THR D1753 " pdb=" N THR D1753 " pdb=" C THR D1753 " pdb=" CB THR D1753 " both_signs ideal model delta sigma weight residual False 2.53 2.28 0.24 2.00e-01 2.50e+01 1.50e+00 ... (remaining 4503 not shown) Planarity restraints: 4850 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A2017 " -0.046 5.00e-02 4.00e+02 6.94e-02 7.70e+00 pdb=" N PRO A2018 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO A2018 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A2018 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D2017 " 0.046 5.00e-02 4.00e+02 6.92e-02 7.66e+00 pdb=" N PRO D2018 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO D2018 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO D2018 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 789 " -0.009 2.00e-02 2.50e+03 1.77e-02 3.13e+00 pdb=" C ARG D 789 " 0.031 2.00e-02 2.50e+03 pdb=" O ARG D 789 " -0.012 2.00e-02 2.50e+03 pdb=" N GLY D 790 " -0.010 2.00e-02 2.50e+03 ... (remaining 4847 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2679 2.74 - 3.28: 29721 3.28 - 3.82: 47219 3.82 - 4.36: 56470 4.36 - 4.90: 94785 Nonbonded interactions: 230874 Sorted by model distance: nonbonded pdb=" OD1 ASP A 769 " pdb=" OG1 THR A 772 " model vdw 2.202 3.040 nonbonded pdb=" OD1 ASP D 769 " pdb=" OG1 THR D 772 " model vdw 2.203 3.040 nonbonded pdb=" OE1 GLU D1381 " pdb="MN MN D2301 " model vdw 2.208 2.320 nonbonded pdb=" OE1 GLU A1381 " pdb="MN MN A2301 " model vdw 2.208 2.320 nonbonded pdb=" OD1 ASP D1420 " pdb=" NH1 ARG D1476 " model vdw 2.218 3.120 ... (remaining 230869 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 31.970 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.070 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 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 : 0.003 0.096 28666 Z= 0.155 Angle : 0.912 63.150 38776 Z= 0.353 Chirality : 0.040 0.277 4506 Planarity : 0.003 0.069 4850 Dihedral : 14.911 89.859 10588 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.98 % Favored : 88.88 % Rotamer: Outliers : 2.99 % Allowed : 10.32 % Favored : 86.69 % Cbeta Deviations : 0.06 % 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: -3.18 (0.13), residues: 3488 helix: -0.84 (0.11), residues: 1692 sheet: -2.04 (0.27), residues: 280 loop : -3.70 (0.14), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 209 TYR 0.007 0.001 TYR D2095 PHE 0.017 0.001 PHE D 533 TRP 0.005 0.001 TRP D 116 HIS 0.003 0.000 HIS A 472 Details of bonding type rmsd covalent geometry : bond 0.00251 (28630) covalent geometry : angle 0.58347 (38732) SS BOND : bond 0.00244 ( 4) SS BOND : angle 9.53810 ( 8) hydrogen bonds : bond 0.13370 ( 1292) hydrogen bonds : angle 5.96169 ( 3768) metal coordination : bond 0.06798 ( 32) metal coordination : angle 22.58593 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 947 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 854 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 ASN cc_start: 0.8203 (t0) cc_final: 0.7993 (t0) REVERT: A 341 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7882 (mmmt) REVERT: A 376 ARG cc_start: 0.6935 (mmt180) cc_final: 0.6497 (mmt180) REVERT: A 419 LYS cc_start: 0.8758 (tmtt) cc_final: 0.7675 (tptt) REVERT: A 438 GLN cc_start: 0.6053 (pp30) cc_final: 0.5688 (pp30) REVERT: A 481 PHE cc_start: 0.7391 (t80) cc_final: 0.6926 (t80) REVERT: A 526 ARG cc_start: 0.6994 (mtt180) cc_final: 0.6765 (mtt90) REVERT: A 722 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7293 (mm-30) REVERT: A 1150 GLU cc_start: 0.7414 (tm-30) cc_final: 0.6956 (tm-30) REVERT: A 1513 GLU cc_start: 0.7324 (mt-10) cc_final: 0.7068 (mt-10) REVERT: A 1538 GLU cc_start: 0.6741 (pm20) cc_final: 0.6505 (pm20) REVERT: A 1623 LYS cc_start: 0.8731 (ttmt) cc_final: 0.8127 (tttt) REVERT: A 1670 LYS cc_start: 0.7862 (mtmt) cc_final: 0.7657 (mtmt) REVERT: A 1717 TRP cc_start: 0.8182 (p-90) cc_final: 0.7694 (p-90) REVERT: A 1907 PHE cc_start: 0.4681 (m-10) cc_final: 0.4437 (m-10) REVERT: A 2108 LEU cc_start: 0.8220 (mt) cc_final: 0.7949 (mt) REVERT: A 2153 LEU cc_start: 0.7657 (mt) cc_final: 0.7425 (mp) REVERT: D 376 ARG cc_start: 0.6973 (mmt180) cc_final: 0.6596 (mmt180) REVERT: D 419 LYS cc_start: 0.8750 (tmtt) cc_final: 0.7576 (tptt) REVERT: D 481 PHE cc_start: 0.7389 (t80) cc_final: 0.6929 (t80) REVERT: D 1111 ASN cc_start: 0.8678 (m-40) cc_final: 0.8422 (p0) REVERT: D 1150 GLU cc_start: 0.7410 (tm-30) cc_final: 0.6913 (tm-30) REVERT: D 1623 LYS cc_start: 0.8794 (ttmt) cc_final: 0.8196 (tttm) REVERT: D 1654 ILE cc_start: 0.7460 (mp) cc_final: 0.7173 (mp) REVERT: D 1717 TRP cc_start: 0.8207 (p-90) cc_final: 0.7762 (p-90) REVERT: D 1907 PHE cc_start: 0.4678 (m-10) cc_final: 0.4430 (m-10) REVERT: D 1978 ASP cc_start: 0.7611 (p0) cc_final: 0.7264 (p0) REVERT: D 2108 LEU cc_start: 0.8172 (mt) cc_final: 0.7925 (mt) REVERT: D 2153 LEU cc_start: 0.7647 (mt) cc_final: 0.7398 (mp) outliers start: 93 outliers final: 54 residues processed: 922 average time/residue: 0.2000 time to fit residues: 288.1621 Evaluate side-chains 655 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 600 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 791 LYS Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1162 ASN Chi-restraints excluded: chain A residue 1290 MET Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1409 CYS Chi-restraints excluded: chain A residue 1426 CYS Chi-restraints excluded: chain A residue 1455 THR Chi-restraints excluded: chain A residue 1460 ILE Chi-restraints excluded: chain A residue 1463 GLN Chi-restraints excluded: chain A residue 1527 LEU Chi-restraints excluded: chain A residue 1625 MET Chi-restraints excluded: chain A residue 1731 LEU Chi-restraints excluded: chain A residue 1770 LEU Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1838 LEU Chi-restraints excluded: chain A residue 1884 VAL Chi-restraints excluded: chain A residue 1968 VAL Chi-restraints excluded: chain A residue 1998 VAL Chi-restraints excluded: chain A residue 2099 PHE Chi-restraints excluded: chain A residue 2151 LYS Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 680 SER Chi-restraints excluded: chain D residue 735 VAL Chi-restraints excluded: chain D residue 791 LYS Chi-restraints excluded: chain D residue 1133 VAL Chi-restraints excluded: chain D residue 1162 ASN Chi-restraints excluded: chain D residue 1290 MET Chi-restraints excluded: chain D residue 1323 VAL Chi-restraints excluded: chain D residue 1409 CYS Chi-restraints excluded: chain D residue 1426 CYS Chi-restraints excluded: chain D residue 1455 THR Chi-restraints excluded: chain D residue 1460 ILE Chi-restraints excluded: chain D residue 1463 GLN Chi-restraints excluded: chain D residue 1527 LEU Chi-restraints excluded: chain D residue 1625 MET Chi-restraints excluded: chain D residue 1731 LEU Chi-restraints excluded: chain D residue 1770 LEU Chi-restraints excluded: chain D residue 1825 LEU Chi-restraints excluded: chain D residue 1968 VAL Chi-restraints excluded: chain D residue 1998 VAL Chi-restraints excluded: chain D residue 2053 LEU Chi-restraints excluded: chain D residue 2099 PHE Chi-restraints excluded: chain D residue 2151 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 0.0000 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 10.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN A 189 HIS A 288 ASN A 348 ASN A 359 ASN ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 ASN A 449 GLN A 522 ASN A 546 GLN A 628 ASN A 644 ASN A 647 HIS ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 771 GLN ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1128 ASN A1206 GLN A1231 HIS A1296 HIS A1297 ASN A1463 GLN A1503 ASN ** A1812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1829 GLN A1837 GLN ** A1886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1984 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2043 ASN ** A2074 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2123 GLN A2146 HIS B 48 ASN ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 GLN D 288 ASN ** D 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 359 ASN ** D 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 449 GLN D 522 ASN D 546 GLN D 607 ASN D 628 ASN D 647 HIS D 771 GLN ** D 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1111 ASN D1128 ASN D1206 GLN D1231 HIS D1296 HIS D1297 ASN ** D1308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1429 ASN D1463 GLN D1503 ASN D1829 GLN D1833 ASN D1837 GLN ** D1886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1984 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2043 ASN D2123 GLN D2146 HIS E 48 ASN ** E 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.175489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.140013 restraints weight = 46812.281| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 2.87 r_work: 0.3653 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 28666 Z= 0.203 Angle : 0.712 14.201 38776 Z= 0.347 Chirality : 0.043 0.196 4506 Planarity : 0.004 0.072 4850 Dihedral : 9.623 77.596 4094 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.78 % Favored : 88.10 % Rotamer: Outliers : 4.98 % Allowed : 17.52 % Favored : 77.49 % 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: -2.33 (0.14), residues: 3488 helix: 0.04 (0.12), residues: 1696 sheet: -1.97 (0.28), residues: 294 loop : -3.45 (0.15), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 423 TYR 0.019 0.002 TYR D2095 PHE 0.021 0.002 PHE D 475 TRP 0.012 0.001 TRP A2125 HIS 0.004 0.001 HIS A 472 Details of bonding type rmsd covalent geometry : bond 0.00461 (28630) covalent geometry : angle 0.68460 (38732) SS BOND : bond 0.00492 ( 4) SS BOND : angle 2.57770 ( 8) hydrogen bonds : bond 0.03765 ( 1292) hydrogen bonds : angle 5.08338 ( 3768) metal coordination : bond 0.01526 ( 32) metal coordination : angle 6.28977 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 816 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 661 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7922 (mm-30) REVERT: A 341 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.8073 (mmmt) REVERT: A 376 ARG cc_start: 0.7421 (mmt180) cc_final: 0.6997 (mmt180) REVERT: A 401 LYS cc_start: 0.8848 (mmtm) cc_final: 0.8542 (mmtm) REVERT: A 438 GLN cc_start: 0.6328 (pp30) cc_final: 0.5908 (pp30) REVERT: A 591 MET cc_start: 0.8038 (ttm) cc_final: 0.7788 (ttm) REVERT: A 713 ARG cc_start: 0.8421 (ttt-90) cc_final: 0.8127 (ttt-90) REVERT: A 1150 GLU cc_start: 0.7893 (tm-30) cc_final: 0.7326 (tm-30) REVERT: A 1463 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.7440 (pp30) REVERT: A 1623 LYS cc_start: 0.9018 (ttmt) cc_final: 0.8424 (tttt) REVERT: A 1670 LYS cc_start: 0.8373 (mtmt) cc_final: 0.8075 (mtmt) REVERT: A 1717 TRP cc_start: 0.8577 (p-90) cc_final: 0.7883 (p-90) REVERT: A 2051 LEU cc_start: 0.6996 (tp) cc_final: 0.6736 (tt) REVERT: D 376 ARG cc_start: 0.7414 (mmt180) cc_final: 0.6984 (mmt180) REVERT: D 401 LYS cc_start: 0.8844 (mmtm) cc_final: 0.8554 (mmtm) REVERT: D 438 GLN cc_start: 0.6287 (pp30) cc_final: 0.5858 (pp30) REVERT: D 476 GLN cc_start: 0.8097 (tm-30) cc_final: 0.7892 (tm-30) REVERT: D 591 MET cc_start: 0.8007 (ttm) cc_final: 0.7767 (ttm) REVERT: D 713 ARG cc_start: 0.8302 (ttt-90) cc_final: 0.8022 (ttt-90) REVERT: D 1150 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7286 (tm-30) REVERT: D 1157 LYS cc_start: 0.7601 (tptp) cc_final: 0.7393 (tptt) REVERT: D 1463 GLN cc_start: 0.8303 (OUTLIER) cc_final: 0.7479 (pp30) REVERT: D 1623 LYS cc_start: 0.9021 (ttmt) cc_final: 0.8417 (tttt) REVERT: D 1654 ILE cc_start: 0.7852 (mp) cc_final: 0.7413 (mp) REVERT: D 1693 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8923 (pp) REVERT: D 1717 TRP cc_start: 0.8576 (p-90) cc_final: 0.7946 (p-90) REVERT: E 65 MET cc_start: 0.7903 (mtm) cc_final: 0.7686 (mtm) outliers start: 155 outliers final: 99 residues processed: 769 average time/residue: 0.1820 time to fit residues: 226.1144 Evaluate side-chains 672 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 569 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 450 HIS Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1162 ASN Chi-restraints excluded: chain A residue 1208 LEU Chi-restraints excluded: chain A residue 1237 GLU Chi-restraints excluded: chain A residue 1290 MET Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1379 VAL Chi-restraints excluded: chain A residue 1388 VAL Chi-restraints excluded: chain A residue 1409 CYS Chi-restraints excluded: chain A residue 1413 THR Chi-restraints excluded: chain A residue 1426 CYS Chi-restraints excluded: chain A residue 1427 ILE Chi-restraints excluded: chain A residue 1460 ILE Chi-restraints excluded: chain A residue 1463 GLN Chi-restraints excluded: chain A residue 1514 ASN Chi-restraints excluded: chain A residue 1527 LEU Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1625 MET Chi-restraints excluded: chain A residue 1722 LYS Chi-restraints excluded: chain A residue 1731 LEU Chi-restraints excluded: chain A residue 1781 MET Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1830 ILE Chi-restraints excluded: chain A residue 1842 SER Chi-restraints excluded: chain A residue 1864 LEU Chi-restraints excluded: chain A residue 1872 ILE Chi-restraints excluded: chain A residue 1961 PHE Chi-restraints excluded: chain A residue 1968 VAL Chi-restraints excluded: chain A residue 2099 PHE Chi-restraints excluded: chain A residue 2104 VAL Chi-restraints excluded: chain A residue 2151 LYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 215 ASP Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 337 ILE Chi-restraints excluded: chain D residue 348 ASN Chi-restraints excluded: chain D residue 368 CYS Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 450 HIS Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 585 ASP Chi-restraints excluded: chain D residue 606 MET Chi-restraints excluded: chain D residue 667 VAL Chi-restraints excluded: chain D residue 735 VAL Chi-restraints excluded: chain D residue 1133 VAL Chi-restraints excluded: chain D residue 1162 ASN Chi-restraints excluded: chain D residue 1282 SER Chi-restraints excluded: chain D residue 1323 VAL Chi-restraints excluded: chain D residue 1379 VAL Chi-restraints excluded: chain D residue 1388 VAL Chi-restraints excluded: chain D residue 1409 CYS Chi-restraints excluded: chain D residue 1413 THR Chi-restraints excluded: chain D residue 1426 CYS Chi-restraints excluded: chain D residue 1427 ILE Chi-restraints excluded: chain D residue 1460 ILE Chi-restraints excluded: chain D residue 1463 GLN Chi-restraints excluded: chain D residue 1514 ASN Chi-restraints excluded: chain D residue 1625 MET Chi-restraints excluded: chain D residue 1693 LEU Chi-restraints excluded: chain D residue 1722 LYS Chi-restraints excluded: chain D residue 1731 LEU Chi-restraints excluded: chain D residue 1825 LEU Chi-restraints excluded: chain D residue 1830 ILE Chi-restraints excluded: chain D residue 1842 SER Chi-restraints excluded: chain D residue 1864 LEU Chi-restraints excluded: chain D residue 1872 ILE Chi-restraints excluded: chain D residue 1961 PHE Chi-restraints excluded: chain D residue 1968 VAL Chi-restraints excluded: chain D residue 2028 LEU Chi-restraints excluded: chain D residue 2053 LEU Chi-restraints excluded: chain D residue 2099 PHE Chi-restraints excluded: chain D residue 2104 VAL Chi-restraints excluded: chain D residue 2151 LYS Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 64 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 204 optimal weight: 2.9990 chunk 84 optimal weight: 8.9990 chunk 308 optimal weight: 3.9990 chunk 157 optimal weight: 40.0000 chunk 350 optimal weight: 8.9990 chunk 282 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 166 optimal weight: 2.9990 chunk 304 optimal weight: 0.8980 chunk 241 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 698 ASN ** A 704 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 771 GLN ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1405 HIS A1429 ASN A1539 GLN A1738 GLN ** A1886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1984 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2074 GLN B 55 HIS D 189 HIS ** D 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 698 ASN D 771 GLN ** D 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1405 HIS D1738 GLN ** D1812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1984 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2074 GLN E 55 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.175977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.143115 restraints weight = 46988.821| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 2.92 r_work: 0.3680 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.132 28666 Z= 0.146 Angle : 0.674 15.383 38776 Z= 0.325 Chirality : 0.042 0.243 4506 Planarity : 0.004 0.042 4850 Dihedral : 9.395 75.615 4064 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.89 % Favored : 88.99 % Rotamer: Outliers : 4.57 % Allowed : 19.55 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.99 (0.14), residues: 3488 helix: 0.35 (0.13), residues: 1706 sheet: -1.76 (0.28), residues: 298 loop : -3.37 (0.15), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 231 TYR 0.018 0.001 TYR A 214 PHE 0.022 0.002 PHE D 475 TRP 0.008 0.001 TRP D1192 HIS 0.007 0.001 HIS A1751 Details of bonding type rmsd covalent geometry : bond 0.00327 (28630) covalent geometry : angle 0.64584 (38732) SS BOND : bond 0.00498 ( 4) SS BOND : angle 2.89632 ( 8) hydrogen bonds : bond 0.03449 ( 1292) hydrogen bonds : angle 4.93159 ( 3768) metal coordination : bond 0.03391 ( 32) metal coordination : angle 6.22370 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 783 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 641 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7842 (mm-30) REVERT: A 322 ASN cc_start: 0.8400 (t0) cc_final: 0.8136 (t0) REVERT: A 341 LYS cc_start: 0.8399 (OUTLIER) cc_final: 0.7972 (mmmt) REVERT: A 350 LEU cc_start: 0.9481 (mm) cc_final: 0.9275 (mm) REVERT: A 376 ARG cc_start: 0.7414 (mmt180) cc_final: 0.6980 (mmt180) REVERT: A 398 GLU cc_start: 0.7383 (mt-10) cc_final: 0.7179 (mp0) REVERT: A 401 LYS cc_start: 0.8852 (mmtm) cc_final: 0.8519 (mmtm) REVERT: A 438 GLN cc_start: 0.6328 (pp30) cc_final: 0.5858 (pp30) REVERT: A 591 MET cc_start: 0.7972 (ttm) cc_final: 0.7740 (ttm) REVERT: A 713 ARG cc_start: 0.8451 (ttt-90) cc_final: 0.8211 (ttt-90) REVERT: A 783 CYS cc_start: 0.8581 (t) cc_final: 0.8095 (t) REVERT: A 1141 MET cc_start: 0.8519 (mmp) cc_final: 0.7931 (mmt) REVERT: A 1150 GLU cc_start: 0.7846 (tm-30) cc_final: 0.7283 (tm-30) REVERT: A 1623 LYS cc_start: 0.9055 (ttmt) cc_final: 0.8475 (tttm) REVERT: A 1670 LYS cc_start: 0.8360 (mtmt) cc_final: 0.8109 (mtmt) REVERT: A 1717 TRP cc_start: 0.8540 (p-90) cc_final: 0.7887 (p-90) REVERT: A 1782 MET cc_start: 0.8732 (mmm) cc_final: 0.7950 (ppp) REVERT: D 268 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7878 (mm-30) REVERT: D 376 ARG cc_start: 0.7349 (mmt180) cc_final: 0.6896 (mmt180) REVERT: D 401 LYS cc_start: 0.8860 (mmtm) cc_final: 0.8507 (mmtm) REVERT: D 438 GLN cc_start: 0.6301 (pp30) cc_final: 0.5840 (pp30) REVERT: D 591 MET cc_start: 0.7878 (ttm) cc_final: 0.7627 (ttm) REVERT: D 630 THR cc_start: 0.8583 (m) cc_final: 0.8212 (p) REVERT: D 713 ARG cc_start: 0.8385 (ttt-90) cc_final: 0.8173 (ttt-90) REVERT: D 1141 MET cc_start: 0.8496 (mmp) cc_final: 0.7914 (mmt) REVERT: D 1150 GLU cc_start: 0.7816 (tm-30) cc_final: 0.7213 (tm-30) REVERT: D 1536 CYS cc_start: 0.7311 (OUTLIER) cc_final: 0.6509 (t) REVERT: D 1623 LYS cc_start: 0.9014 (ttmt) cc_final: 0.8437 (tttm) REVERT: D 1693 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8838 (pp) REVERT: D 1717 TRP cc_start: 0.8541 (p-90) cc_final: 0.7956 (p-90) REVERT: D 1978 ASP cc_start: 0.7842 (p0) cc_final: 0.7391 (p0) REVERT: E 65 MET cc_start: 0.7823 (mtm) cc_final: 0.7590 (mtm) outliers start: 142 outliers final: 89 residues processed: 743 average time/residue: 0.1783 time to fit residues: 216.3013 Evaluate side-chains 683 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 591 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 450 HIS Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 585 ASP Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1212 THR Chi-restraints excluded: chain A residue 1237 GLU Chi-restraints excluded: chain A residue 1244 GLU Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1388 VAL Chi-restraints excluded: chain A residue 1409 CYS Chi-restraints excluded: chain A residue 1413 THR Chi-restraints excluded: chain A residue 1427 ILE Chi-restraints excluded: chain A residue 1455 THR Chi-restraints excluded: chain A residue 1460 ILE Chi-restraints excluded: chain A residue 1514 ASN Chi-restraints