Starting phenix.real_space_refine on Mon Sep 14 05:17:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7el9_31177/09_2026/7el9_31177.cif Found real_map, /net/cci-nas-00/data/ceres_data/7el9_31177/09_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_31177/09_2026/7el9_31177.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7el9_31177/09_2026/7el9_31177.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7el9_31177/09_2026/7el9_31177.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7el9_31177/09_2026/7el9_31177.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7el9_31177/09_2026/7el9_31177.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7el9_31177/09_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): 0.19s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: {'RNAv2': 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: {'RNAv2': 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: 6.05, 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: 2.78 Conformation dependent library (CDL) restraints added in 1.5 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: 1.28 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: 6.95 Time building geometry restraints manager: 3.75 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: 38067 1.91 - 3.83: 552 3.83 - 5.74: 89 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: 15561 17.97 - 35.94: 1304 35.94 - 53.92: 304 53.92 - 71.89: 81 71.89 - 89.86: 26 Dihedral angle restraints: 17276 sinusoidal: 6914 harmonic: 10362 Sorted by residual: dihedral pdb=" C4' U C 16 " pdb=" C3' U C 16 " pdb=" C2' U C 16 " pdb=" C1' U C 16 " ideal model delta sinusoidal sigma weight residual 36.35 -35.03 71.37 1 3.10e+00 1.04e-01 6.80e+02 dihedral pdb=" C4' U F 16 " pdb=" C3' U F 16 " pdb=" C2' U F 16 " pdb=" C1' U F 16 " ideal model delta sinusoidal sigma weight residual 36.34 -34.97 71.32 1 3.10e+00 1.04e-01 6.79e+02 dihedral pdb=" C4' C F 18 " pdb=" C3' C F 18 " pdb=" C2' C F 18 " pdb=" C1' C F 18 " ideal model delta sinusoidal sigma weight residual 36.35 -34.83 71.18 1 3.10e+00 1.04e-01 6.77e+02 ... (remaining 17273 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3828 0.055 - 0.111: 605 0.111 - 0.166: 40 0.166 - 0.222: 10 0.222 - 0.277: 23 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=" C2' C C 18 " pdb=" C3' C C 18 " pdb=" O2' C C 18 " pdb=" C1' C C 18 " both_signs ideal model delta sigma weight residual False -2.79 -2.52 -0.27 2.00e-01 2.50e+01 1.88e+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: 0.06 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: 1.690 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: 0.030 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 32.290 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 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= 0.156 Angle : 0.920 63.150 38776 Z= 0.355 Chirality : 0.043 0.277 4506 Planarity : 0.003 0.069 4850 Dihedral : 14.758 89.859 10520 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/Z covalent geometry : bond 0.00253 / 0.13 (28630) covalent geometry : angle 0.59471 / 0.32 (38732) SS BOND : bond 0.00244 / 0.12 ( 4) SS BOND : angle 9.53810 / 4.69 ( 8) hydrogen bonds : bond 0.13370 / 9.24 ( 1292) hydrogen bonds : angle 5.96169 / 4.07 ( 3768) metal coordination : bond 0.06798 / 3.99 ( 32) metal coordination : angle 22.58593 / 12.65 ( 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 : 1.187 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: 0.2012 time to fit residues: 291.9882 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 : 1.082 ------------------------------------------------------------------------------- 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... 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 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** D1405 HIS 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 Total number of N/Q/H flips: 53 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.175551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.141544 restraints weight = 46856.407| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 2.96 r_work: 0.3661 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.120 28666 Z= 0.203 Angle : 0.759 21.122 38776 Z= 0.360 Chirality : 0.047 0.660 4506 Planarity : 0.004 0.073 4850 Dihedral : 8.551 132.423 4026 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.81 % Favored : 88.07 % Rotamer: Outliers : 5.02 % Allowed : 17.36 % Favored : 77.62 % 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: 1694 sheet: -1.97 (0.28), residues: 294 loop : -3.45 (0.15), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 423 TYR 0.019 0.002 TYR D2095 PHE 0.022 0.002 PHE D 533 TRP 0.012 0.002 TRP A2125 HIS 0.004 0.001 HIS D1954 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.20 (28630) covalent geometry : angle 0.73388 / 0.36 (38732) SS BOND : bond 0.00516 / 0.25 ( 4) SS BOND : angle 2.53005 / 1.50 ( 8) hydrogen bonds : bond 0.03742 / 2.51 ( 1292) hydrogen bonds : angle 5.08322 / 3.48 ( 3768) metal coordination : bond 0.02555 / 1.24 ( 32) metal coordination : angle 6.31382 / 3.96 ( 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 818 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 662 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7914 (mm-30) REVERT: A 341 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.8072 (mmmt) REVERT: A 376 ARG cc_start: 0.7387 (mmt180) cc_final: 0.6984 (mmt180) REVERT: A 401 LYS cc_start: 0.8845 (mmtm) cc_final: 0.8540 (mmtm) REVERT: A 438 GLN cc_start: 0.6324 (pp30) cc_final: 0.5903 (pp30) REVERT: A 591 MET cc_start: 0.7974 (ttm) cc_final: 0.7726 (ttm) REVERT: A 713 ARG cc_start: 0.8443 (ttt-90) cc_final: 0.8152 (ttt-90) REVERT: A 1150 GLU cc_start: 0.7835 (tm-30) cc_final: 0.7271 (tm-30) REVERT: A 1463 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.7440 (pp30) REVERT: A 1623 LYS cc_start: 0.9012 (ttmt) cc_final: 0.8388 (tttt) REVERT: A 1670 LYS cc_start: 0.8352 (mtmt) cc_final: 0.8062 (mtmt) REVERT: A 1717 TRP cc_start: 0.8563 (p-90) cc_final: 0.7884 (p-90) REVERT: A 2051 LEU cc_start: 0.7008 (tp) cc_final: 0.6603 (tt) REVERT: D 376 ARG cc_start: 0.7387 (mmt180) cc_final: 0.6999 (mmt180) REVERT: D 401 LYS cc_start: 0.8854 (mmtm) cc_final: 0.8543 (mmtm) REVERT: D 438 GLN cc_start: 0.6285 (pp30) cc_final: 0.5856 (pp30) REVERT: D 476 GLN cc_start: 0.8066 (tm-30) cc_final: 0.7864 (tm-30) REVERT: D 591 MET cc_start: 0.7964 (ttm) cc_final: 0.7739 (ttm) REVERT: D 713 ARG cc_start: 0.8316 (ttt-90) cc_final: 0.8035 (ttt-90) REVERT: D 1150 GLU cc_start: 0.7853 (tm-30) cc_final: 0.7250 (tm-30) REVERT: D 1463 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7475 (pp30) REVERT: D 1623 LYS cc_start: 0.9051 (ttmt) cc_final: 0.8458 (tttm) REVERT: D 1654 ILE cc_start: 0.7854 (mp) cc_final: 0.7417 (mp) REVERT: D 1693 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8930 (pp) REVERT: D 1717 TRP cc_start: 0.8562 (p-90) cc_final: 0.7943 (p-90) REVERT: D 1782 MET cc_start: 0.8750 (mmm) cc_final: 0.7838 (ppp) REVERT: