Starting phenix.real_space_refine on Thu Jun 19 10:46:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rf0_19114/06_2025/8rf0_19114.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rf0_19114/06_2025/8rf0_19114.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rf0_19114/06_2025/8rf0_19114.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rf0_19114/06_2025/8rf0_19114.map" model { file = "/net/cci-nas-00/data/ceres_data/8rf0_19114/06_2025/8rf0_19114.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rf0_19114/06_2025/8rf0_19114.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.019 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 70 5.16 5 C 13815 2.51 5 N 3881 2.21 5 O 4154 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21922 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 21699 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 2780, 21677 Classifications: {'peptide': 2780} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PTRANS': 114, 'TRANS': 2665} Chain breaks: 4 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 286 Unresolved non-hydrogen angles: 368 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 9, 'ASN:plan1': 3, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 158 Conformer: "B" Number of residues, atoms: 2780, 21677 Classifications: {'peptide': 2780} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PTRANS': 114, 'TRANS': 2665} Chain breaks: 4 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 286 Unresolved non-hydrogen angles: 368 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 9, 'ASN:plan1': 3, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 158 bond proxies already assigned to first conformer: 22150 Chain: "B" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 99 Unusual residues: {'BGC': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 99 Unusual residues: {'BGC': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'UPG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 5 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AARG A 194 " occ=0.60 ... (20 atoms not shown) pdb=" NH2BARG A 194 " occ=0.40 residue: pdb=" N AARG A1355 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A1355 " occ=0.50 Time building chain proxies: 21.74, per 1000 atoms: 0.99 Number of scatterers: 21922 At special positions: 0 Unit cell: (102.648, 122.388, 213.192, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 70 16.00 P 2 15.00 O 4154 8.00 N 3881 7.00 C 13815 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-2 " BGC B 1 " - " BGC B 2 " " BGC B 2 " - " BGC B 3 " " BGC B 3 " - " BGC B 4 " " BGC B 4 " - " BGC B 5 " " BGC B 5 " - " BGC B 6 " " BGC B 6 " - " BGC B 7 " " BGC B 7 " - " BGC B 8 " " BGC B 8 " - " BGC B 9 " " BGC C 2 " - " BGC C 3 " " BGC C 3 " - " BGC C 4 " " BGC C 5 " - " BGC C 6 " " BGC C 6 " - " BGC C 7 " " BGC C 7 " - " BGC C 8 " " BGC C 8 " - " BGC C 9 " BETA1-3 " BGC C 1 " - " BGC C 2 " " BGC C 4 " - " BGC C 5 " Time building additional restraints: 6.19 Conformation dependent library (CDL) restraints added in 5.4 seconds 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5172 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 24 sheets defined 45.9% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.68 Creating SS restraints... Processing helix chain 'A' and resid 34 through 45 removed outlier: 3.754A pdb=" N ARG A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 79 removed outlier: 3.971A pdb=" N TYR A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N THR A 76 " --> pdb=" O VAL A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 96 removed outlier: 4.074A pdb=" N TRP A 92 " --> pdb=" O PRO A 88 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU A 93 " --> pdb=" O ALA A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 105 removed outlier: 3.562A pdb=" N ILE A 100 " --> pdb=" O ASN A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 118 removed outlier: 3.739A pdb=" N GLN A 118 " --> pdb=" O LYS A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 142 removed outlier: 3.597A pdb=" N GLY A 136 " --> pdb=" O VAL A 132 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TRP A 137 " --> pdb=" O MET A 133 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA A 141 " --> pdb=" O TRP A 137 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N HIS A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 160 Processing helix chain 'A' and resid 172 through 212 removed outlier: 4.182A pdb=" N ARG A 178 " --> pdb=" O PRO A 174 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N PHE A 179 " --> pdb=" O SER A 175 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG A 191 " --> pdb=" O ARG A 187 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG A 197 " --> pdb=" O GLU A 193 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG A 199 " --> pdb=" O SER A 195 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ALA A 202 " --> pdb=" O MET A 198 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ASN A 203 " --> pdb=" O ARG A 199 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU A 204 " --> pdb=" O GLN A 200 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL A 205 " --> pdb=" O LYS A 201 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 212 " --> pdb=" O GLU A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 225 removed outlier: 3.938A pdb=" N ALA A 220 " --> pdb=" O GLU A 216 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLN A 224 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N VAL A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 229 removed outlier: 3.694A pdb=" N VAL A 229 " --> pdb=" O ASP A 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 226 through 229' Processing helix chain 'A' and resid 233 through 244 removed outlier: 3.867A pdb=" N GLN A 237 " --> pdb=" O THR A 233 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR A 240 " --> pdb=" O THR A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 254 Processing helix chain 'A' and resid 255 through 261 Processing helix chain 'A' and resid 262 through 265 removed outlier: 4.175A pdb=" N THR A 265 " --> pdb=" O ALA A 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 262 through 265' Processing helix chain 'A' and resid 267 through 276 removed outlier: 3.719A pdb=" N MET A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N HIS A 275 " --> pdb=" O MET A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 298 removed outlier: 3.533A pdb=" N VAL A 289 " --> pdb=" O MET A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 308 Processing helix chain 'A' and resid 309 through 314 removed outlier: 4.111A pdb=" N VAL A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU A 314 " --> pdb=" O ILE A 310 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 309 through 314' Processing helix chain 'A' and resid 319 through 323 removed outlier: 4.001A pdb=" N LEU A 323 " --> pdb=" O TYR A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 342 removed outlier: 3.519A pdb=" N ARG A 341 " --> pdb=" O LEU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 358 removed outlier: 3.543A pdb=" N ALA A 353 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N VAL A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 361 No H-bonds generated for 'chain 'A' and resid 359 through 361' Processing helix chain 'A' and resid 373 through 378 Processing helix chain 'A' and resid 381 through 390 Processing helix chain 'A' and resid 394 through 407 Processing helix chain 'A' and resid 408 through 430 Proline residue: A 414 - end of helix Processing helix chain 'A' and resid 439 through 467 removed outlier: 4.421A pdb=" N LEU A 449 " --> pdb=" O LEU A 445 " (cutoff:3.500A) Proline residue: A 450 - end of helix Processing helix chain 'A' and resid 499 through 515 removed outlier: 3.986A pdb=" N GLU A 503 " --> pdb=" O ASP A 499 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN A 515 " --> pdb=" O HIS A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 557 removed outlier: 4.506A pdb=" N ILE A 542 " --> pdb=" O GLU A 538 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG A 556 " --> pdb=" O ALA A 552 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N TYR A 557 " --> pdb=" O LEU A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 599 removed outlier: 3.503A pdb=" N LEU A 597 " --> pdb=" O GLU A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 643 removed outlier: 3.661A pdb=" N GLY A 639 " --> pdb=" O THR A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 647 Processing helix chain 'A' and resid 679 through 685 Processing helix chain 'A' and resid 702 through 707 Processing helix chain 'A' and resid 719 through 730 removed outlier: 3.993A pdb=" N ARG A 729 " --> pdb=" O ALA A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 746 removed outlier: 3.740A pdb=" N LEU A 741 " --> pdb=" O SER A 737 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA A 746 " --> pdb=" O GLU A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 781 Processing helix chain 'A' and resid 781 through 787 Processing helix chain 'A' and resid 793 through 824 Proline residue: A 810 - end of helix removed outlier: 3.599A pdb=" N TYR A 822 " --> pdb=" O ILE A 818 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N MET A 824 " --> pdb=" O GLY A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 850 removed outlier: 4.409A pdb=" N TRP A 832 " --> pdb=" O GLY A 828 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN A 833 " --> pdb=" O