excluded: chain A residue 1527 LEU Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain A residue 1625 MET Chi-restraints excluded: chain A residue 1722 LYS Chi-restraints excluded: chain A residue 1731 LEU Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1830 ILE Chi-restraints excluded: chain A residue 1842 SER Chi-restraints excluded: chain A residue 1864 LEU Chi-restraints excluded: chain A residue 1872 ILE Chi-restraints excluded: chain A residue 1968 VAL Chi-restraints excluded: chain A residue 1998 VAL Chi-restraints excluded: chain A residue 2099 PHE Chi-restraints excluded: chain A residue 2151 LYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 215 ASP Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 450 HIS Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 585 ASP Chi-restraints excluded: chain D residue 606 MET Chi-restraints excluded: chain D residue 658 GLU Chi-restraints excluded: chain D residue 735 VAL Chi-restraints excluded: chain D residue 1133 VAL Chi-restraints excluded: chain D residue 1208 LEU Chi-restraints excluded: chain D residue 1212 THR Chi-restraints excluded: chain D residue 1244 GLU Chi-restraints excluded: chain D residue 1323 VAL Chi-restraints excluded: chain D residue 1388 VAL Chi-restraints excluded: chain D residue 1409 CYS Chi-restraints excluded: chain D residue 1413 THR Chi-restraints excluded: chain D residue 1427 ILE Chi-restraints excluded: chain D residue 1455 THR Chi-restraints excluded: chain D residue 1460 ILE Chi-restraints excluded: chain D residue 1514 ASN Chi-restraints excluded: chain D residue 1536 CYS Chi-restraints excluded: chain D residue 1544 VAL Chi-restraints excluded: chain D residue 1625 MET Chi-restraints excluded: chain D residue 1693 LEU Chi-restraints excluded: chain D residue 1722 LYS Chi-restraints excluded: chain D residue 1731 LEU Chi-restraints excluded: chain D residue 1825 LEU Chi-restraints excluded: chain D residue 1830 ILE Chi-restraints excluded: chain D residue 1838 LEU Chi-restraints excluded: chain D residue 1842 SER Chi-restraints excluded: chain D residue 1864 LEU Chi-restraints excluded: chain D residue 1872 ILE Chi-restraints excluded: chain D residue 1968 VAL Chi-restraints excluded: chain D residue 1998 VAL Chi-restraints excluded: chain D residue 2053 LEU Chi-restraints excluded: chain D residue 2099 PHE Chi-restraints excluded: chain D residue 2151 LYS Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 54 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 222 optimal weight: 10.0000 chunk 213 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 252 optimal weight: 4.9990 chunk 352 optimal weight: 10.0000 chunk 58 optimal weight: 0.3980 chunk 152 optimal weight: 20.0000 chunk 123 optimal weight: 0.9990 chunk 67 optimal weight: 0.0050 chunk 346 optimal weight: 0.9990 overall best weight: 1.4800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 ASN ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1712 ASN A1738 GLN ** A1886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1954 HIS A1984 ASN ** D 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1712 ASN D1738 GLN ** D1886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1954 HIS D1984 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.174544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.139191 restraints weight = 46644.520| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 2.93 r_work: 0.3649 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 28666 Z= 0.158 Angle : 0.686 14.359 38776 Z= 0.334 Chirality : 0.042 0.239 4506 Planarity : 0.004 0.047 4850 Dihedral : 9.300 74.324 4046 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.55 % Favored : 88.33 % Rotamer: Outliers : 4.73 % Allowed : 20.61 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.82 (0.14), residues: 3488 helix: 0.45 (0.13), residues: 1704 sheet: -1.49 (0.30), residues: 278 loop : -3.26 (0.15), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 789 TYR 0.017 0.001 TYR A 534 PHE 0.022 0.002 PHE A 475 TRP 0.009 0.001 TRP E 43 HIS 0.008 0.001 HIS D1954 Details of bonding type rmsd covalent geometry : bond 0.00366 (28630) covalent geometry : angle 0.66463 (38732) SS BOND : bond 0.00792 ( 4) SS BOND : angle 2.83515 ( 8) hydrogen bonds : bond 0.03395 ( 1292) hydrogen bonds : angle 4.88982 ( 3768) metal coordination : bond 0.01154 ( 32) metal coordination : angle 5.43231 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 774 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 627 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 TRP cc_start: 0.5009 (OUTLIER) cc_final: 0.3229 (t60) REVERT: A 120 MET cc_start: 0.3511 (mmm) cc_final: 0.2967 (mtt) REVERT: A 227 LYS cc_start: 0.7505 (OUTLIER) cc_final: 0.7035 (pttm) REVERT: A 322 ASN cc_start: 0.8517 (t0) cc_final: 0.8270 (t0) REVERT: A 350 LEU cc_start: 0.9524 (mm) cc_final: 0.9304 (mm) REVERT: A 376 ARG cc_start: 0.7554 (mmt180) cc_final: 0.7105 (mmt180) REVERT: A 401 LYS cc_start: 0.8891 (mmtm) cc_final: 0.8532 (mmtm) REVERT: A 438 GLN cc_start: 0.6460 (pp30) cc_final: 0.5972 (pp30) REVERT: A 697 LEU cc_start: 0.8590 (tp) cc_final: 0.8298 (tp) REVERT: A 783 CYS cc_start: 0.8631 (t) cc_final: 0.8160 (t) REVERT: A 1121 TYR cc_start: 0.8531 (p90) cc_final: 0.8200 (p90) REVERT: A 1141 MET cc_start: 0.8552 (mmp) cc_final: 0.8006 (mmt) REVERT: A 1148 PHE cc_start: 0.9150 (t80) cc_final: 0.8908 (t80) REVERT: A 1150 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7368 (tm-30) REVERT: A 1208 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.8047 (tp) REVERT: A 1513 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7716 (mt-10) REVERT: A 1623 LYS cc_start: 0.9053 (ttmt) cc_final: 0.8414 (tttm) REVERT: A 1670 LYS cc_start: 0.8452 (mtmt) cc_final: 0.8128 (mtmt) REVERT: A 1717 TRP cc_start: 0.8554 (p-90) cc_final: 0.7860 (p-90) REVERT: A 1782 MET cc_start: 0.8767 (mmm) cc_final: 0.7900 (ppp) REVERT: D 227 LYS cc_start: 0.7383 (OUTLIER) cc_final: 0.6857 (pttm) REVERT: D 336 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8759 (mmmt) REVERT: D 341 LYS cc_start: 0.8337 (mmtm) cc_final: 0.7919 (mmtt) REVERT: D 350 LEU cc_start: 0.9528 (mm) cc_final: 0.9314 (mm) REVERT: D 376 ARG cc_start: 0.7510 (mmt180) cc_final: 0.7064 (mmt180) REVERT: D 401 LYS cc_start: 0.8942 (mmtm) cc_final: 0.8567 (mmtm) REVERT: D 438 GLN cc_start: 0.6440 (pp30) cc_final: 0.5974 (pp30) REVERT: D 1141 MET cc_start: 0.8506 (mmp) cc_final: 0.7963 (mmt) REVERT: D 1150 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7289 (tm-30) REVERT: D 1623 LYS cc_start: 0.9001 (ttmt) cc_final: 0.8384 (tttm) REVERT: D 1670 LYS cc_start: 0.8527 (mttt) cc_final: 0.8319 (mttp) REVERT: D 1693 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8840 (pp) REVERT: D 1717 TRP cc_start: 0.8503 (p-90) cc_final: 0.7907 (p-90) REVERT: E 65 MET cc_start: 0.7867 (mtm) cc_final: 0.7633 (mtm) outliers start: 147 outliers final: 107 residues processed: 732 average time/residue: 0.1815 time to fit residues: 215.9937 Evaluate side-chains 680 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 567 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 116 TRP Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 227 LYS Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 450 HIS Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 585 ASP Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1162 ASN Chi-restraints excluded: chain A residue 1208 LEU Chi-restraints excluded: chain A residue 1212 THR Chi-restraints excluded: chain A residue 1244 GLU Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1388 VAL Chi-restraints excluded: chain A residue 1409 CYS Chi-restraints excluded: chain A residue 1413 THR Chi-restraints excluded: chain A residue 1425 GLN Chi-restraints excluded: chain A residue 1426 CYS Chi-restraints excluded: chain A residue 1427 ILE Chi-restraints excluded: chain A residue 1455 THR Chi-restraints excluded: chain A residue 1460 ILE Chi-restraints excluded: chain A residue 1465 VAL Chi-restraints excluded: chain A residue 1514 ASN Chi-restraints excluded: chain A residue 1527 LEU Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain A residue 1625 MET Chi-restraints excluded: chain A residue 1722 LYS Chi-restraints excluded: chain A residue 1731 LEU Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1830 ILE Chi-restraints excluded: chain A residue 1838 LEU Chi-restraints excluded: chain A residue 1842 SER Chi-restraints excluded: chain A residue 1864 LEU Chi-restraints excluded: chain A residue 1872 ILE Chi-restraints excluded: chain A residue 1961 PHE Chi-restraints excluded: chain A residue 1968 VAL Chi-restraints excluded: chain A residue 2099 PHE Chi-restraints excluded: chain A residue 2151 LYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 215 ASP Chi-restraints excluded: chain D residue 227 LYS Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 336 LYS Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 368 CYS Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 450 HIS Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 585 ASP Chi-restraints excluded: chain D residue 606 MET Chi-restraints excluded: chain D residue 658 GLU Chi-restraints excluded: chain D residue 667 VAL Chi-restraints excluded: chain D residue 735 VAL Chi-restraints excluded: chain D residue 1133 VAL Chi-restraints excluded: chain D residue 1162 ASN Chi-restraints excluded: chain D residue 1208 LEU Chi-restraints excluded: chain D residue 1212 THR Chi-restraints excluded: chain D residue 1244 GLU Chi-restraints excluded: chain D residue 1323 VAL Chi-restraints excluded: chain D residue 1388 VAL Chi-restraints excluded: chain D residue 1409 CYS Chi-restraints excluded: chain D residue 1413 THR Chi-restraints excluded: chain D residue 1425 GLN Chi-restraints excluded: chain D residue 1427 ILE Chi-restraints excluded: chain D residue 1455 THR Chi-restraints excluded: chain D residue 1460 ILE Chi-restraints excluded: chain D residue 1465 VAL Chi-restraints excluded: chain D residue 1514 ASN Chi-restraints excluded: chain D residue 1527 LEU Chi-restraints excluded: chain D residue 1544 VAL Chi-restraints excluded: chain D residue 1625 MET Chi-restraints excluded: chain D residue 1693 LEU Chi-restraints excluded: chain D residue 1722 LYS Chi-restraints excluded: chain D residue 1731 LEU Chi-restraints excluded: chain D residue 1825 