E 65 MET cc_start: 0.7900 (mtm) cc_final: 0.7685 (mtm) outliers start: 156 outliers final: 98 residues processed: 769 average time/residue: 0.1769 time to fit residues: 220.3327 Evaluate side-chains 668 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 566 time to evaluate : 1.069 ------------------------------------------------------------------------------- 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 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 540 VAL 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 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 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 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: 0.8980 chunk 308 optimal weight: 0.5980 chunk 157 optimal weight: 40.0000 chunk 350 optimal weight: 7.9990 chunk 282 optimal weight: 0.8980 chunk 39 optimal weight: 0.3980 chunk 166 optimal weight: 0.1980 chunk 304 optimal weight: 0.6980 chunk 241 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 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 A1712 ASN A1738 GLN ** A1886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1984 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2074 GLN A2146 HIS B 55 HIS ** D 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 704 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 771 GLN ** D 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1738 GLN ** D1886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1984 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2074 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.178370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.143431 restraints weight = 46973.089| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 3.07 r_work: 0.3710 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.121 28666 Z= 0.125 Angle : 0.693 14.085 38776 Z= 0.327 Chirality : 0.044 0.347 4506 Planarity : 0.004 0.041 4850 Dihedral : 8.079 136.218 3993 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.67 % Favored : 89.31 % Rotamer: Outliers : 4.34 % Allowed : 19.36 % Favored : 76.30 % 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: -1.97 (0.14), residues: 3488 helix: 0.37 (0.13), residues: 1706 sheet: -1.73 (0.28), residues: 296 loop : -3.37 (0.15), residues: 1486 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 0.023 0.001 PHE D 475 TRP 0.008 0.001 TRP A1192 HIS 0.004 0.001 HIS D1954 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (28630) covalent geometry : angle 0.66655 / 0.32 (38732) SS BOND : bond 0.00389 / 0.19 ( 4) SS BOND : angle 2.92543 / 1.62 ( 8) hydrogen bonds : bond 0.03357 / 2.24 ( 1292) hydrogen bonds : angle 4.88848 / 3.34 ( 3768) metal coordination : bond 0.02431 / 1.64 ( 32) metal coordination : angle 6.09019 / 3.79 ( 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 779 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 644 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7851 (mm-30) REVERT: A 322 ASN cc_start: 0.8496 (t0) cc_final: 0.8217 (t0) REVERT: A 341 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.8057 (mmmt) REVERT: A 376 ARG cc_start: 0.7359 (mmt180) cc_final: 0.6876 (mmt180) REVERT: A 398 GLU cc_start: 0.7395 (mt-10) cc_final: 0.7115 (mp0) REVERT: A 401 LYS cc_start: 0.8863 (mmtm) cc_final: 0.8515 (mmtm) REVERT: A 438 GLN cc_start: 0.6279 (pp30) cc_final: 0.5822 (pp30) REVERT: A 526 ARG cc_start: 0.7342 (mtt-85) cc_final: 0.6902 (mtt90) REVERT: A 591 MET cc_start: 0.7892 (ttm) cc_final: 0.7650 (ttm) REVERT: A 630 THR cc_start: 0.8433 (m) cc_final: 0.8054 (p) REVERT: A 713 ARG cc_start: 0.8431 (ttt-90) cc_final: 0.8176 (ttt-90) REVERT: A 783 CYS cc_start: 0.8583 (t) cc_final: 0.8094 (t) REVERT: A 1141 MET cc_start: 0.8495 (mmp) cc_final: 0.7879 (mmt) REVERT: A 1150 GLU cc_start: 0.7855 (tm-30) cc_final: 0.7284 (tm-30) REVERT: A 1623 LYS cc_start: 0.8952 (ttmt) cc_final: 0.8312 (tttt) REVERT: A 1717 TRP cc_start: 0.8522 (p-90) cc_final: 0.7830 (p-90) REVERT: A 1782 MET cc_start: 0.8723 (mmm) cc_final: 0.7926 (ppp) REVERT: D 268 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7875 (mm-30) REVERT: D 336 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8614 (mmmt) REVERT: D 376 ARG cc_start: 0.7330 (mmt180) cc_final: 0.6861 (mmt180) REVERT: D 401 LYS cc_start: 0.8862 (mmtm) cc_final: 0.8509 (mmtm) REVERT: D 438 GLN cc_start: 0.6288 (pp30) cc_final: 0.5801 (pp30) REVERT: D 591 MET cc_start: 0.7874 (ttm) cc_final: 0.7613 (ttm) REVERT: D 630 THR cc_start: 0.8432 (m) cc_final: 0.8049 (p) REVERT: D 697 LEU cc_start: 0.8523 (tp) cc_final: 0.8238 (tp) REVERT: D 713 ARG cc_start: 0.8350 (ttt-90) cc_final: 0.8142 (ttt-90) REVERT: D 1141 MET cc_start: 0.8455 (mmp) cc_final: 0.7840 (mmt) REVERT: D 1150 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7281 (tm-30) REVERT: D 1536 CYS cc_start: 0.7320 (m) cc_final: 0.6477 (t) REVERT: D 1623 LYS cc_start: 0.9016 (ttmt) cc_final: 0.8359 (tttm) REVERT: D 1693 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8786 (pp) REVERT: D 1717 TRP cc_start: 0.8514 (p-90) cc_final: 0.7931 (p-90) REVERT: D 1782 MET cc_start: 0.8728 (mmm) cc_final: 0.7911 (ppp) REVERT: D 1978 ASP cc_start: 0.7875 (p0) cc_final: 0.7404 (p0) REVERT: E 65 MET cc_start: 0.7819 (mtm) cc_final: 0.7588 (mtm) outliers start: 135 outliers final: 82 residues processed: 741 average time/residue: 0.1771 time to fit residues: 214.9980 Evaluate side-chains 672 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 587 time to evaluate : 1.348 ------------------------------------------------------------------------------- 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 261 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 341 LYS 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 658 GLU Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1135 ASP Chi-restraints excluded: chain A residue 1212 THR Chi-restraints excluded: chain A residue 1237 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 1544 VAL Chi-restraints excluded: chain A residue 1552 LEU 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 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 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 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 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 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 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 2099 PHE Chi-restraints excluded: chain D residue 2151 LYS Chi-restraints excluded: chain E residue 51 THR 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: 4.9990 chunk 91 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 252 optimal weight: 5.9990 chunk 352 optimal weight: 9.9990 chunk 58 optimal weight: 0.0870 chunk 152 optimal weight: 30.0000 chunk 123 optimal weight: 1.9990 chunk 67 optimal weight: 0.0020 chunk 346 optimal weight: 0.8980 overall best weight: 1.5970 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 348 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 ** 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 