ALA A 829 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A 840 " --> pdb=" O LEU A 836 " (cutoff:3.500A) Proline residue: A 844 - end of helix removed outlier: 5.343A pdb=" N SER A 847 " --> pdb=" O ALA A 843 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU A 848 " --> pdb=" O PRO A 844 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER A 850 " --> pdb=" O LEU A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 906 removed outlier: 4.430A pdb=" N GLU A 871 " --> pdb=" O THR A 867 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ALA A 887 " --> pdb=" O ILE A 883 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N ASP A 888 " --> pdb=" O VAL A 884 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG A 903 " --> pdb=" O ARG A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 936 removed outlier: 3.553A pdb=" N TYR A 932 " --> pdb=" O ILE A 928 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ARG A 933 " --> pdb=" O VAL A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 951 removed outlier: 4.082A pdb=" N LEU A 951 " --> pdb=" O LEU A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 969 Proline residue: A 962 - end of helix Processing helix chain 'A' and resid 969 through 979 removed outlier: 3.934A pdb=" N VAL A 973 " --> pdb=" O LEU A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 1005 Processing helix chain 'A' and resid 1005 through 1011 removed outlier: 3.692A pdb=" N GLU A1009 " --> pdb=" O TRP A1005 " (cutoff:3.500A) Processing helix chain 'A' and resid 1037 through 1055 Processing helix chain 'A' and resid 1058 through 1076 removed outlier: 3.851A pdb=" N THR A1062 " --> pdb=" O SER A1058 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A1063 " --> pdb=" O PHE A1059 " (cutoff:3.500A) Processing helix chain 'A' and resid 1102 through 1125 removed outlier: 3.549A pdb=" N ALA A1114 " --> pdb=" O GLY A1110 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ALA A1125 " --> pdb=" O ASP A1121 " (cutoff:3.500A) Processing helix chain 'A' and resid 1135 through 1150 removed outlier: 3.640A pdb=" N ALA A1141 " --> pdb=" O ILE A1137 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA A1150 " --> pdb=" O GLU A1146 " (cutoff:3.500A) Processing helix chain 'A' and resid 1159 through 1182 removed outlier: 3.581A pdb=" N ARG A1163 " --> pdb=" O ARG A1159 " (cutoff:3.500A) Processing helix chain 'A' and resid 1186 through 1209 removed outlier: 3.909A pdb=" N VAL A1190 " --> pdb=" O ALA A1186 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN A1192 " --> pdb=" O ILE A1188 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU A1193 " --> pdb=" O ARG A1189 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA A1194 " --> pdb=" O VAL A1190 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N VAL A1195 " --> pdb=" O ILE A1191 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A1196 " --> pdb=" O ASN A1192 " (cutoff:3.500A) Processing helix chain 'A' and resid 1213 through 1238 Processing helix chain 'A' and resid 1244 through 1263 removed outlier: 3.696A pdb=" N LEU A1261 " --> pdb=" O ARG A1257 " (cutoff:3.500A) Processing helix chain 'A' and resid 1285 through 1287 No H-bonds generated for 'chain 'A' and resid 1285 through 1287' Processing helix chain 'A' and resid 1301 through 1312 removed outlier: 3.565A pdb=" N GLY A1312 " --> pdb=" O ALA A1308 " (cutoff:3.500A) Processing helix chain 'A' and resid 1315 through 1320 removed outlier: 4.258A pdb=" N TRP A1319 " --> pdb=" O PRO A1315 " (cutoff:3.500A) Processing helix chain 'A' and resid 1342 through 1352 removed outlier: 4.664A pdb=" N MET A1347 " --> pdb=" O PHE A1343 " (cutoff:3.500A) Proline residue: A1348 - end of helix Processing helix chain 'A' and resid 1358 through 1379 removed outlier: 3.522A pdb=" N GLN A1362 " --> pdb=" O GLY A1358 " (cutoff:3.500A) Processing helix chain 'A' and resid 1421 through 1428 removed outlier: 4.008A pdb=" N SER A1425 " --> pdb=" O ALA A1421 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE A1426 " --> pdb=" O PRO A1422 " (cutoff:3.500A) Processing helix chain 'A' and resid 1432 through 1446 removed outlier: 3.512A pdb=" N ALA A1436 " --> pdb=" O ASP A1432 " (cutoff:3.500A) Processing helix chain 'A' and resid 1482 through 1494 Processing helix chain 'A' and resid 1496 through 1503 removed outlier: 4.177A pdb=" N GLU A1500 " --> pdb=" O GLY A1496 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N HIS A1503 " --> pdb=" O ARG A1499 " (cutoff:3.500A) Processing helix chain 'A' and resid 1505 through 1511 removed outlier: 3.945A pdb=" N ALA A1511 " --> pdb=" O VAL A1507 " (cutoff:3.500A) Processing helix chain 'A' and resid 1512 through 1515 Processing helix chain 'A' and resid 1552 through 1556 Processing helix chain 'A' and resid 1696 through 1703 removed outlier: 3.986A pdb=" N SER A1700 " --> pdb=" O HIS A1696 " (cutoff:3.500A) Processing helix chain 'A' and resid 1750 through 1756 Processing helix chain 'A' and resid 1810 through 1822 removed outlier: 3.630A pdb=" N VAL A1814 " --> pdb=" O SER A1810 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP A1815 " --> pdb=" O ARG A1811 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS A1816 " --> pdb=" O GLU A1812 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP A1819 " --> pdb=" O ASP A1815 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N ARG A1820 " --> pdb=" O LYS A1816 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR A1821 " --> pdb=" O ALA A1817 " (cutoff:3.500A) Processing helix chain 'A' and resid 1830 through 1845 removed outlier: 3.537A pdb=" N VAL A1845 " --> pdb=" O GLN A1841 " (cutoff:3.500A) Processing helix chain 'A' and resid 1848 through 1864 Processing helix chain 'A' and resid 1909 through 1923 Processing helix chain 'A' and resid 1937 through 1957 removed outlier: 4.542A pdb=" N GLN A1942 " --> pdb=" O ALA A1938 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ASP A1943 " --> pdb=" O SER A1939 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE A1951 " --> pdb=" O ALA A1947 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N THR A1954 " --> pdb=" O HIS A1950 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N GLN A1955 " --> pdb=" O ILE A1951 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG A1957 " --> pdb=" O GLU A1953 " (cutoff:3.500A) Processing helix chain 'A' and resid 1977 through 1988 Processing helix chain 'A' and resid 2001 through 2011 removed outlier: 3.676A pdb=" N VAL A2007 " --> pdb=" O ILE A2003 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA A2011 " --> pdb=" O VAL A2007 " (cutoff:3.500A) Processing helix chain 'A' and resid 2212 through 2216 Processing helix chain 'A' and resid 2256 through 2261 Processing helix chain 'A' and resid 2316 through 2331 removed outlier: 3.605A pdb=" N GLN A2329 " --> pdb=" O LYS A2325 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ASP A2331 " --> pdb=" O VAL A2327 " (cutoff:3.500A) Processing helix chain 'A' and resid 2332 through 2348 Processing helix chain 'A' and resid 2358 through 2364 removed outlier: 3.899A pdb=" N ASN A2364 " --> pdb=" O ASN A2360 " (cutoff:3.500A) Processing helix chain 'A' and resid 2365 through 2376 Processing helix chain 'A' and resid 2391 through 2396 removed outlier: 3.679A pdb=" N LEU A2395 " --> pdb=" O PHE A2391 " (cutoff:3.500A) Processing helix chain 'A' and resid 2397 through 2401 removed outlier: 3.908A pdb=" N ALA A2400 " --> pdb=" O ASP A2397 " (cutoff:3.500A) Processing helix chain 'A' and resid 2407 through 2418 removed outlier: 3.633A pdb=" N GLY A2418 " --> pdb=" O LEU A2414 " (cutoff:3.500A) Processing helix chain 'A' and resid 2444 through 2460 removed outlier: 3.521A pdb=" N TRP A2448 " --> pdb=" O ASP A2444 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LEU A2449 " --> pdb=" O ASP A2445 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N ALA A2450 " --> pdb=" O VAL A2446 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR A2451 " --> pdb=" O VAL A2447 " (cutoff:3.500A) Processing helix chain 'A' and resid 2462 through 2467 removed outlier: 3.764A pdb=" N ILE A2465 " --> pdb=" O ASP A2462 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP A2467 " --> pdb=" O ALA A2464 " (cutoff:3.500A) Processing helix chain 'A' and resid 2497 through 2512 removed outlier: 3.676A pdb=" N ALA A2505 " --> pdb=" O HIS A2501 " (cutoff:3.500A) Processing helix chain 'A' and resid 2542 through 2562 removed outlier: 3.940A pdb=" N ASP A2554 " --> pdb=" O GLY A2550 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLU A2557 " --> pdb=" O ARG A2553 " (cutoff:3.500A) Processing helix chain 'A' and resid 2564 through 2585 removed outlier: 3.676A pdb=" N LYS A2570 " --> pdb=" O ASP A2566 " (cutoff:3.500A) Processing helix chain 'A' and resid 2614 through 2625 removed outlier: 3.853A pdb=" N GLN A2618 " --> pdb=" O ASP A2614 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL A2622 " --> pdb=" O GLN A2618 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY A2625 " --> pdb=" O SER A2621 " (cutoff:3.500A) Processing helix chain 'A' and resid 2628 through 2644 removed outlier: 3.856A pdb=" N MET A2640 " --> pdb=" O MET A2636 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLU A2641 " --> pdb=" O ASP A2637 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N HIS A2642 " --> pdb=" O ALA A2638 " (cutoff:3.500A) Processing helix chain 'A' and resid 2666 through 2671 removed outlier: 4.039A pdb=" N LYS A2669 " --> pdb=" O GLY A2666 " (cutoff:3.500A) Processing helix chain 'A' and