LEU Chi-restraints excluded: chain D residue 1830 ILE Chi-restraints excluded: chain D residue 1838 LEU Chi-restraints excluded: chain D residue 1842 SER Chi-restraints excluded: chain D residue 1864 LEU Chi-restraints excluded: chain D residue 1872 ILE Chi-restraints excluded: chain D residue 1961 PHE Chi-restraints excluded: chain D residue 1968 VAL Chi-restraints excluded: chain D residue 1994 VAL Chi-restraints excluded: chain D residue 2099 PHE Chi-restraints excluded: chain D residue 2151 LYS Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 54 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 267 optimal weight: 1.9990 chunk 254 optimal weight: 6.9990 chunk 295 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 219 optimal weight: 0.7980 chunk 286 optimal weight: 2.9990 chunk 128 optimal weight: 0.1980 chunk 221 optimal weight: 4.9990 chunk 248 optimal weight: 0.9990 chunk 285 optimal weight: 2.9990 chunk 244 optimal weight: 0.3980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 GLN A 698 ASN ** A 704 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1111 ASN ** A1231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1712 ASN A1738 GLN ** A1751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2123 GLN ** D 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 698 ASN ** D 704 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1712 ASN ** D1886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.176824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.141411 restraints weight = 46689.989| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 2.98 r_work: 0.3686 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28666 Z= 0.125 Angle : 0.669 14.881 38776 Z= 0.327 Chirality : 0.042 0.234 4506 Planarity : 0.004 0.054 4850 Dihedral : 9.155 73.272 4040 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.15 % Favored : 88.76 % Rotamer: Outliers : 4.69 % Allowed : 21.13 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.72 (0.14), residues: 3488 helix: 0.53 (0.13), residues: 1708 sheet: -1.36 (0.30), residues: 290 loop : -3.24 (0.15), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 231 TYR 0.027 0.001 TYR D 214 PHE 0.024 0.001 PHE A 475 TRP 0.010 0.001 TRP D1192 HIS 0.009 0.001 HIS A1751 Details of bonding type rmsd covalent geometry : bond 0.00280 (28630) covalent geometry : angle 0.65316 (38732) SS BOND : bond 0.00140 ( 4) SS BOND : angle 2.02393 ( 8) hydrogen bonds : bond 0.03209 ( 1292) hydrogen bonds : angle 4.76447 ( 3768) metal coordination : bond 0.00801 ( 32) metal coordination : angle 4.64593 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 770 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 624 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 LYS cc_start: 0.7352 (OUTLIER) cc_final: 0.6927 (pttm) REVERT: A 268 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7886 (mm-30) REVERT: A 322 ASN cc_start: 0.8433 (t0) cc_final: 0.8196 (t0) REVERT: A 350 LEU cc_start: 0.9489 (mm) cc_final: 0.9231 (mm) REVERT: A 376 ARG cc_start: 0.7399 (mmt180) cc_final: 0.7030 (mmt180) REVERT: A 401 LYS cc_start: 0.8877 (mmtm) cc_final: 0.8548 (mmtm) REVERT: A 438 GLN cc_start: 0.6410 (pp30) cc_final: 0.5939 (pp30) REVERT: A 630 THR cc_start: 0.8454 (m) cc_final: 0.8072 (p) REVERT: A 1121 TYR cc_start: 0.8498 (p90) cc_final: 0.8196 (p90) REVERT: A 1141 MET cc_start: 0.8497 (mmp) cc_final: 0.7998 (mmt) REVERT: A 1150 GLU cc_start: 0.7946 (tm-30) cc_final: 0.7377 (tm-30) REVERT: A 1207 MET cc_start: 0.7934 (mmm) cc_final: 0.7720 (mmm) REVERT: A 1513 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7766 (mt-10) REVERT: A 1623 LYS cc_start: 0.9011 (ttmt) cc_final: 0.8348 (tttm) REVERT: A 1670 LYS cc_start: 0.8376 (mtmt) cc_final: 0.8082 (mtmt) REVERT: A 1717 TRP cc_start: 0.8526 (p-90) cc_final: 0.7873 (p-90) REVERT: A 1751 HIS cc_start: 0.7199 (m170) cc_final: 0.6953 (m170) REVERT: A 1782 MET cc_start: 0.8743 (mmm) cc_final: 0.7941 (ppp) REVERT: A 1791 HIS cc_start: 0.8795 (m-70) cc_final: 0.8448 (m-70) REVERT: A 1794 LYS cc_start: 0.8736 (mtpp) cc_final: 0.8439 (mtmt) REVERT: D 227 LYS cc_start: 0.7271 (OUTLIER) cc_final: 0.6824 (pttm) REVERT: D 268 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7903 (mm-30) REVERT: D 322 ASN cc_start: 0.8489 (t0) cc_final: 0.8203 (t0) REVERT: D 350 LEU cc_start: 0.9481 (mm) cc_final: 0.9245 (mm) REVERT: D 363 ASP cc_start: 0.8665 (m-30) cc_final: 0.8393 (t0) REVERT: D 376 ARG cc_start: 0.7374 (mmt180) cc_final: 0.6987 (mmt180) REVERT: D 401 LYS cc_start: 0.8935 (mmtm) cc_final: 0.8514 (mmtm) REVERT: D 438 GLN cc_start: 0.6405 (pp30) cc_final: 0.5928 (pp30) REVERT: D 630 THR cc_start: 0.8484 (m) cc_final: 0.8091 (p) REVERT: D 1141 MET cc_start: 0.8515 (mmp) cc_final: 0.7988 (mmt) REVERT: D 1150 GLU cc_start: 0.7909 (tm-30) cc_final: 0.7319 (tm-30) REVERT: D 1623 LYS cc_start: 0.8966 (ttmt) cc_final: 0.8315 (tttm) REVERT: D 1717 TRP cc_start: 0.8481 (p-90) cc_final: 0.7899 (p-90) REVERT: D 1782 MET cc_start: 0.8747 (mmm) cc_final: 0.8019 (ppp) REVERT: D 1794 LYS cc_start: 0.8829 (mtpp) cc_final: 0.8507 (mtmt) outliers start: 146 outliers final: 104 residues processed: 727 average time/residue: 0.1706 time to fit residues: 203.8044 Evaluate side-chains 675 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 569 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 227 LYS Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 450 HIS Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 585 ASP Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1212 THR Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1388 VAL Chi-restraints excluded: chain A residue 1409 CYS Chi-restraints excluded: chain A residue 1413 THR Chi-restraints excluded: chain A residue 1425 GLN Chi-restraints excluded: chain A residue 1426 CYS Chi-restraints excluded: chain A residue 1427 ILE Chi-restraints excluded: chain A residue 1455 THR Chi-restraints excluded: chain A residue 1460 ILE Chi-restraints excluded: chain A residue 1514 ASN Chi-restraints excluded: chain A residue 1527 LEU Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain A residue 1625 MET Chi-restraints excluded: chain A residue 1701 VAL Chi-restraints excluded: chain A residue 1722 LYS Chi-restraints excluded: chain A residue 1731 LEU Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1830 ILE Chi-restraints excluded: chain A residue 1842 SER Chi-restraints excluded: chain A residue 1864 LEU Chi-restraints excluded: chain A residue 1872 ILE Chi-restraints excluded: chain A residue 1961 PHE Chi-restraints excluded: chain A residue 1968 VAL Chi-restraints excluded: chain A residue 1998 VAL Chi-restraints excluded: chain A residue 2099 PHE Chi-restraints excluded: chain A residue 2151 LYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 215 ASP Chi-restraints excluded: chain D residue 227 LYS Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 450 HIS Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 565 MET Chi-restraints excluded: chain D residue 606 MET Chi-restraints excluded: chain D residue 735 VAL Chi-restraints excluded: chain D residue 772 THR Chi-restraints excluded: chain D residue 1133 VAL Chi-restraints excluded: chain D residue 1208 LEU Chi-restraints excluded: chain D residue 1212 THR Chi-restraints excluded: chain D residue 1323 VAL Chi-restraints excluded: chain D residue 1388 VAL Chi-restraints excluded: chain D residue 1409 CYS Chi-restraints excluded: chain D residue 1413 THR Chi-restraints excluded: chain D residue 1425 GLN Chi-restraints excluded: chain D residue 1426 CYS Chi-restraints excluded: chain D residue 1427 ILE Chi-restraints excluded: chain D residue 1455 THR Chi-restraints excluded: chain D residue 1514 ASN Chi-restraints excluded: chain D residue 1527 LEU Chi-restraints excluded: chain D residue 1544 VAL Chi-restraints excluded: chain D residue 1625 MET Chi-restraints excluded: chain D residue 1722 LYS Chi-restraints excluded: chain D residue 1731 LEU Chi-restraints excluded: chain D residue 1825 LEU Chi-restraints excluded: chain D residue 1830 ILE Chi-restraints excluded: chain D residue 1838 LEU Chi-restraints excluded: chain D residue 1842 SER Chi-restraints excluded: chain D residue 1864 LEU Chi-restraints excluded: chain D residue 1872 ILE Chi-restraints excluded: chain D residue 1961 PHE Chi-restraints excluded: chain D residue 1968 VAL Chi-restraints excluded: chain D residue 1998 VAL Chi-restraints excluded: chain D residue 2099 PHE Chi-restraints excluded: chain D residue 2151 LYS Chi-restraints excluded: chain E residue 51 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 10 optimal weight: 0.0980 chunk 295 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 154 optimal weight: 10.0000 chunk 345 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 228 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 ASN ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1308 GLN A1712 ASN ** A1886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 288 ASN ** D 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1292 GLN ** D1308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1712 ASN ** D1886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1984 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.177454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.143804 restraints weight = 46955.736| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 2.88 r_work: 0.3703 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28666 Z= 0.123 Angle : 0.668 13.329 38776 Z= 0.325 Chirality : 0.042 0.224 4506 Planarity : 0.004 0.058 4850 Dihedral : 9.028 73.299 4038 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.12 % Favored : 88.79 % Rotamer: Outliers : 4.69 % Allowed : 21.70 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.64 (0.14), residues: 3488 helix: 0.58 (0.13), residues: 1710 sheet: -1.26 (0.32), residues: 268 loop : -3.18 (0.15), residues: 1510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 459 TYR 0.026 0.001 TYR D 214 PHE 0.028 0.001 PHE D 475 TRP 0.009 0.001 TRP A1192 HIS 0.006 0.001 HIS A1751 Details of bonding type rmsd covalent geometry : bond 0.00277 (28630) covalent geometry : angle 0.64945 (38732) SS BOND : bond 0.01044 ( 4) SS BOND : angle 2.40532 ( 8) hydrogen bonds : bond 0.03176 ( 1292) hydrogen bonds : angle 4.73555 ( 3768) metal coordination : bond 0.00888 ( 32) metal