189 HIS D 644 ASN D 698 ASN ** D 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1712 ASN D1738 GLN D1954 HIS D1984 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.175331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.138959 restraints weight = 46675.815| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 2.74 r_work: 0.3666 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 28666 Z= 0.163 Angle : 0.706 13.765 38776 Z= 0.339 Chirality : 0.044 0.328 4506 Planarity : 0.004 0.046 4850 Dihedral : 7.862 135.056 3974 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.61 % Favored : 88.27 % Rotamer: Outliers : 4.57 % Allowed : 20.48 % Favored : 74.95 % 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: -1.84 (0.14), residues: 3488 helix: 0.46 (0.13), residues: 1706 sheet: -1.62 (0.29), residues: 298 loop : -3.29 (0.15), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 789 TYR 0.017 0.001 TYR A 534 PHE 0.020 0.002 PHE A 475 TRP 0.007 0.001 TRP A1192 HIS 0.008 0.001 HIS A1954 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 (28630) covalent geometry : angle 0.68540 / 0.34 (38732) SS BOND : bond 0.00522 / 0.26 ( 4) SS BOND : angle 2.59964 / 1.34 ( 8) hydrogen bonds : bond 0.03375 / 2.23 ( 1292) hydrogen bonds : angle 4.86853 / 3.32 ( 3768) metal coordination : bond 0.01066 / 0.62 ( 32) metal coordination : angle 5.48961 / 3.43 ( 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 763 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 621 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 LYS cc_start: 0.7425 (OUTLIER) cc_final: 0.7052 (pttm) REVERT: A 236 ARG cc_start: 0.8719 (mtp85) cc_final: 0.8516 (mtp85) REVERT: A 322 ASN cc_start: 0.8464 (t0) cc_final: 0.8221 (t0) REVERT: A 376 ARG cc_start: 0.7456 (mmt180) cc_final: 0.7021 (mmt180) REVERT: A 398 GLU cc_start: 0.7474 (mt-10) cc_final: 0.7145 (mp0) REVERT: A 401 LYS cc_start: 0.8923 (mmtm) cc_final: 0.8570 (mmtm) REVERT: A 438 GLN cc_start: 0.6425 (pp30) cc_final: 0.5933 (pp30) REVERT: A 476 GLN cc_start: 0.7963 (tm-30) cc_final: 0.7757 (tm-30) REVERT: A 526 ARG cc_start: 0.7434 (mtt-85) cc_final: 0.6947 (mtt90) REVERT: A 595 MET cc_start: 0.8407 (mmm) cc_final: 0.8187 (mtt) REVERT: A 783 CYS cc_start: 0.8562 (t) cc_final: 0.8090 (t) REVERT: A 1141 MET cc_start: 0.8503 (mmp) cc_final: 0.7941 (mmt) REVERT: A 1150 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7304 (tm-30) REVERT: A 1207 MET cc_start: 0.8060 (mmm) cc_final: 0.7786 (mmm) REVERT: A 1513 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7674 (mt-10) REVERT: A 1623 LYS cc_start: 0.8985 (ttmt) cc_final: 0.8335 (tttm) REVERT: A 1717 TRP cc_start: 0.8551 (p-90) cc_final: 0.7883 (p-90) REVERT: A 1782 MET cc_start: 0.8771 (mmm) cc_final: 0.7918 (ppp) REVERT: D 336 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8647 (mmmt) REVERT: D 376 ARG cc_start: 0.7434 (mmt180) cc_final: 0.6989 (mmt180) REVERT: D 401 LYS cc_start: 0.8949 (mmtm) cc_final: 0.8583 (mmtm) REVERT: D 438 GLN cc_start: 0.6433 (pp30) cc_final: 0.5999 (pp30) REVERT: D 595 MET cc_start: 0.8396 (mmm) cc_final: 0.8187 (mtt) REVERT: D 1141 MET cc_start: 0.8484 (mmp) cc_final: 0.7912 (mmt) REVERT: D 1150 GLU cc_start: 0.7868 (tm-30) cc_final: 0.7232 (tm-30) REVERT: D 1623 LYS cc_start: 0.9020 (ttmt) cc_final: 0.8369 (tttm) REVERT: D 1717 TRP cc_start: 0.8484 (p-90) cc_final: 0.7921 (p-90) REVERT: E 65 MET cc_start: 0.7851 (mtm) cc_final: 0.7626 (mtm) outliers start: 142 outliers final: 101 residues processed: 721 average time/residue: 0.1761 time to fit residues: 206.1278 Evaluate side-chains 664 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 561 time to evaluate : 1.009 ------------------------------------------------------------------------------- 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 348 ASN Chi-restraints excluded: chain A residue 351 LEU 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 565 MET 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 735 VAL Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1135 ASP 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 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 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 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 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 565 MET 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 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 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 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 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: 0.1980 chunk 254 optimal weight: 6.9990 chunk 295 optimal weight: 0.0770 chunk 75 optimal weight: 3.9990 chunk 219 optimal weight: 0.6980 chunk 286 optimal weight: 2.9990 chunk 128 optimal weight: 0.4980 chunk 221 optimal weight: 0.9990 chunk 248 optimal weight: 0.9980 chunk 285 optimal weight: 1.9990 chunk 244 optimal weight: 0.0970 overall best weight: 0.3136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 472 HIS ** 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 788 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 ** A1886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 704 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1231 HIS ** 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.178916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.144664 restraints weight = 46592.599| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 3.03 r_work: 0.3714 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2533 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= 0.120 Angle : 0.686 15.200 38776 Z= 0.330 Chirality : 0.044 0.251 4506 Planarity : 0.004 0.055 4850 Dihedral : 7.718 134.942 3970 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.12 % Favored : 88.88 % Rotamer: Outliers : 4.34 % Allowed : 21.48 % 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: -1.73 (0.14), residues: 3488 helix: 0.54 (0.13), residues: 1702 sheet: -1.39 (0.30), residues: 290 loop : -3.25 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 231 TYR 0.016 0.001 TYR D 558 PHE 0.026 0.001 PHE A 475 TRP 0.011 0.001 TRP A1192 HIS 0.003 0.000 HIS A1791 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (28630) covalent geometry : angle 0.67125 / 0.33 (38732) SS BOND : bond 0.00269 / 0.13 ( 4) SS BOND : angle 1.94449 / 1.11 ( 8) hydrogen bonds : bond 0.03166 / 2.11 ( 1292) hydrogen bonds : angle 4.73212 / 3.23 ( 3768) metal coordination : bond 0.00788 / 0.46 ( 32) metal coordination : angle 4.54598 / 2.84 ( 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 763 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 628 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 LYS cc_start: 0.7198 (OUTLIER) cc_final: 0.6729 (pttm) REVERT: A 268 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7884 (mm-30) REVERT: A 322 ASN cc_start: 0.8445 (t0) cc_final: 0.8212 (t0) REVERT: A 376 ARG cc_start: 0.7311 (mmt180) cc_final: 0.6946 (mmt180) REVERT: A 398 GLU cc_start: 