resid 2682 through 2697 removed outlier: 4.284A pdb=" N TRP A2688 " --> pdb=" O HIS A2684 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N VAL A2689 " --> pdb=" O ALA A2685 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL A2690 " --> pdb=" O ALA A2686 " (cutoff:3.500A) Processing helix chain 'A' and resid 2698 through 2710 Processing helix chain 'A' and resid 2753 through 2764 Processing sheet with id=AA1, first strand: chain 'A' and resid 565 through 569 removed outlier: 8.873A pdb=" N TYR A 566 " --> pdb=" O ILE A 520 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N PHE A 522 " --> pdb=" O TYR A 566 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N LEU A 568 " --> pdb=" O PHE A 522 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N LEU A 524 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL A 491 " --> pdb=" O SER A 523 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL A 620 " --> pdb=" O TYR A 717 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N TYR A 717 " --> pdb=" O VAL A 620 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 628 through 629 removed outlier: 3.586A pdb=" N ARG A 628 " --> pdb=" O VAL A 757 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1024 through 1025 Processing sheet with id=AA4, first strand: chain 'A' and resid 1035 through 1036 Processing sheet with id=AA5, first strand: chain 'A' and resid 1099 through 1101 removed outlier: 3.551A pdb=" N ARG A1283 " --> pdb=" O GLU A1288 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU A1288 " --> pdb=" O ARG A1283 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1326 through 1328 removed outlier: 3.586A pdb=" N ALA A1334 " --> pdb=" O VAL A1327 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1419 through 1420 Processing sheet with id=AA8, first strand: chain 'A' and resid 1449 through 1450 removed outlier: 3.599A pdb=" N GLY A1453 " --> pdb=" O GLY A1450 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1549 through 1550 removed outlier: 3.878A pdb=" N LYS A1627 " --> pdb=" O THR A1642 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR A1642 " --> pdb=" O LYS A1627 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLN A1647 " --> pdb=" O LEU A1668 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU A1668 " --> pdb=" O GLN A1647 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A1799 " --> pdb=" O LEU A1667 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TRP A1804 " --> pdb=" O LEU A1734 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1561 through 1564 removed outlier: 3.595A pdb=" N MET A1571 " --> pdb=" O TYR A1579 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1613 through 1615 removed outlier: 3.831A pdb=" N VAL A1793 " --> pdb=" O ARG A1675 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ILE A1677 " --> pdb=" O VAL A1791 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU A1787 " --> pdb=" O SER A1681 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU A1746 " --> pdb=" O ARG A1788 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1968 through 1972 removed outlier: 6.185A pdb=" N LEU A1930 " --> pdb=" O PHE A1969 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N VAL A1971 " --> pdb=" O LEU A1930 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE A1932 " --> pdb=" O VAL A1971 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N PHE A1898 " --> pdb=" O VAL A1931 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL A1933 " --> pdb=" O PHE A1898 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N LEU A1900 " --> pdb=" O VAL A1933 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU A1992 " --> pdb=" O SER A1899 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 2051 through 2053 removed outlier: 3.530A pdb=" N VAL A2061 " --> pdb=" O GLY A2052 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR A2060 " --> pdb=" O HIS A2150 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE A2146 " --> pdb=" O LEU A2064 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY A2312 " --> pdb=" O PHE A2243 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ALA A2226 " --> pdb=" O ASP A2221 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 2051 through 2053 removed outlier: 3.530A pdb=" N VAL A2061 " --> pdb=" O GLY A2052 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR A2060 " --> pdb=" O HIS A2150 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE A2146 " --> pdb=" O LEU A2064 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL A2185 " --> pdb=" O ARG A2305 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG A2305 " --> pdb=" O VAL A2185 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 2075 through 2080 removed outlier: 3.770A pdb=" N PHE A2083 " --> pdb=" O ASN A2080 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 2120 through 2122 removed outlier: 3.586A pdb=" N VAL A2201 " --> pdb=" O ALA A2291 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA A2291 " --> pdb=" O VAL A2201 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 2120 through 2122 removed outlier: 3.575A pdb=" N ARG A2193 " --> pdb=" O LEU A2299 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL A2197 " --> pdb=" O GLN A2295 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLN A2295 " --> pdb=" O VAL A2197 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 2350 through 2352 removed outlier: 3.606A pdb=" N PHE A2788 " --> pdb=" O VAL A2803 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 2389 through 2390 removed outlier: 3.710A pdb=" N TRP A2430 " --> pdb=" O PHE A2389 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 2439 through 2440 removed outlier: 3.791A pdb=" N ALA A2485 " --> pdb=" O ARG A2439 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 2470 through 2474 removed outlier: 6.851A pdb=" N ILE A2470 " --> pdb=" O ARG A2494 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ARG A2494 " --> pdb=" O ILE A2470 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N PHE A2472 " --> pdb=" O SER A2492 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 2540 through 2541 Processing sheet with id=AC5, first strand: chain 'A' and resid 2732 through 2735 removed outlier: 7.360A pdb=" N THR A2732 " --> pdb=" O SER A2748 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N SER A2748 " --> pdb=" O THR A2732 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 2768 through 2770 removed outlier: 3.514A pdb=" N THR A2769 " --> pdb=" O HIS A2776 " (cutoff:3.500A) 948 hydrogen bonds defined for protein. 2725 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: 12.03 Time building geometry restraints manager: 6.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3636 1.31 - 1.44: 6283 1.44 - 1.56: 12373 1.56 - 1.69: 5 1.69 - 1.82: 125 Bond restraints: 22422 Sorted by residual: bond pdb=" O3B UPG A2901 " pdb=" PB UPG A2901 " ideal model delta sigma weight residual 1.652 1.490 0.162 2.00e-02 2.50e+03 6.53e+01 bond pdb=" C PRO A1520 " pdb=" N ARG A1521 " ideal model delta sigma weight residual 1.330 1.434 -0.103 1.38e-02 5.25e+03 5.61e+01 bond pdb=" C ALA A1519 " pdb=" N PRO A1520 " ideal model delta sigma weight residual 1.334 1.472 -0.138 2.34e-02 1.83e+03 3.46e+01 bond pdb=" O1B UPG A2901 " pdb=" PB UPG A2901 " ideal model delta sigma weight residual 1.493 1.600 -0.107 2.00e-02 2.50e+03 2.84e+01 bond pdb=" CA PRO A1520 " pdb=" C PRO A1520 " ideal model delta sigma weight residual 1.520 1.593 -0.073 1.42e-02 4.96e+03 2.65e+01 ... (remaining 22417 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.80: 30449 7.80 - 15.61: 23 15.61 - 23.41: 0 23.41 - 31.21: 0 31.21 - 39.02: 1 Bond angle restraints: 30473 Sorted by residual: angle pdb=" O ALA A1519 " pdb=" C ALA A1519 " pdb=" N PRO A1520 " ideal model delta sigma weight residual 121.32 82.30 39.02 1.15e+00 7.56e-01 1.15e+03 angle pdb=" N PRO A2030 " pdb=" CA PRO A2030 " pdb=" CB PRO A2030 " ideal model delta sigma weight residual 102.81 109.81 -7.00 6.70e-01 2.23e+00 1.09e+02 angle pdb=" CA PRO A1520 " pdb=" C PRO A1520 " pdb=" O PRO A1520 " ideal model delta sigma weight residual 120.60 107.12 13.48 1.82e+00 3.02e-01 5.48e+01 angle pdb=" N PRO A2037 " pdb=" CA PRO A2037 " pdb=" CB PRO A2037 " ideal model delta sigma weight residual 103.25 110.79 -7.54 1.05e+00 9.07e-01 5.16e+01 angle pdb=" N PRO A2028 " pdb=" CA PRO A2028 " pdb=" CB PRO A2028 " ideal model delta sigma weight residual 103.25 110.77 -7.52 1.05e+00 9.07e-01 5.13e+01 ... (remaining 30468 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.68: 12553 23.68 - 47.37: 793 47.37 - 71.05: 83 71.05 - 94.73: 43 94.73 - 118.42: 41 Dihedral angle restraints: 13513 sinusoidal: 5478 harmonic: 8035 Sorted by residual: dihedral pdb=" CA TYR A 139 " pdb=" C TYR A 139 " pdb=" N VAL A 140 " pdb=" CA VAL A 140 " ideal model delta harmonic sigma weight residual 180.00 146.39 33.61 0 5.00e+00 4.00e-02 4.52e+01 dihedral pdb=" N PRO A1520 " pdb=" C PRO A1520 " pdb=" CA PRO A1520 " pdb=" CB PRO A1520 " ideal model delta harmonic sigma weight residual 115.10 127.06 -11.96 0 2.50e+00 1.60e-01 2.29e+01 dihedral pdb=" CA GLN A1015 " pdb=" C GLN A1015 " pdb=" N GLU A1016 " pdb=" CA GLU A1016 " ideal model delta harmonic sigma weight residual 180.00 -156.89 -23.11 0 5.00e+00 4.00e-02 2.14e+01 ... (remaining 13510 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 3082 0.074 - 0.148: 293 0.148 - 0.222: 18 0.222 - 0.296: 11 0.296 - 0.370: 2 Chirality restraints: 3406 Sorted by residual: chirality pdb=" C1 BGC B 2 " pdb=" O2 BGC B 1 " pdb=" C2 BGC