coordination : angle 5.07609 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 748 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 602 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 LYS cc_start: 0.7157 (OUTLIER) cc_final: 0.6755 (pttm) REVERT: A 268 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7899 (mm-30) REVERT: A 322 ASN cc_start: 0.8310 (t0) cc_final: 0.8093 (t0) REVERT: A 350 LEU cc_start: 0.9455 (mm) cc_final: 0.9206 (mm) REVERT: A 376 ARG cc_start: 0.7329 (mmt180) cc_final: 0.7005 (mmt180) REVERT: A 401 LYS cc_start: 0.8878 (mmtm) cc_final: 0.8520 (mmtm) REVERT: A 438 GLN cc_start: 0.6424 (pp30) cc_final: 0.5939 (pp30) REVERT: A 595 MET cc_start: 0.8404 (mmm) cc_final: 0.8099 (mtt) REVERT: A 630 THR cc_start: 0.8392 (m) cc_final: 0.8032 (p) REVERT: A 1141 MET cc_start: 0.8482 (mmp) cc_final: 0.7999 (mmt) REVERT: A 1150 GLU cc_start: 0.7798 (tm-30) cc_final: 0.7273 (tm-30) REVERT: A 1207 MET cc_start: 0.7979 (mmm) cc_final: 0.7713 (mmm) REVERT: A 1389 MET cc_start: 0.8304 (ptm) cc_final: 0.7324 (ptm) REVERT: A 1513 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7712 (mt-10) REVERT: A 1623 LYS cc_start: 0.8991 (ttmt) cc_final: 0.8326 (tttm) REVERT: A 1654 ILE cc_start: 0.7765 (mp) cc_final: 0.7344 (mp) REVERT: A 1717 TRP cc_start: 0.8494 (p-90) cc_final: 0.7910 (p-90) REVERT: A 1751 HIS cc_start: 0.7037 (m170) cc_final: 0.6825 (m170) REVERT: A 1782 MET cc_start: 0.8740 (mmm) cc_final: 0.7950 (ppp) REVERT: A 1791 HIS cc_start: 0.8743 (m-70) cc_final: 0.8399 (m-70) REVERT: A 1794 LYS cc_start: 0.8725 (mtpp) cc_final: 0.8433 (mtmt) REVERT: B 36 ARG cc_start: 0.7502 (ptt90) cc_final: 0.6116 (ptt90) REVERT: D 227 LYS cc_start: 0.7278 (OUTLIER) cc_final: 0.6731 (pttm) REVERT: D 268 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7909 (mm-30) REVERT: D 322 ASN cc_start: 0.8397 (t0) cc_final: 0.8138 (t0) REVERT: D 350 LEU cc_start: 0.9483 (mm) cc_final: 0.9253 (mm) REVERT: D 401 LYS cc_start: 0.8943 (mmtm) cc_final: 0.8587 (mmtm) REVERT: D 438 GLN cc_start: 0.6346 (pp30) cc_final: 0.5856 (pp30) REVERT: D 630 THR cc_start: 0.8412 (m) cc_final: 0.8052 (p) REVERT: D 1141 MET cc_start: 0.8521 (mmp) cc_final: 0.7995 (mmt) REVERT: D 1150 GLU cc_start: 0.7843 (tm-30) cc_final: 0.7267 (tm-30) REVERT: D 1623 LYS cc_start: 0.8989 (ttmt) cc_final: 0.8332 (tttm) REVERT: D 1717 TRP cc_start: 0.8492 (p-90) cc_final: 0.7941 (p-90) REVERT: D 1782 MET cc_start: 0.8748 (mmm) cc_final: 0.7986 (ppp) REVERT: D 2028 LEU cc_start: 0.1415 (OUTLIER) cc_final: 0.1116 (tm) outliers start: 146 outliers final: 109 residues processed: 704 average time/residue: 0.1881 time to fit residues: 218.7803 Evaluate side-chains 681 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 569 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 227 LYS Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 450 HIS Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1212 THR Chi-restraints excluded: chain A residue 1244 GLU Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1388 VAL Chi-restraints excluded: chain A residue 1409 CYS Chi-restraints excluded: chain A residue 1413 THR Chi-restraints excluded: chain A residue 1425 GLN Chi-restraints excluded: chain A residue 1426 CYS Chi-restraints excluded: chain A residue 1427 ILE Chi-restraints excluded: chain A residue 1455 THR Chi-restraints excluded: chain A residue 1465 VAL Chi-restraints excluded: chain A residue 1514 ASN Chi-restraints excluded: chain A residue 1527 LEU Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain A residue 1625 MET Chi-restraints excluded: chain A residue 1701 VAL Chi-restraints excluded: chain A residue 1731 LEU Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1830 ILE Chi-restraints excluded: chain A residue 1838 LEU Chi-restraints excluded: chain A residue 1842 SER Chi-restraints excluded: chain A residue 1864 LEU Chi-restraints excluded: chain A residue 1872 ILE Chi-restraints excluded: chain A residue 1917 VAL Chi-restraints excluded: chain A residue 1961 PHE Chi-restraints excluded: chain A residue 1968 VAL Chi-restraints excluded: chain A residue 1994 VAL Chi-restraints excluded: chain A residue 1998 VAL Chi-restraints excluded: chain A residue 2099 PHE Chi-restraints excluded: chain A residue 2151 LYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 215 ASP Chi-restraints excluded: chain D residue 227 LYS Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 450 HIS Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 473 LYS Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 606 MET Chi-restraints excluded: chain D residue 735 VAL Chi-restraints excluded: chain D residue 772 THR Chi-restraints excluded: chain D residue 798 LEU Chi-restraints excluded: chain D residue 1133 VAL Chi-restraints excluded: chain D residue 1208 LEU Chi-restraints excluded: chain D residue 1212 THR Chi-restraints excluded: chain D residue 1244 GLU Chi-restraints excluded: chain D residue 1323 VAL Chi-restraints excluded: chain D residue 1388 VAL Chi-restraints excluded: chain D residue 1409 CYS Chi-restraints excluded: chain D residue 1413 THR Chi-restraints excluded: chain D residue 1425 GLN Chi-restraints excluded: chain D residue 1426 CYS Chi-restraints excluded: chain D residue 1427 ILE Chi-restraints excluded: chain D residue 1455 THR Chi-restraints excluded: chain D residue 1460 ILE Chi-restraints excluded: chain D residue 1465 VAL Chi-restraints excluded: chain D residue 1514 ASN Chi-restraints excluded: chain D residue 1527 LEU Chi-restraints excluded: chain D residue 1536 CYS Chi-restraints excluded: chain D residue 1544 VAL Chi-restraints excluded: chain D residue 1625 MET Chi-restraints excluded: chain D residue 1731 LEU Chi-restraints excluded: chain D residue 1825 LEU Chi-restraints excluded: chain D residue 1830 ILE Chi-restraints excluded: chain D residue 1838 LEU Chi-restraints excluded: chain D residue 1842 SER Chi-restraints excluded: chain D residue 1864 LEU Chi-restraints excluded: chain D residue 1872 ILE Chi-restraints excluded: chain D residue 1917 VAL Chi-restraints excluded: chain D residue 1961 PHE Chi-restraints excluded: chain D residue 1968 VAL Chi-restraints excluded: chain D residue 1998 VAL Chi-restraints excluded: chain D residue 2020 PHE Chi-restraints excluded: chain D residue 2028 LEU Chi-restraints excluded: chain D residue 2099 PHE Chi-restraints excluded: chain D residue 2151 LYS Chi-restraints excluded: chain E residue 51 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 110 optimal weight: 0.1980 chunk 1 optimal weight: 6.9990 chunk 193 optimal weight: 3.9990 chunk 283 optimal weight: 0.6980 chunk 306 optimal weight: 8.9990 chunk 244 optimal weight: 4.9990 chunk 352 optimal weight: 20.0000 chunk 231 optimal weight: 3.9990 chunk 312 optimal weight: 5.9990 chunk 158 optimal weight: 6.9990 chunk 177 optimal weight: 9.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 ASN A 717 GLN ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 788 ASN ** A1111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1503 ASN A1711 ASN A1712 ASN ** A1984 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 288 ASN D 644 ASN ** D 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 788 ASN ** D1111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1308 GLN D1503 ASN D1712 ASN ** D1833 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1984 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.170114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.135292 restraints weight = 46766.284| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 3.02 r_work: 0.3571 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 28666 Z= 0.240 Angle : 0.752 15.015 38776 Z= 0.374 Chirality : 0.045 0.215 4506 Planarity : 0.004 0.061 4850 Dihedral : 9.288 75.489 4036 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.11 % Allowed : 12.53 % Favored : 87.36 % Rotamer: Outliers : 5.43 % Allowed : 22.80 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.77 (0.14), residues: 3488 helix: 0.42 (0.13), residues: 1712 sheet: -1.38 (0.31), residues: 298 loop : -3.17 (0.15), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 376 TYR 0.025 0.002 TYR D2095 PHE 0.035 0.002 PHE D1148 TRP 0.017 0.002 TRP E 43 HIS 0.004 0.001 HIS D 647 Details of bonding type rmsd covalent geometry : bond 0.00559 (28630) covalent geometry : angle 0.73092 (38732) SS BOND : bond 0.00771 ( 4) SS BOND : angle 2.63535 ( 8) hydrogen bonds : bond 0.03812 ( 1292) hydrogen bonds : angle 4.96255 ( 3768) metal coordination : bond 0.01355 ( 32) metal coordination : angle 5.70032 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 768 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 599 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 TRP cc_start: 0.5203 (OUTLIER) cc_final: 0.3396 (t60) REVERT: A 120 MET cc_start: 0.3722 (mmm) cc_final: 0.3150 (mtt) REVERT: A 227 LYS cc_start: 0.7505 (OUTLIER) cc_final: 0.6818 (mtmm) REVERT: A 322 ASN cc_start: 0.8556 (t0) cc_final: 0.8332 (t0) REVERT: A 350 LEU cc_start: 0.9530 (mm) cc_final: 0.9283 (mm) REVERT: A 376 ARG cc_start: 0.7501 (mmt180) cc_final: 0.6864 (mmp-170) REVERT: A 401 LYS cc_start: 0.8933 (mmtm) cc_final: 0.8605 (mmtm) REVERT: A 1141 MET cc_start: 0.8670 (mmp) cc_final: 0.8254 (mmp) REVERT: A 1150 GLU cc_start: 0.7997 (tm-30) cc_final: 0.7397 (tm-30) REVERT: A 1237 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7309 (mt-10) REVERT: A 1513 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7787 (mt-10) REVERT: A 1623 LYS cc_start: 0.9087 (ttmt) cc_final: 0.8429 (tttm) REVERT: A 1657 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8130 (pt) REVERT: A 1717 TRP cc_start: 0.8567 (p-90) cc_final: 0.7957 (p-90) REVERT: A 1751 HIS cc_start: 0.7199 (m170) cc_final: 0.6979 (m170) REVERT: A 1765 MET cc_start: 0.5736 (mmm) cc_final: 0.5278 (mmm) REVERT: A 1794 LYS cc_start: 0.8788 (mtpp) cc_final: 0.8554 (mtmt) REVERT: A 2028 LEU cc_start: 0.2133 (OUTLIER) cc_final: 0.1740 (tm) REVERT: D 116 TRP cc_start: 0.5260 (OUTLIER) cc_final: 0.3464 (t60) REVERT: D 120 MET cc_start: 0.3625 (mmm) cc_final: 0.3037 (mtt) REVERT: D 227 LYS cc_start: 0.7710 (OUTLIER) cc_final: 0.7177 (pttm) REVERT: D 322 ASN cc_start: 0.8548 (t0) cc_final: 0.8315 (t0) REVERT: D 350 LEU cc_start: 0.9519 (mm) cc_final: 0.9250 (mm) REVERT: D 363 ASP cc_start: 0.8800 (m-30) cc_final: 0.8433 (t0) REVERT: D 401 