0.7461 (mt-10) cc_final: 0.7140 (mp0) REVERT: A 401 LYS cc_start: 0.8930 (mmtm) cc_final: 0.8511 (mmtm) REVERT: A 438 GLN cc_start: 0.6308 (pp30) cc_final: 0.5836 (pp30) REVERT: A 526 ARG cc_start: 0.7442 (mtt-85) cc_final: 0.6994 (mtt90) REVERT: A 595 MET cc_start: 0.8422 (mmm) cc_final: 0.8164 (mtt) REVERT: A 630 THR cc_start: 0.8361 (m) cc_final: 0.7991 (p) REVERT: A 1141 MET cc_start: 0.8456 (mmp) cc_final: 0.7898 (mmt) REVERT: A 1150 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7316 (tm-30) REVERT: A 1623 LYS cc_start: 0.8876 (ttmt) cc_final: 0.8145 (tttm) REVERT: A 1670 LYS cc_start: 0.8392 (mttt) cc_final: 0.8189 (mttp) REVERT: A 1717 TRP cc_start: 0.8526 (p-90) cc_final: 0.7863 (p-90) REVERT: A 1782 MET cc_start: 0.8746 (mmm) cc_final: 0.7949 (ppp) REVERT: A 1791 HIS cc_start: 0.8767 (m-70) cc_final: 0.8429 (m-70) REVERT: A 1794 LYS cc_start: 0.8794 (mtpp) cc_final: 0.8466 (mtmt) REVERT: D 227 LYS cc_start: 0.7172 (OUTLIER) cc_final: 0.6848 (pttm) REVERT: D 268 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7893 (mm-30) REVERT: D 322 ASN cc_start: 0.8397 (t0) cc_final: 0.8042 (t0) REVERT: D 332 SER cc_start: 0.8926 (p) cc_final: 0.8608 (m) REVERT: D 336 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8612 (mmmt) REVERT: D 363 ASP cc_start: 0.8648 (m-30) cc_final: 0.8396 (t0) REVERT: D 376 ARG cc_start: 0.7341 (mmt180) cc_final: 0.7067 (mmt180) REVERT: D 385 MET cc_start: 0.7712 (mtm) cc_final: 0.7430 (mtp) REVERT: D 401 LYS cc_start: 0.8943 (mmtm) cc_final: 0.8537 (mmtm) REVERT: D 438 GLN cc_start: 0.6289 (pp30) cc_final: 0.5819 (pp30) REVERT: D 595 MET cc_start: 0.8419 (mmm) cc_final: 0.8131 (mtt) REVERT: D 630 THR cc_start: 0.8372 (m) cc_final: 0.7992 (p) REVERT: D 1141 MET cc_start: 0.8555 (mmp) cc_final: 0.7994 (mmt) REVERT: D 1150 GLU cc_start: 0.7868 (tm-30) cc_final: 0.7286 (tm-30) REVERT: D 1207 MET cc_start: 0.7959 (mmm) cc_final: 0.7656 (mmm) REVERT: D 1623 LYS cc_start: 0.8968 (ttmt) cc_final: 0.8253 (tttm) REVERT: D 1717 TRP cc_start: 0.8433 (p-90) cc_final: 0.7899 (p-90) REVERT: D 1782 MET cc_start: 0.8750 (mmm) cc_final: 0.7960 (ppp) REVERT: D 1794 LYS cc_start: 0.8829 (mtpp) cc_final: 0.8504 (mtmt) outliers start: 135 outliers final: 91 residues processed: 723 average time/residue: 0.1684 time to fit residues: 200.1838 Evaluate side-chains 670 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 576 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU 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 375 LEU 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 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 1135 ASP 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 1409 CYS Chi-restraints excluded: chain A residue 1413 THR Chi-restraints excluded: chain A residue 1425 GLN 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 1544 VAL Chi-restraints excluded: chain A residue 1625 MET 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 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 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 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 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 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 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 1425 GLN Chi-restraints excluded: chain D residue 1427 ILE Chi-restraints excluded: chain D residue 1455 THR 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 1842 SER 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: 3.9990 chunk 295 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 44 optimal weight: 8.9990 chunk 154 optimal weight: 7.9990 chunk 345 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 228 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 ASN ** A 704 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 717 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** A1308 GLN A1712 ASN ** A1886 ASN ** 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** D1308 GLN D1712 ASN ** D1738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.178013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.143842 restraints weight = 47058.688| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 2.94 r_work: 0.3703 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28666 Z= 0.129 Angle : 0.689 13.557 38776 Z= 0.330 Chirality : 0.043 0.284 4506 Planarity : 0.004 0.058 4850 Dihedral : 7.653 133.901 3966 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.24 % Favored : 88.70 % Rotamer: Outliers : 4.37 % Allowed : 21.96 % Favored : 73.67 % 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: 0.61 (0.13), residues: 1698 sheet: -1.20 (0.31), residues: 282 loop : -3.21 (0.15), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 231 TYR 0.013 0.001 TYR D 558 PHE 0.035 0.002 PHE A1148 TRP 0.008 0.001 TRP D1192 HIS 0.002 0.001 HIS D1735 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (28630) covalent geometry : angle 0.66842 / 0.33 (38732) SS BOND : bond 0.00505 / 0.26 ( 4) SS BOND : angle 2.02230 / 1.24 ( 8) hydrogen bonds : bond 0.03207 / 2.13 ( 1292) hydrogen bonds : angle 4.70806 / 3.21 ( 3768) metal coordination : bond 0.00874 / 0.51 ( 32) metal coordination : angle 5.48559 / 3.58 ( 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 741 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 605 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7911 (mm-30) REVERT: A 322 ASN cc_start: 0.8364 (t0) cc_final: 0.8155 (t0) REVERT: A 350 LEU cc_start: 0.9437 (mm) cc_final: 0.9084 (mm) REVERT: A 376 ARG cc_start: 0.7375 (mmt180) cc_final: 0.7080 (mmt180) REVERT: A 398 GLU cc_start: 0.7439 (mt-10) cc_final: 0.7074 (mp0) REVERT: A 401 LYS cc_start: 0.8926 (mmtm) cc_final: 0.8555 (mmtm) REVERT: A 438 GLN cc_start: 0.6403 (pp30) cc_final: 0.5906 (pp30) REVERT: A 526 ARG cc_start: 0.7441 (mtt-85) cc_final: 0.6991 (mtt90) REVERT: A 793 LYS cc_start: 0.9068 (mttt) cc_final: 0.8847 (mttt) REVERT: A 1141 MET cc_start: 0.8475 (mmp) cc_final: 0.7959 (mmt) REVERT: A 1150 GLU cc_start: 0.7863 (tm-30) cc_final: 0.7330 (tm-30) REVERT: A 1623 LYS cc_start: 0.8918 (ttmt) cc_final: 0.8182 (tttm) REVERT: A 1654 ILE cc_start: 0.7716 (mp) cc_final: 0.7188 (mp) REVERT: A 1670 LYS cc_start: 0.8361 (mttt) cc_final: 0.8112 (mttp) REVERT: A 1717 TRP cc_start: 0.8503 (p-90) cc_final: 0.7905 (p-90) REVERT: A 1782 MET cc_start: 0.8771 (mmm) cc_final: 0.7953 (ppp) REVERT: A 1791 HIS cc_start: 0.8766 (m-70) cc_final: 0.8512 (m-70) REVERT: A 1794 LYS cc_start: 0.8810 (mtpp) cc_final: 0.8609 (mtmt) REVERT: D 60 CYS cc_start: 0.2061 (OUTLIER) cc_final: 0.1824 (t) REVERT: D 227 LYS cc_start: 0.7035 (OUTLIER) cc_final: 0.6695 (pttm) REVERT: D 268 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7908 (mm-30) REVERT: D 322 ASN cc_start: 0.8327 (t0) cc_final: 0.8003 (t0) REVERT: D 336 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8625 (mmmt) REVERT: D 401 LYS cc_start: 0.8943 (mmtm) cc_final: 0.8590 (mmtm) REVERT: D 438 GLN cc_start: 0.6394 (pp30) cc_final: 0.6174 (pp30) REVERT: D 595 MET