B 2 " pdb=" O5 BGC B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-02 2.50e+03 1.57e+02 chirality pdb=" C1 BGC B 3 " pdb=" O2 BGC B 2 " pdb=" C2 BGC B 3 " pdb=" O5 BGC B 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-02 2.50e+03 9.20e+01 chirality pdb=" C1 BGC B 7 " pdb=" O2 BGC B 6 " pdb=" C2 BGC B 7 " pdb=" O5 BGC B 7 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.43e+01 ... (remaining 3403 not shown) Planarity restraints: 3947 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A1519 " -0.141 2.00e-02 2.50e+03 2.15e-01 4.64e+02 pdb=" C ALA A1519 " 0.372 2.00e-02 2.50e+03 pdb=" O ALA A1519 " -0.137 2.00e-02 2.50e+03 pdb=" N PRO A1520 " -0.093 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 100 " -0.033 2.00e-02 2.50e+03 6.51e-02 4.24e+01 pdb=" C ILE A 100 " 0.113 2.00e-02 2.50e+03 pdb=" O ILE A 100 " -0.042 2.00e-02 2.50e+03 pdb=" N GLU A 101 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 585 " -0.023 2.00e-02 2.50e+03 4.68e-02 2.19e+01 pdb=" C GLU A 585 " 0.081 2.00e-02 2.50e+03 pdb=" O GLU A 585 " -0.032 2.00e-02 2.50e+03 pdb=" N ARG A 586 " -0.027 2.00e-02 2.50e+03 ... (remaining 3944 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 783 2.72 - 3.26: 22642 3.26 - 3.81: 35281 3.81 - 4.35: 42152 4.35 - 4.90: 70791 Nonbonded interactions: 171649 Sorted by model distance: nonbonded pdb=" OG SER A1337 " pdb=" OH TYR A1345 " model vdw 2.171 3.040 nonbonded pdb=" OG1 THR A2255 " pdb=" O THR A2282 " model vdw 2.204 3.040 nonbonded pdb=" O ASN A1417 " pdb=" OG1 THR A1461 " model vdw 2.223 3.040 nonbonded pdb=" O LEU A2466 " pdb=" OG1 THR A2497 " model vdw 2.228 3.040 nonbonded pdb=" O TRP A2343 " pdb=" OG1 THR A2347 " model vdw 2.228 3.040 ... (remaining 171644 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.40 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: 2.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.800 Check model and map are aligned: 0.150 Set scattering table: 0.210 Process input model: 67.850 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.130 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5833 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 : 0.004 0.162 22438 Z= 0.212 Angle : 0.738 39.017 30521 Z= 0.429 Chirality : 0.045 0.370 3406 Planarity : 0.006 0.215 3947 Dihedral : 16.919 118.415 8341 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.90 % Allowed : 8.84 % Favored : 90.25 % Rotamer: Outliers : 0.45 % Allowed : 0.32 % Favored : 99.23 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.16), residues: 2776 helix: 0.93 (0.17), residues: 1128 sheet: 0.16 (0.31), residues: 316 loop : -2.48 (0.16), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP A 967 HIS 0.004 0.001 HIS A 569 PHE 0.016 0.001 PHE A 238 TYR 0.012 0.001 TYR A 931 ARG 0.005 0.000 ARG A1324 Details of bonding type rmsd link_BETA1-2 : bond 0.01056 ( 14) link_BETA1-2 : angle 2.92920 ( 42) hydrogen bonds : bond 0.19549 ( 917) hydrogen bonds : angle 7.05529 ( 2725) link_BETA1-3 : bond 0.01226 ( 2) link_BETA1-3 : angle 1.54776 ( 6) covalent geometry : bond 0.00374 (22422) covalent geometry : angle 0.73031 (30473) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 2299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 538 time to evaluate : 2.428 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: symmetry clash REVERT: A 25 ILE cc_start: 0.4396 (mt) cc_final: 0.3371 (mm) REVERT: A 232 PRO cc_start: 0.8523 (Cg_endo) cc_final: 0.8302 (Cg_exo) REVERT: A 251 PHE cc_start: 0.6085 (t80) cc_final: 0.5750 (t80) REVERT: A 356 MET cc_start: 0.7515 (ttm) cc_final: 0.7220 (tmm) REVERT: A 467 VAL cc_start: 0.7893 (t) cc_final: 0.7231 (m) REVERT: A 505 MET cc_start: 0.7514 (mmp) cc_final: 0.7264 (mmt) REVERT: A 524 LEU cc_start: 0.7879 (tt) cc_final: 0.7224 (tt) REVERT: A 582 MET cc_start: 0.6806 (ppp) cc_final: 0.6061 (ppp) REVERT: A 643 HIS cc_start: 0.7334 (t70) cc_final: 0.7054 (t70) REVERT: A 798 TRP cc_start: 0.7048 (t60) cc_final: 0.6843 (t-100) REVERT: A 800 MET cc_start: 0.4891 (mtm) cc_final: 0.4434 (tpt) REVERT: A 824 MET cc_start: 0.5377 (mtt) cc_final: 0.5115 (mmp) REVERT: A 892 MET cc_start: 0.7368 (mmp) cc_final: 0.7089 (mmp) REVERT: A 911 MET cc_start: 0.5015 (ppp) cc_final: 0.4581 (tpp) REVERT: A 931 TYR cc_start: 0.6049 (m-10) cc_final: 0.5758 (m-10) REVERT: A 1750 ASP cc_start: 0.7783 (t0) cc_final: 0.7192 (p0) REVERT: A 1782 ASP cc_start: 0.6176 (t0) cc_final: 0.5715 (t0) REVERT: A 1822 ARG cc_start: 0.7511 (ttm-80) cc_final: 0.6398 (tpm170) REVERT: A 2105 LEU cc_start: 0.7617 (mt) cc_final: 0.7132 (mt) REVERT: A 2198 TYR cc_start: 0.4472 (m-10) cc_final: 0.4046 (m-10) REVERT: A 2273 ILE cc_start: 0.5792 (tt) cc_final: 0.5549 (tt) REVERT: A 2299 LEU cc_start: 0.6635 (mt) cc_final: 0.6407 (mt) REVERT: A 2401 PHE cc_start: 0.3035 (t80) cc_final: 0.2666 (t80) REVERT: A 2420 GLN cc_start: 0.7030 (tt0) cc_final: 0.6614 (tt0) REVERT: A 2527 ASN cc_start: 0.7327 (t160) cc_final: 0.6697 (t0) REVERT: A 2603 LEU cc_start: 0.6639 (tp) cc_final: 0.6179 (tp) REVERT: A 2684 HIS cc_start: 0.7282 (t-170) cc_final: 0.7072 (t-90) REVERT: A 2712 VAL cc_start: 0.5730 (t) cc_final: 0.5389 (t) outliers start: 6 outliers final: 3 residues processed: 543 average time/residue: 0.4509 time to fit residues: 357.1080 Evaluate side-chains 257 residues out of total 2299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 254 time to evaluate : 2.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 1327 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 234 optimal weight: 1.9990 chunk 210 optimal weight: 0.8980 chunk 116 optimal weight: 5.9990 chunk 71 optimal weight: 7.9990 chunk 142 optimal weight: 6.9990 chunk 112 optimal weight: 7.9990 chunk 217 optimal weight: 0.4980 chunk 84 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 162 optimal weight: 0.6980 chunk 252 optimal weight: 0.3980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 515 ASN ** A 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1053 GLN A1111 HIS A1362 GLN A1480 HIS ** A1516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1720 ASN ** A1823 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2306 HIS ** A2364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2428 HIS A2527 ASN A2776 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.146211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.127167 restraints weight = 90539.322| |-----------------------------------------------------------------------------| r_work (start): 0.4270 rms_B_bonded: 5.16 r_work (final): 0.4270 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4270 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4270 r_free = 0.4270 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4270 r_free = 0.4270 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.4270 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6873 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 22438 Z= 0.159 Angle : 0.750 13.741 30521 Z= 0.374 Chirality : 0.046 0.223 3406 Planarity : 0.006 0.133 3947 Dihedral : 12.235 114.927 3452 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.61 % Allowed : 8.88 % Favored : 90.51 % Rotamer: Outliers : 1.76 % Allowed : 10.62 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.16), residues: 2776 helix: 0.77 (0.16), residues: 1166 sheet: 0.21 (0.30), residues: 329 loop : -2.52 (0.16), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A2785 HIS 0.011 0.001 HIS A1823 PHE 0.028 0.002 PHE A2359 TYR 0.035 0.002 TYR A 139 ARG 0.012 0.001 ARG A1248 Details of bonding type rmsd link_BETA1-2 : bond 0.00583 ( 14) link_BETA1-2 : angle 2.82353 ( 42) hydrogen bonds : bond 0.04357 ( 917) hydrogen bonds : angle 5.18889 ( 2725) link_BETA1-3 : bond 0.00959 ( 2) link_BETA1-3 : angle 3.17178 ( 6) covalent geometry : bond 0.00330 (22422) covalent geometry : angle 0.74184 (30473) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 259 time to evaluate : 2.323 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 25 ILE cc_start: 0.3975 (mt) cc_final: 0.3135 (mm) REVERT: A 290 LYS cc_start: 0.8909 (mttp) cc_final: 0.8624 (mptt) REVERT: A 785 ILE cc_start: 0.7700 (mt) cc_final: 0.7418 (mm) REVERT: A 800 MET cc_start: 0.5398 (mtm) cc_final: 0.5166 (tpt) REVERT: A 1153 ASP cc_start: 0.4048 (m-30) cc_final: 0.2842 (m-30) REVERT: A 1185 PHE cc_start: 0.6432 (t80) cc_final: 0.6159 (t80) REVERT: A 1816 LYS cc_start: 0.8541 (mmtm) cc_final: 0.8159 (tmmt) REVERT: A 1822 ARG cc_start: 0.7666 (ttm-80) cc_final: 0.6948 (tpm170) REVERT: A 2273 ILE cc_start: 0.6536 (tt) cc_final: 0.6300 (tt) REVERT: A 2571 TRP cc_start: 0.6627 (m-10) cc_final: 0.6416 (m-90) outliers start: 35 outliers final: 23 residues processed: 284 average time/residue: 0.3659 time to fit residues: 160.6142 Evaluate side-chains 232 residues out of total 2299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 209 time to evaluate : 2.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 466 PHE Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 1048 VAL Chi-restraints excluded: chain A residue 1166 GLU Chi-restraints excluded: chain A residue 1362 GLN Chi-restraints excluded: chain A residue 1408 LEU Chi-restraints excluded: chain A residue 1501 LEU Chi-restraints excluded: chain A residue 1603 ILE Chi-restraints excluded: chain A residue 1991 VAL Chi-restraints excluded: chain A residue 2075 ILE Chi-restraints excluded: chain A residue 2082 ASN Chi-restraints excluded: chain A residue 2145 MET Chi-restraints excluded: chain A residue 2238 SER Chi-restraints excluded: chain A residue 2335 VAL Chi-restraints excluded: chain A residue 2414 LEU Chi-restraints excluded: chain A residue 2457 VAL Chi-restraints excluded: chain A residue 2687 THR Chi-restraints excluded: chain A residue 2691 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 164 optimal weight: 3.9990 chunk 90 optimal weight: 20.0000 chunk 48 optimal weight: 1.9990 chunk 249 optimal weight: 2.9990 chunk 161 optimal weight: 7.9990 chunk 181 optimal weight: 4.9990 chunk 168 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 215 optimal weight: 8.9990 chunk 255 optimal weight: 0.5980 chunk 266 optimal weight: 8.