LYS cc_start: 0.8975 (mmtm) cc_final: 0.8633 (mmtm) REVERT: D 595 MET cc_start: 0.8486 (mmm) cc_final: 0.8173 (mtt) REVERT: D 1141 MET cc_start: 0.8666 (mmp) cc_final: 0.8208 (mmp) REVERT: D 1150 GLU cc_start: 0.7939 (tm-30) cc_final: 0.7332 (tm-30) REVERT: D 1623 LYS cc_start: 0.8997 (ttmt) cc_final: 0.8341 (tttt) REVERT: D 1657 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8201 (pt) REVERT: D 1670 LYS cc_start: 0.8600 (mttt) cc_final: 0.8347 (mtmp) REVERT: D 1717 TRP cc_start: 0.8559 (p-90) cc_final: 0.7975 (p-90) REVERT: D 1782 MET cc_start: 0.8789 (mmm) cc_final: 0.8060 (ppp) REVERT: D 2028 LEU cc_start: 0.1908 (OUTLIER) cc_final: 0.1592 (tm) outliers start: 169 outliers final: 123 residues processed: 717 average time/residue: 0.1821 time to fit residues: 214.2112 Evaluate side-chains 682 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 551 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 116 TRP Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 227 LYS Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 585 ASP Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1162 ASN Chi-restraints excluded: chain A residue 1208 LEU Chi-restraints excluded: chain A residue 1212 THR Chi-restraints excluded: chain A residue 1244 GLU Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1388 VAL Chi-restraints excluded: chain A residue 1409 CYS Chi-restraints excluded: chain A residue 1413 THR Chi-restraints excluded: chain A residue 1425 GLN Chi-restraints excluded: chain A residue 1426 CYS Chi-restraints excluded: chain A residue 1427 ILE Chi-restraints excluded: chain A residue 1455 THR Chi-restraints excluded: chain A residue 1460 ILE Chi-restraints excluded: chain A residue 1514 ASN Chi-restraints excluded: chain A residue 1527 LEU Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain A residue 1625 MET Chi-restraints excluded: chain A residue 1657 LEU Chi-restraints excluded: chain A residue 1731 LEU Chi-restraints excluded: chain A residue 1773 LEU Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1830 ILE Chi-restraints excluded: chain A residue 1838 LEU Chi-restraints excluded: chain A residue 1842 SER Chi-restraints excluded: chain A residue 1864 LEU Chi-restraints excluded: chain A residue 1872 ILE Chi-restraints excluded: chain A residue 1917 VAL Chi-restraints excluded: chain A residue 1961 PHE Chi-restraints excluded: chain A residue 1968 VAL Chi-restraints excluded: chain A residue 1994 VAL Chi-restraints excluded: chain A residue 1998 VAL Chi-restraints excluded: chain A residue 2017 LEU Chi-restraints excluded: chain A residue 2020 PHE Chi-restraints excluded: chain A residue 2028 LEU Chi-restraints excluded: chain A residue 2079 VAL Chi-restraints excluded: chain A residue 2099 PHE Chi-restraints excluded: chain A residue 2151 LYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 116 TRP Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 215 ASP Chi-restraints excluded: chain D residue 227 LYS Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 606 MET Chi-restraints excluded: chain D residue 667 VAL Chi-restraints excluded: chain D residue 735 VAL Chi-restraints excluded: chain D residue 772 THR Chi-restraints excluded: chain D residue 798 LEU Chi-restraints excluded: chain D residue 1133 VAL Chi-restraints excluded: chain D residue 1162 ASN Chi-restraints excluded: chain D residue 1208 LEU Chi-restraints excluded: chain D residue 1212 THR Chi-restraints excluded: chain D residue 1244 GLU Chi-restraints excluded: chain D residue 1323 VAL Chi-restraints excluded: chain D residue 1388 VAL Chi-restraints excluded: chain D residue 1413 THR Chi-restraints excluded: chain D residue 1425 GLN Chi-restraints excluded: chain D residue 1426 CYS Chi-restraints excluded: chain D residue 1427 ILE Chi-restraints excluded: chain D residue 1455 THR Chi-restraints excluded: chain D residue 1460 ILE Chi-restraints excluded: chain D residue 1465 VAL Chi-restraints excluded: chain D residue 1514 ASN Chi-restraints excluded: chain D residue 1527 LEU Chi-restraints excluded: chain D residue 1544 VAL Chi-restraints excluded: chain D residue 1614 VAL Chi-restraints excluded: chain D residue 1625 MET Chi-restraints excluded: chain D residue 1657 LEU Chi-restraints excluded: chain D residue 1731 LEU Chi-restraints excluded: chain D residue 1773 LEU Chi-restraints excluded: chain D residue 1825 LEU Chi-restraints excluded: chain D residue 1830 ILE Chi-restraints excluded: chain D residue 1838 LEU Chi-restraints excluded: chain D residue 1842 SER Chi-restraints excluded: chain D residue 1864 LEU Chi-restraints excluded: chain D residue 1872 ILE Chi-restraints excluded: chain D residue 1917 VAL Chi-restraints excluded: chain D residue 1961 PHE Chi-restraints excluded: chain D residue 1968 VAL Chi-restraints excluded: chain D residue 1994 VAL Chi-restraints excluded: chain D residue 1998 VAL Chi-restraints excluded: chain D residue 2020 PHE Chi-restraints excluded: chain D residue 2028 LEU Chi-restraints excluded: chain D residue 2099 PHE Chi-restraints excluded: chain D residue 2151 LYS Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 59 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 119 optimal weight: 0.0270 chunk 251 optimal weight: 7.9990 chunk 313 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 335 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 149 optimal weight: 10.0000 chunk 116 optimal weight: 0.0980 chunk 34 optimal weight: 9.9990 chunk 124 optimal weight: 0.6980 chunk 257 optimal weight: 0.7980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 ASN A 633 GLN ** A 704 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1712 ASN ** A1751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1791 HIS ** A1886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1984 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 149 ASN D 476 GLN D 633 GLN ** D 704 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1712 ASN ** D1886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1984 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.175498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.140799 restraints weight = 47037.103| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 2.89 r_work: 0.3662 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28666 Z= 0.130 Angle : 0.700 11.442 38776 Z= 0.344 Chirality : 0.043 0.206 4506 Planarity : 0.004 0.066 4850 Dihedral : 9.075 75.450 4035 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.01 % Favored : 88.85 % Rotamer: Outliers : 3.95 % Allowed : 24.69 % Favored : 71.35 % 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: -1.66 (0.14), residues: 3488 helix: 0.48 (0.13), residues: 1712 sheet: -1.22 (0.32), residues: 290 loop : -3.11 (0.15), residues: 1486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 459 TYR 0.021 0.001 TYR D 214 PHE 0.030 0.002 PHE A 475 TRP 0.011 0.001 TRP A1351 HIS 0.004 0.001 HIS A1751 Details of bonding type rmsd covalent geometry : bond 0.00290 (28630) covalent geometry : angle 0.68291 (38732) SS BOND : bond 0.00272 ( 4) SS BOND : angle 1.90148 ( 8) hydrogen bonds : bond 0.03350 ( 1292) hydrogen bonds : angle 4.77042 ( 3768) metal coordination : bond 0.00734 ( 32) metal coordination : angle 5.07777 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 734 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 611 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 TRP cc_start: 0.5135 (OUTLIER) cc_final: 0.3617 (t60) REVERT: A 120 MET cc_start: 0.3697 (mmm) cc_final: 0.3129 (mtt) REVERT: A 227 LYS cc_start: 0.7343 (OUTLIER) cc_final: 0.6863 (pttm) REVERT: A 268 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7879 (mm-30) REVERT: A 350 LEU cc_start: 0.9497 (mm) cc_final: 0.9231 (mm) REVERT: A 376 ARG cc_start: 0.7411 (mmt180) cc_final: 0.6833 (mmp-170) REVERT: A 401 LYS cc_start: 0.8896 (mmtm) cc_final: 0.8533 (mmtm) REVERT: A 438 GLN cc_start: 0.6600 (pp30) cc_final: 0.6310 (pp30) REVERT: A 440 ASP cc_start: 0.7577 (t70) cc_final: 0.7320 (t70) REVERT: A 1141 MET cc_start: 0.8526 (mmt) cc_final: 0.8208 (mmp) REVERT: A 1150 GLU cc_start: 0.7831 (tm-30) cc_final: 0.7315 (tm-30) REVERT: A 1168 GLU cc_start: 0.8304 (mm-30) cc_final: 0.8010 (tp30) REVERT: A 1237 GLU cc_start: 0.7542 (mt-10) cc_final: 0.7337 (mt-10) REVERT: A 1623 LYS cc_start: 0.8941 (ttmt) cc_final: 0.8262 (tttm) REVERT: A 1717 TRP cc_start: 0.8514 (p-90) cc_final: 0.7937 (p-90) REVERT: A 1751 HIS cc_start: 0.7073 (m170) cc_final: 0.6857 (m170) REVERT: A 1765 MET cc_start: 0.5594 (mmm) cc_final: 0.5205 (mmm) REVERT: A 1794 LYS cc_start: 0.8703 (mtpp) cc_final: 0.8500 (mtmt) REVERT: D 116 TRP cc_start: 0.5119 (OUTLIER) cc_final: 0.3526 (t60) REVERT: D 120 MET cc_start: 0.3618 (mmm) cc_final: 0.3033 (mtt) REVERT: D 268 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7929 (mm-30) REVERT: D 350 LEU cc_start: 0.9519 (mm) cc_final: 0.9291 (mm) REVERT: D 401 LYS cc_start: 0.8932 (mmtm) cc_final: 0.8599 (mmtm) REVERT: D 630 THR cc_start: 0.8466 (m) cc_final: 0.8067 (p) REVERT: D 697 LEU cc_start: 0.8560 (tp) cc_final: 0.8299 (tp) REVERT: D 1141 MET cc_start: 0.8541 (mmp) cc_final: 0.8106 (mmt) REVERT: D 1150 GLU cc_start: 0.7932 (tm-30) cc_final: 0.7364 (tm-30) REVERT: D 1588 LYS cc_start: 0.8197 (ttmm) cc_final: 0.7405 (tttp) REVERT: D 1623 LYS cc_start: 0.8915 (ttmt) cc_final: 0.8186 (tttm) REVERT: D 1670 LYS cc_start: 0.8505 (mttt) cc_final: 0.8253 (mttp) REVERT: D 1717 TRP cc_start: 0.8490 (p-90) cc_final: 0.7959 (p-90) REVERT: D 1751 HIS cc_start: 0.7026 (m90) cc_final: 0.6682 (m90) REVERT: D 1782 MET cc_start: 0.8742 (mmm) cc_final: 0.8062 (ppp) REVERT: D 1791 HIS cc_start: 0.8708 (m-70) cc_final: 0.8481 (m-70) REVERT: D 2028 LEU cc_start: 0.1859 (OUTLIER) cc_final: 0.1526 (tm) outliers start: 123 outliers final: 92 residues processed: 698 average time/residue: 0.1791 time to fit residues: 204.4774 Evaluate side-chains 672 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 576 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 116 TRP Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 227 LYS Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 585 ASP Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1162 ASN Chi-restraints excluded: chain A residue 1212 THR Chi-restraints excluded: chain A residue 1244 GLU Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1388 VAL Chi-restraints