cc_start: 0.8424 (mmm) cc_final: 0.8217 (mtt) REVERT: D 1141 MET cc_start: 0.8439 (mmp) cc_final: 0.7899 (mmt) REVERT: D 1150 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7257 (tm-30) REVERT: D 1623 LYS cc_start: 0.8966 (ttmt) cc_final: 0.8273 (tttm) REVERT: D 1717 TRP cc_start: 0.8463 (p-90) cc_final: 0.7941 (p-90) REVERT: D 1782 MET cc_start: 0.8744 (mmm) cc_final: 0.7986 (ppp) REVERT: D 1791 HIS cc_start: 0.8748 (m-70) cc_final: 0.8485 (m-70) REVERT: D 1794 LYS cc_start: 0.8870 (mtpp) cc_final: 0.8540 (mtmt) REVERT: D 2028 LEU cc_start: 0.1385 (OUTLIER) cc_final: 0.1073 (tm) outliers start: 136 outliers final: 108 residues processed: 705 average time/residue: 0.1762 time to fit residues: 204.5254 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 : 1.089 ------------------------------------------------------------------------------- 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 375 LEU 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 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 1135 ASP 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 1409 CYS Chi-restraints excluded: chain A residue 1413 THR Chi-restraints excluded: chain A residue 1425 GLN 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 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 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 60 CYS 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 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 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 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 1138 THR 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 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 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 1954 HIS 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 110 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 193 optimal weight: 0.9990 chunk 283 optimal weight: 0.7980 chunk 306 optimal weight: 0.0970 chunk 244 optimal weight: 3.9990 chunk 352 optimal weight: 20.0000 chunk 231 optimal weight: 0.9990 chunk 312 optimal weight: 1.9990 chunk 158 optimal weight: 0.6980 chunk 177 optimal weight: 10.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 288 ASN ** A 704 HIS ** 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** A1712 ASN ** A1886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1984 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 288 ASN ** D 704 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1292 GLN D1712 ASN ** D1738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1833 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1984 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.178848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.144714 restraints weight = 46816.004| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 2.97 r_work: 0.3723 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2835 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= 0.128 Angle : 0.689 12.018 38776 Z= 0.332 Chirality : 0.043 0.267 4506 Planarity : 0.004 0.063 4850 Dihedral : 7.626 133.548 3966 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.18 % Favored : 88.82 % Rotamer: Outliers : 4.31 % Allowed : 23.25 % Favored : 72.44 % 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: -1.57 (0.14), residues: 3488 helix: 0.64 (0.13), residues: 1700 sheet: -1.20 (0.31), residues: 288 loop : -3.14 (0.15), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 231 TYR 0.013 0.001 TYR A 558 PHE 0.027 0.001 PHE A 475 TRP 0.008 0.001 TRP D1351 HIS 0.013 0.001 HIS D1751 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (28630) covalent geometry : angle 0.67254 / 0.33 (38732) SS BOND : bond 0.00365 / 0.18 ( 4) SS BOND : angle 1.89223 / 1.16 ( 8) hydrogen bonds : bond 0.03160 / 2.11 ( 1292) hydrogen bonds : angle 4.64956 / 3.17 ( 3768) metal coordination : bond 0.00811 / 0.47 ( 32) metal coordination : angle 4.96159 / 3.23 ( 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 734 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 600 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7859 (mm-30) REVERT: A 322 ASN cc_start: 0.8385 (t0) cc_final: 0.8170 (t0) REVERT: A 350 LEU cc_start: 0.9411 (mm) cc_final: 0.9027 (mm) REVERT: A 376 ARG cc_start: 0.7313 (mmt180) cc_final: 0.7056 (mmt180) REVERT: A 398 GLU cc_start: 0.7424 (mt-10) cc_final: 0.7055 (mp0) REVERT: A 401 LYS cc_start: 0.8905 (mmtm) cc_final: 0.8538 (mmtm) REVERT: A 438 GLN cc_start: 0.6307 (pp30) cc_final: 0.5826 (pp30) REVERT: A 526 ARG cc_start: 0.7440 (mtt-85) cc_final: 0.7035 (mtt90) REVERT: A 630 THR cc_start: 0.8378 (m) cc_final: 0.8005 (p) REVERT: A 1141 MET cc_start: 0.8439 (mmp) cc_final: 0.7933 (mmt) REVERT: A 1148 PHE cc_start: 0.9076 (t80) cc_final: 0.8777 (t80) REVERT: A 1150 GLU cc_start: 0.7795 (tm-30) cc_final: 0.7307 (tm-30) REVERT: A 1623 LYS cc_start: 0.8905 (ttmt) cc_final: 0.8172 (tttm) REVERT: A 1654 ILE cc_start: 0.7736 (mp) cc_final: 0.7280 (mp) REVERT: A 1717 TRP cc_start: 0.8502 (p-90) cc_final: 0.7947 (p-90) REVERT: A 1765 MET cc_start: 0.5209 (mmm) cc_final: 0.4696 (mmm) REVERT: A 1791 HIS cc_start: 0.8686 (m-70) cc_final: 0.8451 (m-70) REVERT: A 1794 LYS cc_start: 0.8815 (mtpp) cc_final: 0.8608 (mtmt) REVERT: D 60 CYS cc_start: 0.2037 (OUTLIER) cc_final: 0.1753 (t) REVERT: D 116 TRP cc_start: 0.5120 (OUTLIER) cc_final: 0.3541 (t60) REVERT: D 120 MET cc_start: 0.3607 (mmm) cc_final: 0.2979 (mtt) REVERT: D 227 LYS cc_start: 0.7111 (OUTLIER) cc_final: 0.6721 (pttm) REVERT: D 268 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7865 (mm-30) REVERT: D 322 ASN cc_start: 0.8299 (t0) cc_final: 0.8002 (t0) REVERT: D 332 SER cc_start: 0.8955 (p) cc_final: 0.8625 (m) REVERT: D 336 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8632 (mmmt) REVERT: D 363 ASP cc_start: 0.8700 (m-30) cc_final: 0.8422 (t0) REVERT: D 401 LYS cc_start: 0.8916 (mmtm) cc_final: 0.8565 (mmtm) REVERT: D 481 PHE cc_start: 0.7887 (t80) cc_final: 0.6679 (t80) REVERT: D 484 MET cc_start: 0.7350 (ppp) cc_final: 0.7133 (ppp) REVERT: D 630 THR cc_start: 0.8378 (m) cc_final: 0.8025 (p) REVERT: D 1141 MET cc_start: 0.8470 (mmp) cc_final: 0.7974 (mmt) REVERT: D 1148 PHE cc_start: 0.9067 (t80) cc_final: 0.8840 (t80) REVERT: D 1150 GLU cc_start: 0.7782 (tm-30) cc_final: 0.7285 (tm-30) REVERT: D 1209 GLU cc_start: 0.7392 (mm-30) cc_final: 0.7163 (mm-30) REVERT: D 1389 MET cc_start: 0.8488 (ptm) cc_final: 0.7156 (ptm) REVERT: D 1513 GLU cc_start: 0.8063 (mp0) cc_final: 0.7555 (mp0) REVERT: D 1623 LYS cc_start: 0.8932 (ttmt) cc_final: 0.8231 (tttm) REVERT: D 1654 ILE cc_start: 0.7739 (mp) cc_final: 0.7330 (mp) REVERT: D 1717 TRP cc_start: 0.8466 (p-90) cc_final: 0.7951 (p-90) REVERT: D 1751 HIS cc_start: 0.7332 (m170) cc_final: 0.7009 (m90) REVERT: D 1782 MET cc_start: 0.8722 (mmm) cc_final: 0.7927 (ppp) REVERT: D 1791 HIS cc_start: 0.8651 (m-70) cc_final: 0.8386 (m-70) REVERT: D 1794 LYS cc_start: 0.8781 (mtpp) cc_final: 0.8474 (mtmt) REVERT: D 2028 LEU cc_start: 0.1478 (OUTLIER) cc_final: 