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1325 GLN A1451 GLN A1480 HIS ** A1516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1823 HIS A2364 ASN ** A2412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2527 ASN A2642 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.138326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.118356 restraints weight = 118917.502| |-----------------------------------------------------------------------------| r_work (start): 0.4138 rms_B_bonded: 5.93 r_work (final): 0.4138 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4138 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4138 r_free = 0.4138 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4138 r_free = 0.4138 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4138 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 22438 Z= 0.178 Angle : 0.757 12.334 30521 Z= 0.385 Chirality : 0.046 0.216 3406 Planarity : 0.006 0.095 3947 Dihedral : 10.006 123.131 3448 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.76 % Allowed : 8.38 % Favored : 90.87 % Rotamer: Outliers : 2.25 % Allowed : 12.87 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.16), residues: 2776 helix: 0.64 (0.16), residues: 1193 sheet: 0.33 (0.30), residues: 337 loop : -2.54 (0.16), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 581 HIS 0.010 0.001 HIS A 592 PHE 0.022 0.002 PHE A2359 TYR 0.026 0.002 TYR A 320 ARG 0.015 0.001 ARG A 572 Details of bonding type rmsd link_BETA1-2 : bond 0.00607 ( 14) link_BETA1-2 : angle 2.81884 ( 42) hydrogen bonds : bond 0.04514 ( 917) hydrogen bonds : angle 4.86889 ( 2725) link_BETA1-3 : bond 0.00777 ( 2) link_BETA1-3 : angle 2.96953 ( 6) covalent geometry : bond 0.00397 (22422) covalent geometry : angle 0.74916 (30473) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 226 time to evaluate : 2.226 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 466 PHE cc_start: 0.6753 (OUTLIER) cc_final: 0.6459 (m-80) REVERT: A 799 LYS cc_start: 0.8378 (pttp) cc_final: 0.8089 (pttp) REVERT: A 800 MET cc_start: 0.5962 (mtm) cc_final: 0.5370 (tpt) REVERT: A 1747 PHE cc_start: 0.7513 (p90) cc_final: 0.7270 (p90) REVERT: A 1822 ARG cc_start: 0.7717 (ttm-80) cc_final: 0.6987 (tpm170) REVERT: A 1979 GLU cc_start: 0.7527 (mm-30) cc_final: 0.7183 (pp20) REVERT: A 2425 ASP cc_start: 0.7610 (m-30) cc_final: 0.7089 (p0) outliers start: 46 outliers final: 31 residues processed: 261 average time/residue: 0.3446 time to fit residues: 141.9881 Evaluate side-chains 223 residues out of total 2299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 191 time to evaluate : 2.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 466 PHE Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 621 MET Chi-restraints excluded: chain A residue 630 MET Chi-restraints excluded: chain A residue 1048 VAL Chi-restraints excluded: chain A residue 1166 GLU Chi-restraints excluded: chain A residue 1408 LEU Chi-restraints excluded: chain A residue 1476 ASN Chi-restraints excluded: chain A residue 1648 SER Chi-restraints excluded: chain A residue 1686 VAL Chi-restraints excluded: chain A residue 1731 ILE Chi-restraints excluded: chain A residue 1990 VAL Chi-restraints excluded: chain A residue 1991 VAL Chi-restraints excluded: chain A residue 2082 ASN Chi-restraints excluded: chain A residue 2236 ASP Chi-restraints excluded: chain A residue 2238 SER Chi-restraints excluded: chain A residue 2245 THR Chi-restraints excluded: chain A residue 2293 LEU Chi-restraints excluded: chain A residue 2335 VAL Chi-restraints excluded: chain A residue 2414 LEU Chi-restraints excluded: chain A residue 2433 LEU Chi-restraints excluded: chain A residue 2438 VAL Chi-restraints excluded: chain A residue 2457 VAL Chi-restraints excluded: chain A residue 2578 LEU Chi-restraints excluded: chain A residue 2687 THR Chi-restraints excluded: chain A residue 2691 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 128 optimal weight: 3.9990 chunk 236 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 chunk 231 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 249 optimal weight: 5.9990 chunk 95 optimal weight: 0.9980 chunk 89 optimal weight: 5.9990 chunk 138 optimal weight: 2.9990 chunk 85 optimal weight: 9.9990 chunk 25 optimal weight: 0.7980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 HIS ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 803 ASN ** A 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1162 HIS A1206 ASN A1209 HIS A1243 ASN A1480 HIS ** A1516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2104 GLN ** A2412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.136809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.116223 restraints weight = 113447.633| |-----------------------------------------------------------------------------| r_work (start): 0.4111 rms_B_bonded: 5.79 r_work (final): 0.4111 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4111 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4111 r_free = 0.4111 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4111 r_free = 0.4111 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4111 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.4489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22438 Z= 0.148 Angle : 0.713 11.313 30521 Z= 0.358 Chirality : 0.044 0.212 3406 Planarity : 0.005 0.081 3947 Dihedral : 9.128 118.101 3444 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.65 % Allowed : 7.83 % Favored : 91.52 % Rotamer: Outliers : 2.16 % Allowed : 14.58 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.16), residues: 2776 helix: 0.78 (0.16), residues: 1167 sheet: 0.23 (0.30), residues: 338 loop : -2.54 (0.16), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP A2571 HIS 0.012 0.001 HIS A 592 PHE 0.028 0.001 PHE A2359 TYR 0.020 0.002 TYR A 331 ARG 0.007 0.001 ARG A 572 Details of bonding type rmsd link_BETA1-2 : bond 0.00588 ( 14) link_BETA1-2 : angle 2.98057 ( 42) hydrogen bonds : bond 0.03985 ( 917) hydrogen bonds : angle 4.61683 ( 2725) link_BETA1-3 : bond 0.00877 ( 2) link_BETA1-3 : angle 3.68877 ( 6) covalent geometry : bond 0.00327 (22422) covalent geometry : angle 0.70271 (30473) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 207 time to evaluate : 2.601 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 685 PHE cc_start: 0.8027 (OUTLIER) cc_final: 0.7755 (m-80) REVERT: A 799 LYS cc_start: 0.8278 (pttp) cc_final: 0.8053 (pttp) REVERT: A 800 MET cc_start: 0.6427 (mtm) cc_final: 0.5614 (tpt) REVERT: A 1086 TRP cc_start: 0.8478 (m100) cc_final: 0.8277 (m100) REVERT: A 1822 ARG cc_start: 0.7682 (ttm-80) cc_final: 0.7005 (tpm170) REVERT: A 1979 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7274 (pp20) outliers start: 44 outliers final: 34 residues processed: 238 average time/residue: 0.3367 time to fit residues: 129.4563 Evaluate side-chains 222 residues out of total 2299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 187 time to evaluate : 2.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 630 MET Chi-restraints excluded: chain A residue 685 PHE Chi-restraints excluded: chain A residue 1048 VAL Chi-restraints excluded: chain A residue 1166 GLU Chi-restraints excluded: chain A residue 1408 LEU Chi-restraints excluded: chain A residue 1476 ASN Chi-restraints excluded: chain A residue 1501 LEU Chi-restraints excluded: chain A residue 1603 ILE Chi-restraints excluded: chain A residue 1686 VAL Chi-restraints excluded: chain A residue 1706 THR Chi-restraints excluded: chain A residue 1976 MET Chi-restraints excluded: chain A residue 1990 VAL Chi-restraints excluded: chain A residue 1991 VAL Chi-restraints excluded: chain A residue 2075 ILE Chi-restraints excluded: chain A residue 2082 ASN Chi-restraints excluded: chain A residue 2158 THR Chi-restraints excluded: chain A residue 2236 ASP Chi-restraints excluded: chain A residue 2238 SER Chi-restraints excluded: chain A residue 2293 LEU Chi-restraints excluded: chain A residue 2294 MET Chi-restraints excluded: chain A residue 2335 VAL Chi-restraints excluded: chain A residue 2414 LEU Chi-restraints excluded: chain A residue 2433 LEU Chi-restraints excluded: chain A residue 2438 VAL Chi-restraints excluded: chain A residue 2457 VAL Chi-restraints excluded: chain A residue 2691 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 52 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 chunk 246 optimal weight: 5.9990 chunk 250 optimal weight: 0.0970 chunk 92 optimal weight: 0.9990 chunk 222 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 199 optimal weight: 0.0670 chunk 134 optimal weight: 0.9990 chunk 267 optimal weight: 3.9990 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1480 HIS ** A1516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1658 HIS A2056 ASN A2365 ASN ** A2412 GLN ** 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 = 0.4428 r_free = 0.4428 