excluded: chain A residue 1425 GLN Chi-restraints excluded: chain A residue 1426 CYS Chi-restraints excluded: chain A residue 1427 ILE Chi-restraints excluded: chain A residue 1455 THR Chi-restraints excluded: chain A residue 1465 VAL Chi-restraints excluded: chain A residue 1514 ASN Chi-restraints excluded: chain A residue 1527 LEU Chi-restraints excluded: chain A residue 1625 MET Chi-restraints excluded: chain A residue 1731 LEU Chi-restraints excluded: chain A residue 1780 ASP Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1838 LEU Chi-restraints excluded: chain A residue 1842 SER Chi-restraints excluded: chain A residue 1872 ILE Chi-restraints excluded: chain A residue 1917 VAL Chi-restraints excluded: chain A residue 1968 VAL Chi-restraints excluded: chain A residue 1994 VAL Chi-restraints excluded: chain A residue 1998 VAL Chi-restraints excluded: chain A residue 2099 PHE Chi-restraints excluded: chain A residue 2151 LYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 116 TRP Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 215 ASP Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 606 MET Chi-restraints excluded: chain D residue 735 VAL Chi-restraints excluded: chain D residue 772 THR Chi-restraints excluded: chain D residue 798 LEU Chi-restraints excluded: chain D residue 1133 VAL Chi-restraints excluded: chain D residue 1135 ASP Chi-restraints excluded: chain D residue 1162 ASN Chi-restraints excluded: chain D residue 1212 THR Chi-restraints excluded: chain D residue 1244 GLU Chi-restraints excluded: chain D residue 1323 VAL Chi-restraints excluded: chain D residue 1388 VAL Chi-restraints excluded: chain D residue 1425 GLN Chi-restraints excluded: chain D residue 1426 CYS Chi-restraints excluded: chain D residue 1427 ILE Chi-restraints excluded: chain D residue 1455 THR Chi-restraints excluded: chain D residue 1460 ILE Chi-restraints excluded: chain D residue 1465 VAL Chi-restraints excluded: chain D residue 1514 ASN Chi-restraints excluded: chain D residue 1527 LEU Chi-restraints excluded: chain D residue 1544 VAL Chi-restraints excluded: chain D residue 1625 MET Chi-restraints excluded: chain D residue 1731 LEU Chi-restraints excluded: chain D residue 1825 LEU Chi-restraints excluded: chain D residue 1838 LEU Chi-restraints excluded: chain D residue 1872 ILE Chi-restraints excluded: chain D residue 1917 VAL Chi-restraints excluded: chain D residue 1961 PHE Chi-restraints excluded: chain D residue 1968 VAL Chi-restraints excluded: chain D residue 1994 VAL Chi-restraints excluded: chain D residue 1998 VAL Chi-restraints excluded: chain D residue 2017 LEU Chi-restraints excluded: chain D residue 2020 PHE Chi-restraints excluded: chain D residue 2028 LEU Chi-restraints excluded: chain D residue 2099 PHE Chi-restraints excluded: chain D residue 2151 LYS Chi-restraints excluded: chain E residue 51 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 173 optimal weight: 9.9990 chunk 262 optimal weight: 5.9990 chunk 248 optimal weight: 2.9990 chunk 293 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 272 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 chunk 198 optimal weight: 0.8980 chunk 266 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 698 ASN ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1712 ASN A1751 HIS ** A1886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 476 GLN D 698 ASN ** D 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1712 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.172427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.137182 restraints weight = 47038.001| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 3.00 r_work: 0.3616 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 28666 Z= 0.179 Angle : 0.732 12.352 38776 Z= 0.362 Chirality : 0.044 0.244 4506 Planarity : 0.004 0.062 4850 Dihedral : 9.019 75.787 4030 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.75 % Favored : 88.13 % Rotamer: Outliers : 3.83 % Allowed : 25.14 % Favored : 71.03 % 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: -1.71 (0.14), residues: 3488 helix: 0.41 (0.13), residues: 1712 sheet: -1.22 (0.32), residues: 290 loop : -3.11 (0.15), residues: 1486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 231 TYR 0.022 0.002 TYR A 214 PHE 0.025 0.002 PHE A 475 TRP 0.014 0.001 TRP D1351 HIS 0.003 0.001 HIS A1751 Details of bonding type rmsd covalent geometry : bond 0.00413 (28630) covalent geometry : angle 0.71475 (38732) SS BOND : bond 0.00430 ( 4) SS BOND : angle 2.03386 ( 8) hydrogen bonds : bond 0.03530 ( 1292) hydrogen bonds : angle 4.84455 ( 3768) metal coordination : bond 0.01050 ( 32) metal coordination : angle 5.08204 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 574 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 LYS cc_start: 0.7477 (OUTLIER) cc_final: 0.6836 (pttm) REVERT: A 268 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7923 (mm-30) REVERT: A 350 LEU cc_start: 0.9523 (mm) cc_final: 0.9296 (mm) REVERT: A 376 ARG cc_start: 0.7494 (mmt180) cc_final: 0.6929 (mmp-170) REVERT: A 401 LYS cc_start: 0.8904 (mmtm) cc_final: 0.8570 (mmtm) REVERT: A 1141 MET cc_start: 0.8561 (mmt) cc_final: 0.8271 (mmp) REVERT: A 1150 GLU cc_start: 0.7870 (tm-30) cc_final: 0.7325 (tm-30) REVERT: A 1237 GLU cc_start: 0.7584 (mt-10) cc_final: 0.7354 (mt-10) REVERT: A 1623 LYS cc_start: 0.8977 (ttmt) cc_final: 0.8182 (tttt) REVERT: A 1717 TRP cc_start: 0.8528 (p-90) cc_final: 0.7866 (p-90) REVERT: A 1765 MET cc_start: 0.5516 (mmm) cc_final: 0.5148 (mmm) REVERT: A 1794 LYS cc_start: 0.8760 (mtpp) cc_final: 0.8524 (mtmt) REVERT: A 2028 LEU cc_start: 0.1987 (OUTLIER) cc_final: 0.1609 (tm) REVERT: D 116 TRP cc_start: 0.5037 (OUTLIER) cc_final: 0.3583 (t60) REVERT: D 120 MET cc_start: 0.3634 (mmm) cc_final: 0.3044 (mtt) REVERT: D 216 GLU cc_start: 0.8385 (pp20) cc_final: 0.7950 (pm20) REVERT: D 227 LYS cc_start: 0.7124 (OUTLIER) cc_final: 0.6919 (pttm) REVERT: D 350 LEU cc_start: 0.9547 (mm) cc_final: 0.9271 (mm) REVERT: D 401 LYS cc_start: 0.8941 (mmtm) cc_final: 0.8581 (mmtm) REVERT: D 1141 MET cc_start: 0.8582 (mmp) cc_final: 0.8159 (mmp) REVERT: D 1150 GLU cc_start: 0.7960 (tm-30) cc_final: 0.7375 (tm-30) REVERT: D 1588 LYS cc_start: 0.8146 (ttmm) cc_final: 0.7398 (tttp) REVERT: D 1623 LYS cc_start: 0.8952 (ttmt) cc_final: 0.8187 (tttm) REVERT: D 1670 LYS cc_start: 0.8584 (mttt) cc_final: 0.8319 (mtmp) REVERT: D 1717 TRP cc_start: 0.8547 (p-90) cc_final: 0.7907 (p-90) REVERT: D 1751 HIS cc_start: 0.7078 (m90) cc_final: 0.6719 (m90) REVERT: D 1765 MET cc_start: 0.5507 (mmm) cc_final: 0.5160 (mmm) REVERT: D 1782 MET cc_start: 0.8788 (mmm) cc_final: 0.8024 (ppp) REVERT: D 1791 HIS cc_start: 0.8738 (m-70) cc_final: 0.8524 (m-70) REVERT: D 2028 LEU cc_start: 0.1967 (OUTLIER) cc_final: 0.1592 (tm) outliers start: 119 outliers final: 99 residues processed: 658 average time/residue: 0.1845 time to fit residues: 198.1502 Evaluate side-chains 659 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 555 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 227 LYS Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 585 ASP Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1162 ASN Chi-restraints excluded: chain A residue 1212 THR Chi-restraints excluded: chain A residue 1244 GLU Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1388 VAL Chi-restraints excluded: chain A residue 1425 GLN Chi-restraints excluded: chain A residue 1426 CYS Chi-restraints excluded: chain A residue 1427 ILE Chi-restraints excluded: chain A residue 1455 THR Chi-restraints excluded: chain A residue 1460 ILE Chi-restraints excluded: chain A residue 1465 VAL Chi-restraints excluded: chain A residue 1514 ASN Chi-restraints excluded: chain A residue 1527 LEU Chi-restraints excluded: chain A residue 1625 MET Chi-restraints excluded: chain A residue 1731 LEU Chi-restraints excluded: chain A residue 1780 ASP Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1838 LEU Chi-restraints excluded: chain A residue 1842 SER Chi-restraints excluded: chain A residue 1872 ILE Chi-restraints excluded: chain A residue 1917 VAL Chi-restraints excluded: chain A residue 1968 VAL Chi-restraints excluded: chain A residue 1994 VAL Chi-restraints excluded: chain A residue 1998 VAL Chi-restraints excluded: chain A residue 2017 LEU Chi-restraints excluded: chain A residue 2020 PHE Chi-restraints excluded: chain A residue 2028 LEU Chi-restraints excluded: chain A residue 2099 PHE Chi-restraints excluded: chain A residue 2128 LEU Chi-restraints excluded: chain A residue 2151 LYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 116 TRP Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 215 ASP Chi-restraints excluded: chain D residue 227 LYS Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 606 MET Chi-restraints excluded: chain D residue 735 VAL Chi-restraints excluded: chain D residue 772 THR Chi-restraints excluded: chain D residue 798 LEU Chi-restraints excluded: chain D residue 1133 VAL Chi-restraints excluded: chain D residue 1135 ASP Chi-restraints excluded: chain D residue 1162 ASN Chi-restraints excluded: chain D residue 1212 THR Chi-restraints excluded: chain D residue 1244 GLU Chi-restraints excluded: chain D residue 1323 VAL Chi-restraints excluded: chain D residue 1388 VAL Chi-restraints excluded: chain D residue 1425 GLN Chi-restraints excluded: chain D residue 1426 CYS Chi-restraints excluded: chain D residue 1427 ILE Chi-restraints excluded: chain D residue 1455 THR Chi-restraints excluded: chain D residue 1460 ILE Chi-restraints excluded: chain D residue 1465 VAL Chi-restraints excluded: chain D residue 1514 ASN Chi-restraints excluded: chain D residue 1527 LEU Chi-restraints excluded: chain D residue 1544 VAL Chi-restraints excluded: chain D residue 1625 MET Chi-restraints excluded: chain D residue 1731 LEU Chi-restraints excluded: chain D residue 1825 LEU Chi-restraints excluded: chain D residue 1838 LEU Chi-restraints excluded: chain D residue 1842 SER Chi-restraints excluded: chain D residue 1864 LEU Chi-restraints excluded: chain D residue 1872 ILE Chi-restraints excluded: chain D residue 1917 VAL Chi-restraints excluded: chain D residue 1961 PHE Chi-restraints excluded: chain D residue 1968 VAL Chi-restraints excluded: chain D residue 1994 VAL Chi-restraints excluded: chain D residue 1998 VAL Chi-restraints excluded: chain D