0.1166 (tm) REVERT: E 36 ARG cc_start: 0.7464 (ptt90) cc_final: 0.6019 (ptt90) outliers start: 134 outliers final: 105 residues processed: 697 average time/residue: 0.1672 time to fit residues: 191.9609 Evaluate side-chains 684 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 574 time to evaluate : 1.060 ------------------------------------------------------------------------------- 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 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 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 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 1135 ASP Chi-restraints excluded: chain A residue 1162 ASN Chi-restraints excluded: chain A residue 1202 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 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 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 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 60 CYS 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 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 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 564 VAL Chi-restraints excluded: chain D residue 606 MET Chi-restraints excluded: chain D residue 735 VAL Chi-restraints excluded: chain D residue 798 LEU Chi-restraints excluded: chain D residue 1133 VAL Chi-restraints excluded: chain D residue 1138 THR 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 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 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 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 119 optimal weight: 5.9990 chunk 251 optimal weight: 3.9990 chunk 313 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 chunk 335 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 257 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 704 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 788 ASN ** A1111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1503 ASN A1712 ASN ** A1886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 698 ASN ** D 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1712 ASN ** D1738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1833 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.175613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.141729 restraints weight = 47168.578| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 3.02 r_work: 0.3668 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 28666 Z= 0.161 Angle : 0.715 11.284 38776 Z= 0.349 Chirality : 0.045 0.335 4506 Planarity : 0.004 0.064 4850 Dihedral : 7.635 133.019 3964 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.50 % Favored : 88.39 % Rotamer: Outliers : 4.63 % Allowed : 23.34 % Favored : 72.03 % 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: -1.56 (0.14), residues: 3488 helix: 0.60 (0.13), residues: 1702 sheet: -1.19 (0.32), residues: 290 loop : -3.08 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 347 TYR 0.016 0.001 TYR A2095 PHE 0.029 0.002 PHE A1511 TRP 0.010 0.001 TRP D1351 HIS 0.010 0.001 HIS D1751 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (28630) covalent geometry : angle 0.69785 / 0.35 (38732) SS BOND : bond 0.00436 / 0.21 ( 4) SS BOND : angle 1.89456 / 1.17 ( 8) hydrogen bonds : bond 0.03345 / 2.21 ( 1292) hydrogen bonds : angle 4.71385 / 3.22 ( 3768) metal coordination : bond 0.00986 / 0.57 ( 32) metal coordination : angle 5.14855 / 3.30 ( 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 743 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 599 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 TRP cc_start: 0.5256 (OUTLIER) cc_final: 0.3619 (t60) REVERT: A 120 MET cc_start: 0.3273 (mmm) cc_final: 0.2814 (mtt) REVERT: A 191 LEU cc_start: 0.4565 (OUTLIER) cc_final: 0.4225 (mt) REVERT: A 350 LEU cc_start: 0.9454 (mm) cc_final: 0.9118 (mm) REVERT: A 376 ARG cc_start: 0.7358 (mmt180) cc_final: 0.7120 (mmt180) REVERT: A 398 GLU cc_start: 0.7290 (mt-10) cc_final: 0.6832 (mp0) REVERT: A 526 ARG cc_start: 0.7340 (mtt-85) cc_final: 0.7017 (mtt90) REVERT: A 1141 MET cc_start: 0.8479 (mmp) cc_final: 0.7987 (mmt) REVERT: A 1150 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7324 (tm-30) REVERT: A 1237 GLU cc_start: 0.7489 (mt-10) cc_final: 0.7286 (mt-10) REVERT: A 1389 MET cc_start: 0.8500 (ptm) cc_final: 0.7151 (ptm) REVERT: A 1623 LYS cc_start: 0.8929 (ttmt) cc_final: 0.8204 (tttm) REVERT: A 1654 ILE cc_start: 0.7811 (mp) cc_final: 0.7370 (mp) REVERT: A 1717 TRP cc_start: 0.8565 (p-90) cc_final: 0.7953 (p-90) REVERT: A 1751 HIS cc_start: 0.6971 (m90) cc_final: 0.6626 (m90) REVERT: A 1765 MET cc_start: 0.5467 (mmm) cc_final: 0.5005 (mmm) REVERT: A 1791 HIS cc_start: 0.8721 (m-70) cc_final: 0.8498 (m-70) REVERT: B 36 ARG cc_start: 0.7509 (ptt90) cc_final: 0.5807 (ptt90) REVERT: D 60 CYS cc_start: 0.2486 (OUTLIER) cc_final: 0.2133 (t) REVERT: D 116 TRP cc_start: 0.5227 (OUTLIER) cc_final: 0.3569 (t60) REVERT: D 120 MET cc_start: 0.3592 (mmm) cc_final: 0.2998 (mtt) REVERT: D 227 LYS cc_start: 0.7329 (OUTLIER) cc_final: 0.6810 (pttm) REVERT: D 336 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8563 (mmmt) REVERT: D 401 LYS cc_start: 0.8939 (mmtm) cc_final: 0.8609 (mmtm) REVERT: D 438 GLN cc_start: 0.6599 (pp30) cc_final: 0.6252 (pp30) REVERT: D 1141 MET cc_start: 0.8517 (mmp) cc_final: 0.8060 (mmt) REVERT: D 1148 PHE cc_start: 0.9137 (t80) cc_final: 0.8875 (t80) REVERT: D 1150 GLU cc_start: 0.7833 (tm-30) cc_final: 0.7315 (tm-30) REVERT: D 1237 GLU cc_start: 0.7493 (mt-10) cc_final: 0.7261 (mt-10) REVERT: D 1623 LYS cc_start: 0.8933 (ttmt) cc_final: 0.8226 (tttm) REVERT: D 1751 HIS cc_start: 0.7426 (m170) cc_final: 0.7126 (m90) REVERT: D 1791 HIS cc_start: 0.8688 (m-70) cc_final: 0.8434 (m-70) REVERT: D 2028 LEU cc_start: 0.1524 (OUTLIER) cc_final: 0.1185 (tm) outliers start: 144 outliers final: 110 residues processed: 699 average time/residue: 0.1709 time to fit residues: 195.9846 Evaluate side-chains 689 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 572 time to evaluate : 1.085 ------------------------------------------------------------------------------- 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 191 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 337 ILE 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 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 1135 ASP 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 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 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 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 60 CYS Chi-restraints excluded: chain D residue 116 TRP 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 375 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 606 MET Chi-restraints excluded: chain D residue 667 VAL Chi-restraints excluded: chain D residue 735 VAL Chi-restraints excluded: chain D residue 767 THR 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 1138 THR 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 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 