target = 0.137766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.117434 restraints weight = 109605.119| |-----------------------------------------------------------------------------| r_work (start): 0.4128 rms_B_bonded: 5.77 r_work (final): 0.4128 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4128 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4128 r_free = 0.4128 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4128 r_free = 0.4128 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4128 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.4728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22438 Z= 0.125 Angle : 0.684 10.361 30521 Z= 0.341 Chirality : 0.043 0.203 3406 Planarity : 0.005 0.071 3947 Dihedral : 8.856 113.554 3444 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.72 % Allowed : 8.23 % Favored : 91.05 % Rotamer: Outliers : 1.71 % Allowed : 15.21 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.16), residues: 2776 helix: 0.87 (0.16), residues: 1170 sheet: 0.26 (0.30), residues: 338 loop : -2.56 (0.16), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP A 581 HIS 0.009 0.001 HIS A1480 PHE 0.024 0.001 PHE A1747 TYR 0.034 0.001 TYR A 764 ARG 0.009 0.000 ARG A 572 Details of bonding type rmsd link_BETA1-2 : bond 0.00588 ( 14) link_BETA1-2 : angle 2.85486 ( 42) hydrogen bonds : bond 0.03665 ( 917) hydrogen bonds : angle 4.49725 ( 2725) link_BETA1-3 : bond 0.00974 ( 2) link_BETA1-3 : angle 3.37283 ( 6) covalent geometry : bond 0.00268 (22422) covalent geometry : angle 0.67461 (30473) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 201 time to evaluate : 2.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 403 MET cc_start: 0.7906 (mtt) cc_final: 0.7509 (ptt) REVERT: A 534 GLU cc_start: 0.5975 (pm20) cc_final: 0.4612 (tp30) REVERT: A 581 TRP cc_start: 0.4225 (m100) cc_final: 0.3701 (m100) REVERT: A 800 MET cc_start: 0.6182 (mtm) cc_final: 0.5645 (tpt) REVERT: A 1086 TRP cc_start: 0.8429 (m100) cc_final: 0.8202 (m100) REVERT: A 1747 PHE cc_start: 0.7221 (p90) cc_final: 0.6895 (p90) REVERT: A 1822 ARG cc_start: 0.7812 (ttm-80) cc_final: 0.7092 (tpm170) REVERT: A 1979 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7361 (pp20) REVERT: A 1994 VAL cc_start: 0.8147 (m) cc_final: 0.7917 (m) REVERT: A 2520 LEU cc_start: 0.7546 (mt) cc_final: 0.6614 (pp) outliers start: 34 outliers final: 28 residues processed: 223 average time/residue: 0.3797 time to fit residues: 138.1664 Evaluate side-chains 209 residues out of total 2299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 181 time to evaluate : 2.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 466 PHE Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 630 MET Chi-restraints excluded: chain A residue 902 TYR Chi-restraints excluded: chain A residue 1166 GLU Chi-restraints excluded: chain A residue 1243 ASN Chi-restraints excluded: chain A residue 1408 LEU Chi-restraints excluded: chain A residue 1501 LEU Chi-restraints excluded: chain A residue 1603 ILE Chi-restraints excluded: chain A residue 1648 SER Chi-restraints excluded: chain A residue 1731 ILE Chi-restraints excluded: chain A residue 1976 MET Chi-restraints excluded: chain A residue 1991 VAL Chi-restraints excluded: chain A residue 2082 ASN Chi-restraints excluded: chain A residue 2158 THR Chi-restraints excluded: chain A residue 2238 SER Chi-restraints excluded: chain A residue 2294 MET Chi-restraints excluded: chain A residue 2335 VAL Chi-restraints excluded: chain A residue 2414 LEU Chi-restraints excluded: chain A residue 2433 LEU Chi-restraints excluded: chain A residue 2438 VAL Chi-restraints excluded: chain A residue 2691 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 58 optimal weight: 6.9990 chunk 99 optimal weight: 0.8980 chunk 257 optimal weight: 4.9990 chunk 170 optimal weight: 7.9990 chunk 179 optimal weight: 0.9990 chunk 221 optimal weight: 0.9980 chunk 264 optimal weight: 7.9990 chunk 131 optimal weight: 5.9990 chunk 152 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 198 optimal weight: 20.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1353 GLN A1480 HIS ** A1516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1585 GLN A2351 GLN ** A2412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2700 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.130304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.111054 restraints weight = 94471.276| |-----------------------------------------------------------------------------| r_work (start): 0.4045 rms_B_bonded: 4.81 r_work (final): 0.4045 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4041 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4041 r_free = 0.4041 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4041 r_free = 0.4041 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4041 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.5562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 22438 Z= 0.180 Angle : 0.761 11.077 30521 Z= 0.385 Chirality : 0.046 0.191 3406 Planarity : 0.006 0.069 3947 Dihedral : 8.768 102.519 3444 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.72 % Allowed : 8.88 % Favored : 90.40 % Rotamer: Outliers : 1.89 % Allowed : 15.89 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.16), residues: 2776 helix: 0.60 (0.15), residues: 1185 sheet: 0.18 (0.30), residues: 339 loop : -2.62 (0.16), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 581 HIS 0.008 0.001 HIS A 592 PHE 0.026 0.002 PHE A2359 TYR 0.022 0.002 TYR A 29 ARG 0.011 0.001 ARG A2305 Details of bonding type rmsd link_BETA1-2 : bond 0.00574 ( 14) link_BETA1-2 : angle 2.87429 ( 42) hydrogen bonds : bond 0.04585 ( 917) hydrogen bonds : angle 4.62919 ( 2725) link_BETA1-3 : bond 0.00864 ( 2) link_BETA1-3 : angle 3.23360 ( 6) covalent geometry : bond 0.00405 (22422) covalent geometry : angle 0.75268 (30473) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 188 time to evaluate : 2.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.6604 (mmt) cc_final: 0.6331 (mmp) REVERT: A 165 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7480 (tt) REVERT: A 389 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7870 (mm) REVERT: A 800 MET cc_start: 0.6097 (mtm) cc_final: 0.5675 (tpt) REVERT: A 1086 TRP cc_start: 0.8452 (m100) cc_final: 0.8237 (m100) REVERT: A 1747 PHE cc_start: 0.7364 (p90) cc_final: 0.7058 (p90) REVERT: A 1822 ARG cc_start: 0.7715 (ttm-80) cc_final: 0.6895 (tpm170) REVERT: A 1994 VAL cc_start: 0.8183 (m) cc_final: 0.7959 (m) REVERT: A 2620 TRP cc_start: 0.7267 (t-100) cc_final: 0.7023 (t-100) outliers start: 38 outliers final: 25 residues processed: 217 average time/residue: 0.3329 time to fit residues: 118.3852 Evaluate side-chains 200 residues out of total 2299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 173 time to evaluate : 2.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 630 MET Chi-restraints excluded: chain A residue 1166 GLU Chi-restraints excluded: chain A residue 1243 ASN Chi-restraints excluded: chain A residue 1408 LEU Chi-restraints excluded: chain A residue 1686 VAL Chi-restraints excluded: chain A residue 1706 THR Chi-restraints excluded: chain A residue 1976 MET Chi-restraints excluded: chain A residue 1990 VAL Chi-restraints excluded: chain A residue 1991 VAL Chi-restraints excluded: chain A residue 2082 ASN Chi-restraints excluded: chain A residue 2130 LYS Chi-restraints excluded: chain A residue 2158 THR Chi-restraints excluded: chain A residue 2238 SER Chi-restraints excluded: chain A residue 2294 MET Chi-restraints excluded: chain A residue 2335 VAL Chi-restraints excluded: chain A residue 2414 LEU Chi-restraints excluded: chain A residue 2438 VAL Chi-restraints excluded: chain A residue 2457 VAL Chi-restraints excluded: chain A residue 2691 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 117 optimal weight: 9.9990 chunk 119 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 219 optimal weight: 1.9990 chunk 239 optimal weight: 0.6980 chunk 146 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 136 optimal weight: 7.9990 chunk 12 optimal weight: 0.7980 chunk 229 optimal weight: 3.9990 chunk 168 optimal weight: 0.8980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 592 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1430 GLN A1480 HIS ** A1516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1942 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2454 ASN ** A2681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2700 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.130327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.110069 restraints weight = 125478.186| |-----------------------------------------------------------------------------| r_work (start): 0.4039 rms_B_bonded: 5.74 r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4036 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4036 r_free = 0.4036 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4036 r_free = 0.4036 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4036 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.5900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 22438 Z= 0.152 Angle : 0.707 11.733 30521 Z= 0.356 Chirality : 0.044 0.184 3406 Planarity : 0.005 0.068 3947 Dihedral : 8.285 101.677 3444 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.69 % Allowed : 8.45 % Favored : 90.87 % Rotamer: Outliers : 1.80 % Allowed : 16.56 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.16), residues: 2776 helix: 0.71 (0.16), residues: 1182 sheet: 0.18 (0.30), residues: 340 loop : -2.58 (0.16), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 581 HIS 0.006 0.001 HIS A1950 PHE 0.020 0.001 PHE A 465 TYR 0.036 0.002 TYR A 764 ARG 0.010 0.001 ARG A2305 Details of bonding type rmsd link_BETA1-2 : bond 0.00563 ( 14) link_BETA1-2 : angle 2.79957 ( 42) hydrogen bonds : bond 0.04068 ( 917) hydrogen bonds : angle 4.53575 ( 2725) link_BETA1-3 : bond 0.00872 ( 2) link_BETA1-3 : angle 3.73803 ( 6) covalent geometry : bond 0.00340 (22422) covalent geometry : angle 0.69835 (30473) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 184 time to evaluate : 2.