residue 2017 LEU Chi-restraints excluded: chain D residue 2020 PHE Chi-restraints excluded: chain D residue 2028 LEU Chi-restraints excluded: chain D residue 2099 PHE Chi-restraints excluded: chain D residue 2104 VAL Chi-restraints excluded: chain D residue 2128 LEU Chi-restraints excluded: chain D residue 2151 LYS Chi-restraints excluded: chain E residue 51 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 325 optimal weight: 0.1980 chunk 18 optimal weight: 5.9990 chunk 139 optimal weight: 8.9990 chunk 348 optimal weight: 10.0000 chunk 224 optimal weight: 0.8980 chunk 263 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 220 optimal weight: 0.6980 chunk 175 optimal weight: 20.0000 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 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 476 GLN ** A 704 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1272 GLN A1712 ASN ** A1886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 359 ASN D 476 GLN ** D 704 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1712 ASN ** D1886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.173923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.140702 restraints weight = 47037.119| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 2.89 r_work: 0.3645 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28666 Z= 0.149 Angle : 0.726 12.620 38776 Z= 0.358 Chirality : 0.044 0.201 4506 Planarity : 0.004 0.068 4850 Dihedral : 8.924 76.531 4028 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.30 % Favored : 88.56 % Rotamer: Outliers : 3.47 % Allowed : 25.92 % Favored : 70.61 % 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: -1.68 (0.14), residues: 3488 helix: 0.42 (0.13), residues: 1714 sheet: -1.26 (0.31), residues: 292 loop : -3.05 (0.15), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 231 TYR 0.021 0.001 TYR A 214 PHE 0.026 0.002 PHE A 475 TRP 0.016 0.001 TRP A1351 HIS 0.002 0.001 HIS D 472 Details of bonding type rmsd covalent geometry : bond 0.00342 (28630) covalent geometry : angle 0.70990 (38732) SS BOND : bond 0.00370 ( 4) SS BOND : angle 1.88859 ( 8) hydrogen bonds : bond 0.03468 ( 1292) hydrogen bonds : angle 4.79103 ( 3768) metal coordination : bond 0.00803 ( 32) metal coordination : angle 4.91659 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 586 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 GLU cc_start: 0.8443 (pp20) cc_final: 0.8036 (pm20) REVERT: A 227 LYS cc_start: 0.7046 (OUTLIER) cc_final: 0.6811 (pttm) REVERT: A 268 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7829 (mm-30) REVERT: A 376 ARG cc_start: 0.7393 (mmt180) cc_final: 0.6939 (mmp-170) REVERT: A 1141 MET cc_start: 0.8523 (mmt) cc_final: 0.8297 (mmp) REVERT: A 1150 GLU cc_start: 0.7810 (tm-30) cc_final: 0.7302 (tm-30) REVERT: A 1237 GLU cc_start: 0.7494 (mt-10) cc_final: 0.7288 (mt-10) REVERT: A 1460 ILE cc_start: 0.9011 (OUTLIER) cc_final: 0.8786 (tp) REVERT: A 1623 LYS cc_start: 0.8967 (ttmt) cc_final: 0.8215 (tttt) REVERT: A 1717 TRP cc_start: 0.8514 (p-90) cc_final: 0.7875 (p-90) REVERT: A 1765 MET cc_start: 0.5468 (mmm) cc_final: 0.5139 (mmm) REVERT: A 1782 MET cc_start: 0.8772 (mmm) cc_final: 0.8046 (ppp) REVERT: A 1794 LYS cc_start: 0.8769 (mtpp) cc_final: 0.8545 (mtmt) REVERT: A 2028 LEU cc_start: 0.1916 (OUTLIER) cc_final: 0.1586 (tm) REVERT: D 116 TRP cc_start: 0.5263 (OUTLIER) cc_final: 0.3892 (t60) REVERT: D 120 MET cc_start: 0.3587 (mmm) cc_final: 0.3155 (mtt) REVERT: D 216 GLU cc_start: 0.8258 (pp20) cc_final: 0.7983 (pm20) REVERT: D 244 LEU cc_start: 0.8719 (tp) cc_final: 0.8383 (mt) REVERT: D 268 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7879 (mm-30) REVERT: D 350 LEU cc_start: 0.9514 (mm) cc_final: 0.9294 (mm) REVERT: D 401 LYS cc_start: 0.8930 (mmtm) cc_final: 0.8593 (mmtm) REVERT: D 482 GLU cc_start: 0.7371 (pt0) cc_final: 0.6961 (pt0) REVERT: D 1141 MET cc_start: 0.8545 (mmp) cc_final: 0.8143 (mmp) REVERT: D 1150 GLU cc_start: 0.7851 (tm-30) cc_final: 0.7312 (tm-30) REVERT: D 1588 LYS cc_start: 0.8168 (ttmm) cc_final: 0.7378 (tttp) REVERT: D 1623 LYS cc_start: 0.8960 (ttmt) cc_final: 0.8232 (tttm) REVERT: D 1717 TRP cc_start: 0.8531 (p-90) cc_final: 0.7915 (p-90) REVERT: D 1751 HIS cc_start: 0.7108 (m90) cc_final: 0.6740 (m90) REVERT: D 1782 MET cc_start: 0.8765 (mmm) cc_final: 0.8096 (ppp) REVERT: D 1791 HIS cc_start: 0.8691 (m-70) cc_final: 0.8452 (m-70) REVERT: D 2028 LEU cc_start: 0.1942 (OUTLIER) cc_final: 0.1584 (tm) outliers start: 108 outliers final: 98 residues processed: 660 average time/residue: 0.1826 time to fit residues: 196.8150 Evaluate side-chains 665 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 562 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 227 LYS Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 585 ASP Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1162 ASN Chi-restraints excluded: chain A residue 1212 THR Chi-restraints excluded: chain A residue 1244 GLU Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1388 VAL Chi-restraints excluded: chain A residue 1425 GLN Chi-restraints excluded: chain A residue 1426 CYS Chi-restraints excluded: chain A residue 1427 ILE Chi-restraints excluded: chain A residue 1455 THR Chi-restraints excluded: chain A residue 1460 ILE Chi-restraints excluded: chain A residue 1465 VAL Chi-restraints excluded: chain A residue 1514 ASN Chi-restraints excluded: chain A residue 1527 LEU Chi-restraints excluded: chain A residue 1625 MET Chi-restraints excluded: chain A residue 1731 LEU Chi-restraints excluded: chain A residue 1780 ASP Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1838 LEU Chi-restraints excluded: chain A residue 1842 SER Chi-restraints excluded: chain A residue 1872 ILE Chi-restraints excluded: chain A residue 1917 VAL Chi-restraints excluded: chain A residue 1968 VAL Chi-restraints excluded: chain A residue 1994 VAL Chi-restraints excluded: chain A residue 1998 VAL Chi-restraints excluded: chain A residue 2017 LEU Chi-restraints excluded: chain A residue 2020 PHE Chi-restraints excluded: chain A residue 2028 LEU Chi-restraints excluded: chain A residue 2099 PHE Chi-restraints excluded: chain A residue 2128 LEU Chi-restraints excluded: chain A residue 2151 LYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 116 TRP Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 215 ASP Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 361 MET Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 606 MET Chi-restraints excluded: chain D residue 735 VAL Chi-restraints excluded: chain D residue 772 THR Chi-restraints excluded: chain D residue 798 LEU Chi-restraints excluded: chain D residue 1133 VAL Chi-restraints excluded: chain D residue 1135 ASP Chi-restraints excluded: chain D residue 1162 ASN Chi-restraints excluded: chain D residue 1212 THR Chi-restraints excluded: chain D residue 1244 GLU Chi-restraints excluded: chain D residue 1323 VAL Chi-restraints excluded: chain D residue 1328 SER Chi-restraints excluded: chain D residue 1388 VAL Chi-restraints excluded: chain D residue 1425 GLN Chi-restraints excluded: chain D residue 1426 CYS Chi-restraints excluded: chain D residue 1427 ILE Chi-restraints excluded: chain D residue 1455 THR Chi-restraints excluded: chain D residue 1460 ILE Chi-restraints excluded: chain D residue 1465 VAL Chi-restraints excluded: chain D residue 1514 ASN Chi-restraints excluded: chain D residue 1527 LEU Chi-restraints excluded: chain D residue 1544 VAL Chi-restraints excluded: chain D residue 1625 MET Chi-restraints excluded: chain D residue 1731 LEU Chi-restraints excluded: chain D residue 1825 LEU Chi-restraints excluded: chain D residue 1838 LEU Chi-restraints excluded: chain D residue 1842 SER Chi-restraints excluded: chain D residue 1872 ILE Chi-restraints excluded: chain D residue 1917 VAL Chi-restraints excluded: chain D residue 1968 VAL Chi-restraints excluded: chain D residue 1994 VAL Chi-restraints excluded: chain D residue 1998 VAL Chi-restraints excluded: chain D residue 2017 LEU Chi-restraints excluded: chain D residue 2020 PHE Chi-restraints excluded: chain D residue 2028 LEU Chi-restraints excluded: chain D residue 2099 PHE Chi-restraints excluded: chain D residue 2128 LEU Chi-restraints excluded: chain D residue 2151 LYS Chi-restraints excluded: chain E residue 51 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 2 optimal weight: 9.9990 chunk 264 optimal weight: 4.9990 chunk 242 optimal weight: 4.9990 chunk 76 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 285 optimal weight: 0.0570 chunk 324 optimal weight: 10.0000 chunk 215 optimal weight: 4.9990 chunk 298 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 overall best weight: 2.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 476 GLN ** A 704 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1712 ASN ** A1886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 476 GLN ** D 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 704 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1712 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.169411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.138443 restraints weight = 46584.812| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 2.79 r_work: 0.3591 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 28666 Z= 0.217 Angle : 0.767 12.982 38776 Z= 0.382 Chirality : 0.045 0.190 4506 Planarity : 0.004 0.065 4850 Dihedral : 9.022 76.759 4028 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.11 % Allowed : 12.27 % Favored : 87.61 % Rotamer: Outliers : 3.79 % Allowed : 25.92 % Favored : 70.29 % 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: -1.75 (0.14), residues: 3488 helix: 0.37 (0.13), residues: 1708 sheet: -1.39 (0.31), residues: 298 loop : -3.07 (0.15), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 231 TYR 0.021 0.002 TYR A 214 PHE 0.029 0.002 PHE A1502 TRP 0.017 0.002 TRP D1351 HIS 0.003 0.001 HIS A 647 Details of bonding type rmsd covalent geometry : bond 0.00506 (28630) covalent geometry : angle 0.74964 (38732) SS BOND : bond 0.00497 ( 4) SS BOND : angle 2.02759 ( 8) hydrogen bonds : bond 0.03728 ( 1292) hydrogen bonds : angle 4.91732 ( 3768) metal coordination : bond 0.01268 ( 32) metal coordination : angle 5.36414 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8300.33 seconds wall clock time: 142 minutes 59.94 seconds (8579.94 seconds total)