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 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 2128 LEU 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: 4.9990 chunk 262 optimal weight: 2.9990 chunk 248 optimal weight: 4.9990 chunk 293 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 272 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 198 optimal weight: 0.9980 chunk 266 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 288 ASN ** 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 288 ASN ** D 704 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1712 ASN ** D1738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.175724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.139562 restraints weight = 47072.431| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 2.76 r_work: 0.3677 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28666 Z= 0.149 Angle : 0.724 12.071 38776 Z= 0.352 Chirality : 0.045 0.309 4506 Planarity : 0.004 0.069 4850 Dihedral : 7.558 133.744 3961 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.12 % Favored : 88.82 % Rotamer: Outliers : 4.37 % Allowed : 23.60 % Favored : 72.03 % 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: -1.57 (0.14), residues: 3488 helix: 0.59 (0.13), residues: 1702 sheet: -1.36 (0.30), residues: 312 loop : -3.06 (0.15), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG D 789 TYR 0.033 0.001 TYR A 214 PHE 0.045 0.002 PHE A1148 TRP 0.013 0.001 TRP D1351 HIS 0.009 0.001 HIS D1751 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (28630) covalent geometry : angle 0.70770 / 0.35 (38732) SS BOND : bond 0.00411 / 0.20 ( 4) SS BOND : angle 1.76905 / 1.12 ( 8) hydrogen bonds : bond 0.03314 / 2.19 ( 1292) hydrogen bonds : angle 4.70783 / 3.22 ( 3768) metal coordination : bond 0.00854 / 0.50 ( 32) metal coordination : angle 4.97338 / 3.18 ( 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 727 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 591 time to evaluate : 1.049 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: 0.5160 (OUTLIER) cc_final: 0.3520 (t60) REVERT: A 120 MET cc_start: 0.3236 (mmm) cc_final: 0.2785 (mtt) REVERT: A 191 LEU cc_start: 0.4454 (OUTLIER) cc_final: 0.4124 (mt) REVERT: A 268 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7873 (mm-30) REVERT: A 350 LEU cc_start: 0.9455 (mm) cc_final: 0.9114 (mm) REVERT: A 398 GLU cc_start: 0.7261 (mt-10) cc_final: 0.6856 (mp0) REVERT: A 438 GLN cc_start: 0.6583 (pp30) cc_final: 0.6287 (pp30) REVERT: A 1141 MET cc_start: 0.8484 (mmp) cc_final: 0.8025 (mmt) REVERT: A 1150 GLU cc_start: 0.7796 (tm-30) cc_final: 0.7317 (tm-30) REVERT: A 1237 GLU cc_start: 0.7478 (mt-10) cc_final: 0.7274 (mt-10) REVERT: A 1623 LYS cc_start: 0.8966 (ttmt) cc_final: 0.8227 (tttm) REVERT: A 1654 ILE cc_start: 0.7910 (mp) cc_final: 0.7365 (mp) REVERT: A 1717 TRP cc_start: 0.8529 (p-90) cc_final: 0.7930 (p-90) REVERT: A 1751 HIS cc_start: 0.6912 (m90) cc_final: 0.6553 (m90) REVERT: A 1765 MET cc_start: 0.5492 (mmm) cc_final: 0.5068 (mmm) REVERT: A 1782 MET cc_start: 0.8733 (mmm) cc_final: 0.8029 (ppp) REVERT: A 1791 HIS cc_start: 0.8657 (m-70) cc_final: 0.8404 (m-70) REVERT: A 2028 LEU cc_start: 0.1645 (OUTLIER) cc_final: 0.1298 (tm) REVERT: D 60 CYS cc_start: 0.2452 (OUTLIER) cc_final: 0.2072 (t) REVERT: D 116 TRP cc_start: 0.5231 (OUTLIER) cc_final: 0.3574 (t60) REVERT: D 120 MET cc_start: 0.3634 (mmm) cc_final: 0.3026 (mtt) REVERT: D 191 LEU cc_start: 0.4594 (OUTLIER) cc_final: 0.4224 (mt) REVERT: D 268 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7892 (mm-30) REVERT: D 336 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8593 (mmmt) REVERT: D 401 LYS cc_start: 0.8928 (mmtm) cc_final: 0.8583 (mmtm) REVERT: D 438 GLN cc_start: 0.6571 (pp30) cc_final: 0.6284 (pp30) REVERT: D 1141 MET cc_start: 0.8458 (mmp) cc_final: 0.8023 (mmp) REVERT: D 1148 PHE cc_start: 0.9128 (t80) cc_final: 0.8906 (t80) REVERT: D 1150 GLU cc_start: 0.7797 (tm-30) cc_final: 0.7288 (tm-30) REVERT: D 1237 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7343 (mt-10) REVERT: D 1623 LYS cc_start: 0.8907 (ttmt) cc_final: 0.8191 (tttm) REVERT: D 1654 ILE cc_start: 0.7884 (mp) cc_final: 0.7548 (mp) REVERT: D 1751 HIS cc_start: 0.7490 (m170) cc_final: 0.7201 (m90) REVERT: D 1782 MET cc_start: 0.8688 (mmm) cc_final: 0.7915 (ppp) REVERT: D 1791 HIS cc_start: 0.8644 (m-70) cc_final: 0.8388 (m-70) REVERT: D 2028 LEU cc_start: 0.1582 (OUTLIER) cc_final: 0.1243 (tm) outliers start: 136 outliers final: 111 residues processed: 685 average time/residue: 0.1710 time to fit residues: 193.4550 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 : 0.923 ------------------------------------------------------------------------------- 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 191 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 337 ILE 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 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 772 THR Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1135 ASP 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 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 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 1968 VAL Chi-restraints excluded: chain A residue 1998 VAL 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 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 60 CYS Chi-restraints excluded: chain D residue 116 TRP Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 191 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 261 THR Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 336 LYS Chi-restraints excluded: chain D residue 375 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 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 1138 THR Chi-restraints excluded: chain D residue 1162 ASN Chi-restraints excluded: chain D residue 1165 LYS 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 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 1773 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 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 325 optimal weight: 9.9990 chunk 18 optimal weight: 0.2980 chunk 139 optimal weight: 0.0980 chunk 348 optimal weight: 7.9990 chunk 224 optimal weight: 0.9990 chunk 263 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 100 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 220 optimal weight: 0.6980 chunk 175 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 698 ASN ** A 704 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1154 ASN ** A1231 HIS ** 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 149 ASN D 568 GLN ** D 704 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 788 ASN ** D1111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1712 ASN ** D1738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.177834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.144988 restraints weight = 47118.550| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 2.95 r_work: 0.3703 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28666 Z= 0.131 Angle : 0.726 10.492 38776 Z= 0.352 Chirality : 0.044 0.269 4506 Planarity : 0.004 0.073 4850 Dihedral : 7.496 133.523 3961 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.04 % Favored : 88.93 % Rotamer: Outliers : 3.70 % Allowed : 24.50 % Favored : 71.