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 ASP cc_start: 0.7129 (m-30) cc_final: 0.6865 (m-30) REVERT: A 386 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7905 (mt-10) REVERT: A 389 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7901 (mm) REVERT: A 1086 TRP cc_start: 0.8439 (m100) cc_final: 0.8150 (m100) REVERT: A 1747 PHE cc_start: 0.7496 (p90) cc_final: 0.7090 (p90) REVERT: A 1822 ARG cc_start: 0.7757 (ttm-80) cc_final: 0.6842 (tpm170) REVERT: A 2620 TRP cc_start: 0.7314 (t-100) cc_final: 0.6979 (t-100) REVERT: A 2785 TRP cc_start: 0.5422 (m-10) cc_final: 0.4923 (m100) outliers start: 36 outliers final: 27 residues processed: 210 average time/residue: 0.3170 time to fit residues: 109.2287 Evaluate side-chains 197 residues out of total 2299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 169 time to evaluate : 2.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 466 PHE Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 630 MET Chi-restraints excluded: chain A residue 1166 GLU Chi-restraints excluded: chain A residue 1243 ASN Chi-restraints excluded: chain A residue 1408 LEU Chi-restraints excluded: chain A residue 1501 LEU Chi-restraints excluded: chain A residue 1603 ILE Chi-restraints excluded: chain A residue 1648 SER Chi-restraints excluded: chain A residue 1686 VAL Chi-restraints excluded: chain A residue 1706 THR Chi-restraints excluded: chain A residue 1976 MET Chi-restraints excluded: chain A residue 1990 VAL Chi-restraints excluded: chain A residue 1991 VAL Chi-restraints excluded: chain A residue 2082 ASN Chi-restraints excluded: chain A residue 2158 THR Chi-restraints excluded: chain A residue 2238 SER Chi-restraints excluded: chain A residue 2294 MET Chi-restraints excluded: chain A residue 2335 VAL Chi-restraints excluded: chain A residue 2414 LEU Chi-restraints excluded: chain A residue 2438 VAL Chi-restraints excluded: chain A residue 2691 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 0 optimal weight: 10.0000 chunk 106 optimal weight: 7.9990 chunk 96 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 156 optimal weight: 5.9990 chunk 121 optimal weight: 6.9990 chunk 137 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 chunk 243 optimal weight: 9.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 592 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1480 HIS ** A1516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1733 HIS ** A1942 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2527 ASN ** A2681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2700 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.129094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.109323 restraints weight = 104255.734| |-----------------------------------------------------------------------------| r_work (start): 0.3985 rms_B_bonded: 5.08 r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3991 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3991 r_free = 0.3991 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3991 r_free = 0.3991 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3991 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.6262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 22438 Z= 0.170 Angle : 0.747 11.447 30521 Z= 0.378 Chirality : 0.046 0.191 3406 Planarity : 0.005 0.066 3947 Dihedral : 8.120 101.893 3444 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.69 % Allowed : 9.03 % Favored : 90.29 % Rotamer: Outliers : 2.12 % Allowed : 17.28 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.16), residues: 2776 helix: 0.64 (0.15), residues: 1186 sheet: 0.13 (0.31), residues: 333 loop : -2.56 (0.16), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 581 HIS 0.005 0.001 HIS A 62 PHE 0.022 0.002 PHE A 465 TYR 0.017 0.002 TYR A 331 ARG 0.009 0.001 ARG A 259 Details of bonding type rmsd link_BETA1-2 : bond 0.00562 ( 14) link_BETA1-2 : angle 2.80161 ( 42) hydrogen bonds : bond 0.04365 ( 917) hydrogen bonds : angle 4.56928 ( 2725) link_BETA1-3 : bond 0.00900 ( 2) link_BETA1-3 : angle 3.78103 ( 6) covalent geometry : bond 0.00387 (22422) covalent geometry : angle 0.73819 (30473) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 167 time to evaluate : 2.465 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8407 (mtm180) REVERT: A 297 ASP cc_start: 0.7352 (m-30) cc_final: 0.7091 (m-30) REVERT: A 386 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7657 (mt-10) REVERT: A 911 MET cc_start: 0.5772 (tpt) cc_final: 0.5176 (tpp) REVERT: A 1086 TRP cc_start: 0.8475 (m100) cc_final: 0.8210 (m100) REVERT: A 1289 LEU cc_start: 0.7091 (tt) cc_final: 0.6879 (tp) REVERT: A 1747 PHE cc_start: 0.7641 (p90) cc_final: 0.7262 (p90) REVERT: A 1822 ARG cc_start: 0.7643 (ttm-80) cc_final: 0.6962 (tpm170) REVERT: A 2520 LEU cc_start: 0.8380 (mt) cc_final: 0.7978 (mp) REVERT: A 2628 GLU cc_start: 0.5554 (OUTLIER) cc_final: 0.5337 (tm-30) REVERT: A 2785 TRP cc_start: 0.5835 (m-10) cc_final: 0.5473 (m100) outliers start: 43 outliers final: 31 residues processed: 201 average time/residue: 0.3296 time to fit residues: 107.9644 Evaluate side-chains 194 residues out of total 2299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 161 time to evaluate : 2.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 466 PHE Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 630 MET Chi-restraints excluded: chain A residue 1166 GLU Chi-restraints excluded: chain A residue 1408 LEU Chi-restraints excluded: chain A residue 1501 LEU Chi-restraints excluded: chain A residue 1603 ILE Chi-restraints excluded: chain A residue 1646 LEU Chi-restraints excluded: chain A residue 1686 VAL Chi-restraints excluded: chain A residue 1706 THR Chi-restraints excluded: chain A residue 1976 MET Chi-restraints excluded: chain A residue 1990 VAL Chi-restraints excluded: chain A residue 1991 VAL Chi-restraints excluded: chain A residue 2082 ASN Chi-restraints excluded: chain A residue 2130 LYS Chi-restraints excluded: chain A residue 2158 THR Chi-restraints excluded: chain A residue 2204 VAL Chi-restraints excluded: chain A residue 2238 SER Chi-restraints excluded: chain A residue 2294 MET Chi-restraints excluded: chain A residue 2335 VAL Chi-restraints excluded: chain A residue 2414 LEU Chi-restraints excluded: chain A residue 2433 LEU Chi-restraints excluded: chain A residue 2438 VAL Chi-restraints excluded: chain A residue 2457 VAL Chi-restraints excluded: chain A residue 2628 GLU Chi-restraints excluded: chain A residue 2687 THR Chi-restraints excluded: chain A residue 2691 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 126 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 chunk 210 optimal weight: 0.0000 chunk 77 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 128 optimal weight: 0.5980 chunk 248 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 239 optimal weight: 2.9990 chunk 182 optimal weight: 5.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1243 ASN A1480 HIS ** A1516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1585 GLN ** A1942 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2700 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.130959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.111364 restraints weight = 100226.068| |-----------------------------------------------------------------------------| r_work (start): 0.4026 rms_B_bonded: 5.33 r_work (final): 0.4026 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4026 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4026 r_free = 0.4026 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4026 r_free = 0.4026 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4026 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.6314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22438 Z= 0.130 Angle : 0.701 11.492 30521 Z= 0.353 Chirality : 0.044 0.197 3406 Planarity : 0.005 0.066 3947 Dihedral : 7.902 102.082 3444 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.65 % Allowed : 8.34 % Favored : 91.01 % Rotamer: Outliers : 1.80 % Allowed : 17.55 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.16), residues: 2776 helix: 0.71 (0.16), residues: 1201 sheet: 0.34 (0.31), residues: 324 loop : -2.54 (0.16), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.002 TRP A 581 HIS 0.005 0.001 HIS A 511 PHE 0.031 0.001 PHE A 251 TYR 0.036 0.001 TYR A 764 ARG 0.010 0.001 ARG A 572 Details of bonding type rmsd link_BETA1-2 : bond 0.00560 ( 14) link_BETA1-2 : angle 2.72672 ( 42) hydrogen bonds : bond 0.03822 ( 917) hydrogen bonds : angle 4.41331 ( 2725) link_BETA1-3 : bond 0.00935 ( 2) link_BETA1-3 : angle 3.60067 ( 6) covalent geometry : bond 0.00283 (22422) covalent geometry : angle 0.69261 (30473) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 174 time to evaluate : 2.