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.14), residues: 3488 helix: 0.67 (0.13), residues: 1680 sheet: -1.33 (0.30), residues: 312 loop : -3.00 (0.16), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 376 TYR 0.030 0.001 TYR A 214 PHE 0.044 0.002 PHE A1148 TRP 0.013 0.001 TRP D1351 HIS 0.008 0.001 HIS D1751 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (28630) covalent geometry : angle 0.71091 / 0.35 (38732) SS BOND : bond 0.00316 / 0.16 ( 4) SS BOND : angle 1.66863 / 1.05 ( 8) hydrogen bonds : bond 0.03245 / 2.14 ( 1292) hydrogen bonds : angle 4.65980 / 3.19 ( 3768) metal coordination : bond 0.00746 / 0.44 ( 32) metal coordination : angle 4.83056 / 3.08 ( 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 727 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 612 time to evaluate : 1.213 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: A 191 LEU cc_start: 0.4610 (OUTLIER) cc_final: 0.4235 (mt) REVERT: A 244 LEU cc_start: 0.8699 (tp) cc_final: 0.8415 (mt) REVERT: A 268 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7911 (mm-30) REVERT: A 333 LEU cc_start: 0.9098 (mt) cc_final: 0.8890 (mt) REVERT: A 350 LEU cc_start: 0.9443 (mm) cc_final: 0.9098 (mm) REVERT: A 398 GLU cc_start: 0.7209 (mt-10) cc_final: 0.6799 (mp0) REVERT: A 1141 MET cc_start: 0.8465 (mmt) cc_final: 0.8068 (mmt) REVERT: A 1150 GLU cc_start: 0.7806 (tm-30) cc_final: 0.7361 (tm-30) REVERT: A 1623 LYS cc_start: 0.8902 (ttmt) cc_final: 0.8267 (tttm) REVERT: A 1654 ILE cc_start: 0.7818 (mp) cc_final: 0.7420 (mp) REVERT: A 1717 TRP cc_start: 0.8506 (p-90) cc_final: 0.7891 (p-90) REVERT: A 1751 HIS cc_start: 0.6880 (m90) cc_final: 0.6524 (m90) REVERT: A 1765 MET cc_start: 0.5459 (mmm) cc_final: 0.5048 (mmm) REVERT: A 1782 MET cc_start: 0.8738 (mmm) cc_final: 0.7974 (ppp) REVERT: A 1791 HIS cc_start: 0.8610 (m-70) cc_final: 0.8352 (m-70) REVERT: A 1935 GLU cc_start: 0.7128 (mp0) cc_final: 0.6906 (mp0) REVERT: A 2028 LEU cc_start: 0.1565 (OUTLIER) cc_final: 0.1225 (tm) REVERT: D 60 CYS cc_start: 0.2490 (OUTLIER) cc_final: 0.2060 (t) REVERT: D 191 LEU cc_start: 0.4391 (OUTLIER) cc_final: 0.4043 (mt) REVERT: D 216 GLU cc_start: 0.8322 (pp20) cc_final: 0.7984 (pm20) REVERT: D 244 LEU cc_start: 0.8645 (tp) cc_final: 0.8315 (mt) REVERT: D 268 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7923 (mm-30) REVERT: D 401 LYS cc_start: 0.8912 (mmtm) cc_final: 0.8576 (mmtm) REVERT: D 532 ARG cc_start: 0.8478 (ttp80) cc_final: 0.8276 (ttt-90) REVERT: D 1141 MET cc_start: 0.8401 (mmp) cc_final: 0.8000 (mmt) REVERT: D 1150 GLU cc_start: 0.7776 (tm-30) cc_final: 0.7276 (tm-30) REVERT: D 1237 GLU cc_start: 0.7543 (mt-10) cc_final: 0.7339 (mt-10) REVERT: D 1359 GLU cc_start: 0.8681 (tm-30) cc_final: 0.8419 (tm-30) REVERT: D 1623 LYS cc_start: 0.8807 (ttmt) cc_final: 0.8096 (tttm) REVERT: D 1654 ILE cc_start: 0.7827 (mp) cc_final: 0.7487 (mp) REVERT: D 1717 TRP cc_start: 0.8497 (p-90) cc_final: 0.7959 (p-90) REVERT: D 1751 HIS cc_start: 0.7426 (m170) cc_final: 0.7128 (m90) REVERT: D 1782 MET cc_start: 0.8705 (mmm) cc_final: 0.7962 (ppp) REVERT: D 1791 HIS cc_start: 0.8581 (m-70) cc_final: 0.8306 (m-70) REVERT: D 2028 LEU cc_start: 0.1484 (OUTLIER) cc_final: 0.1148 (tm) outliers start: 115 outliers final: 103 residues processed: 691 average time/residue: 0.1806 time to fit residues: 204.7826 Evaluate side-chains 688 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 580 time to evaluate : 1.095 ------------------------------------------------------------------------------- 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 191 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 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 585 ASP 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 1135 ASP 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 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 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 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 1872 ILE Chi-restraints excluded: chain A residue 1917 VAL Chi-restraints excluded: chain A residue 1968 VAL Chi-restraints excluded: chain A residue 1998 VAL 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 60 CYS Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 191 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 375 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 1138 THR Chi-restraints excluded: chain D residue 1162 ASN Chi-restraints excluded: chain D residue 1165 LYS 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 1427 ILE Chi-restraints excluded: chain D residue 1455 THR 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 1773 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 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 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: 6.9990 chunk 264 optimal weight: 6.9990 chunk 242 optimal weight: 3.9990 chunk 76 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 285 optimal weight: 0.6980 chunk 324 optimal weight: 0.4980 chunk 215 optimal weight: 4.9990 chunk 298 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 ASN A 348 ASN A 384 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 ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 288 ASN D 607 ASN D 647 HIS ** D 704 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1503 ASN D1712 ASN ** D1738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.175445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.142051 restraints weight = 47138.233| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 2.84 r_work: 0.3660 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 28666 Z= 0.159 Angle : 0.740 10.325 38776 Z= 0.361 Chirality : 0.045 0.324 4506 Planarity : 0.004 0.068 4850 Dihedral : 7.533 132.783 3961 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.67 % Favored : 88.27 % Rotamer: Outliers : 4.05 % Allowed : 24.50 % Favored : 71.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.14), residues: 3488 helix: 0.60 (0.13), residues: 1698 sheet: -1.16 (0.32), residues: 290 loop : -3.03 (0.15), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 231 TYR 0.030 0.001 TYR A 214 PHE 0.048 0.002 PHE A1148 TRP 0.017 0.001 TRP A 413 HIS 0.008 0.001 HIS D1751 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (28630) covalent geometry : angle 0.72496 / 0.36 (38732) SS BOND : bond 0.00399 / 0.20 ( 4) SS BOND : angle 1.71469 / 1.09 ( 8) hydrogen bonds : bond 0.03391 / 2.22 ( 1292) hydrogen bonds : angle 4.72027 / 3.23 ( 3768) metal coordination : bond 0.00962 / 0.56 ( 32) metal coordination : angle 4.81557 / 3.08 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7806.05 seconds wall clock time: 134 minutes 32.81 seconds (8072.81 seconds total)