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.7420 (OUTLIER) cc_final: 0.6911 (tmm) REVERT: A 297 ASP cc_start: 0.7233 (m-30) cc_final: 0.6966 (m-30) REVERT: A 386 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7657 (mt-10) REVERT: A 591 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8359 (mt) REVERT: A 800 MET cc_start: 0.6363 (mtt) cc_final: 0.5734 (tpt) REVERT: A 911 MET cc_start: 0.5761 (tpt) cc_final: 0.5303 (tpp) REVERT: A 1086 TRP cc_start: 0.8485 (m100) cc_final: 0.8255 (m100) REVERT: A 1747 PHE cc_start: 0.7560 (p90) cc_final: 0.7178 (p90) REVERT: A 1822 ARG cc_start: 0.7539 (ttm-80) cc_final: 0.6552 (tpm170) REVERT: A 2520 LEU cc_start: 0.8349 (mt) cc_final: 0.8003 (mp) REVERT: A 2620 TRP cc_start: 0.7134 (t-100) cc_final: 0.6763 (t-100) REVERT: A 2628 GLU cc_start: 0.5517 (OUTLIER) cc_final: 0.5132 (tm-30) REVERT: A 2785 TRP cc_start: 0.6123 (m-10) cc_final: 0.5737 (m100) REVERT: A 2809 THR cc_start: 0.6265 (m) cc_final: 0.5925 (m) outliers start: 36 outliers final: 29 residues processed: 202 average time/residue: 0.2995 time to fit residues: 100.9743 Evaluate side-chains 199 residues out of total 2299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 167 time to evaluate : 2.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 466 PHE Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 630 MET Chi-restraints excluded: chain A residue 893 MET Chi-restraints excluded: chain A residue 1166 GLU Chi-restraints excluded: chain A residue 1243 ASN Chi-restraints excluded: chain A residue 1408 LEU Chi-restraints excluded: chain A residue 1501 LEU Chi-restraints excluded: chain A residue 1603 ILE Chi-restraints excluded: chain A residue 1646 LEU Chi-restraints excluded: chain A residue 1648 SER Chi-restraints excluded: chain A residue 1686 VAL Chi-restraints excluded: chain A residue 1706 THR Chi-restraints excluded: chain A residue 1976 MET Chi-restraints excluded: chain A residue 1990 VAL Chi-restraints excluded: chain A residue 1991 VAL Chi-restraints excluded: chain A residue 2158 THR Chi-restraints excluded: chain A residue 2204 VAL Chi-restraints excluded: chain A residue 2238 SER Chi-restraints excluded: chain A residue 2294 MET Chi-restraints excluded: chain A residue 2335 VAL Chi-restraints excluded: chain A residue 2414 LEU Chi-restraints excluded: chain A residue 2433 LEU Chi-restraints excluded: chain A residue 2438 VAL Chi-restraints excluded: chain A residue 2457 VAL Chi-restraints excluded: chain A residue 2628 GLU Chi-restraints excluded: chain A residue 2687 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 245 optimal weight: 8.9990 chunk 89 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 140 optimal weight: 0.8980 chunk 6 optimal weight: 0.0030 chunk 114 optimal weight: 0.9990 chunk 77 optimal weight: 7.9990 chunk 232 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 878 GLN A1243 ASN A1480 HIS ** A1516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1942 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.132852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.112852 restraints weight = 135718.983| |-----------------------------------------------------------------------------| r_work (start): 0.4049 rms_B_bonded: 5.86 r_work (final): 0.4049 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4051 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4051 r_free = 0.4051 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4051 r_free = 0.4051 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4051 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.6387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 22438 Z= 0.126 Angle : 0.696 12.337 30521 Z= 0.347 Chirality : 0.044 0.207 3406 Planarity : 0.005 0.065 3947 Dihedral : 7.734 102.030 3444 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.65 % Allowed : 8.52 % Favored : 90.83 % Rotamer: Outliers : 1.67 % Allowed : 17.82 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.16), residues: 2776 helix: 0.78 (0.16), residues: 1195 sheet: 0.37 (0.31), residues: 318 loop : -2.54 (0.16), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.002 TRP A 581 HIS 0.004 0.001 HIS A 511 PHE 0.026 0.001 PHE A 465 TYR 0.037 0.001 TYR A 764 ARG 0.007 0.000 ARG A2305 Details of bonding type rmsd link_BETA1-2 : bond 0.00547 ( 14) link_BETA1-2 : angle 2.70408 ( 42) hydrogen bonds : bond 0.03654 ( 917) hydrogen bonds : angle 4.34084 ( 2725) link_BETA1-3 : bond 0.00831 ( 2) link_BETA1-3 : angle 3.47686 ( 6) covalent geometry : bond 0.00274 (22422) covalent geometry : angle 0.68710 (30473) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 175 time to evaluate : 2.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.7516 (OUTLIER) cc_final: 0.7015 (tmm) REVERT: A 251 PHE cc_start: 0.6775 (t80) cc_final: 0.6544 (t80) REVERT: A 297 ASP cc_start: 0.7211 (m-30) cc_final: 0.6953 (m-30) REVERT: A 386 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7614 (mt-10) REVERT: A 466 PHE cc_start: 0.7008 (OUTLIER) cc_final: 0.6609 (t80) REVERT: A 800 MET cc_start: 0.6544 (mtt) cc_final: 0.5881 (tpt) REVERT: A 876 ASN cc_start: 0.8174 (m-40) cc_final: 0.7765 (t0) REVERT: A 878 GLN cc_start: 0.7904 (OUTLIER) cc_final: 0.6818 (tp40) REVERT: A 911 MET cc_start: 0.5877 (tpt) cc_final: 0.5463 (tpp) REVERT: A 1747 PHE cc_start: 0.7499 (p90) cc_final: 0.7147 (p90) REVERT: A 1822 ARG cc_start: 0.7419 (ttm-80) cc_final: 0.6563 (tpm170) REVERT: A 2520 LEU cc_start: 0.8309 (mt) cc_final: 0.8000 (mp) REVERT: A 2620 TRP cc_start: 0.7207 (t-100) cc_final: 0.6896 (t-100) REVERT: A 2628 GLU cc_start: 0.5676 (OUTLIER) cc_final: 0.5399 (tm-30) REVERT: A 2785 TRP cc_start: 0.6027 (m-10) cc_final: 0.5685 (m100) REVERT: A 2809 THR cc_start: 0.6402 (m) cc_final: 0.6063 (m) outliers start: 33 outliers final: 26 residues processed: 200 average time/residue: 0.3107 time to fit residues: 103.7424 Evaluate side-chains 197 residues out of total 2299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 167 time to evaluate : 2.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 466 PHE Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 630 MET Chi-restraints excluded: chain A residue 878 GLN Chi-restraints excluded: chain A residue 1166 GLU Chi-restraints excluded: chain A residue 1243 ASN Chi-restraints excluded: chain A residue 1408 LEU Chi-restraints excluded: chain A residue 1501 LEU Chi-restraints excluded: chain A residue 1603 ILE Chi-restraints excluded: chain A residue 1646 LEU Chi-restraints excluded: chain A residue 1648 SER Chi-restraints excluded: chain A residue 1686 VAL Chi-restraints excluded: chain A residue 1706 THR Chi-restraints excluded: chain A residue 1976 MET Chi-restraints excluded: chain A residue 1990 VAL Chi-restraints excluded: chain A residue 1991 VAL Chi-restraints excluded: chain A residue 2158 THR Chi-restraints excluded: chain A residue 2204 VAL Chi-restraints excluded: chain A residue 2236 ASP Chi-restraints excluded: chain A residue 2238 SER Chi-restraints excluded: chain A residue 2294 MET Chi-restraints excluded: chain A residue 2335 VAL Chi-restraints excluded: chain A residue 2414 LEU Chi-restraints excluded: chain A residue 2438 VAL Chi-restraints excluded: chain A residue 2457 VAL Chi-restraints excluded: chain A residue 2628 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 247 optimal weight: 2.9990 chunk 223 optimal weight: 0.0870 chunk 246 optimal weight: 0.9990 chunk 241 optimal weight: 0.9990 chunk 212 optimal weight: 0.9990 chunk 170 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 138 optimal weight: 0.7980 chunk 84 optimal weight: 5.9990 chunk 171 optimal weight: 4.9990 chunk 187 optimal weight: 0.8980 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1480 HIS ** A1516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1942 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.131283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.111764 restraints weight = 110517.193| |-----------------------------------------------------------------------------| r_work (start): 0.4056 rms_B_bonded: 5.44 r_work (final): 0.4056 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4058 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4058 r_free = 0.4058 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4058 r_free = 0.4058 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4058 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.6405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.266 22438 Z= 0.228 Angle : 0.882 59.196 30521 Z= 0.491 Chirality : 0.048 1.161 3406 Planarity : 0.006 0.205 3947 Dihedral : 7.754 102.124 3444 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.69 % Allowed : 8.52 % Favored : 90.79 % Rotamer: Outliers : 1.58 % Allowed : 17.87 % Favored : 80.56 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.16), residues: 2776 helix: 0.77 (0.16), residues: 1195 sheet: 0.38 (0.31), residues: 318 loop : -2.55 (0.16), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.094 0.002 TRP A 581 HIS 0.004 0.001 HIS A 511 PHE 0.026 0.001 PHE A 465 TYR 0.045 0.002 TYR A 574 ARG 0.007 0.000 ARG A2305 Details of bonding type rmsd link_BETA1-2 : bond 0.00532 ( 14) link_BETA1-2 : angle 2.70740 ( 42) hydrogen bonds : bond 0.03701 ( 917) hydrogen bonds : angle 4.34567 ( 2725) link_BETA1-3 : bond 0.01009 ( 2) link_BETA1-3 : angle 3.63348 ( 6) covalent geometry : bond 0.00454 (22422) covalent geometry : angle 0.87595 (30473) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9762.36 seconds wall clock time: 169 minutes 50.52 seconds (10190.52 seconds total)