Starting phenix.real_space_refine on Fri Sep 19 02:26:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rf0_19114/09_2025/8rf0_19114.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rf0_19114/09_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_19114/09_2025/8rf0_19114.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rf0_19114/09_2025/8rf0_19114.map" model { file = "/net/cci-nas-00/data/ceres_data/8rf0_19114/09_2025/8rf0_19114.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rf0_19114/09_2025/8rf0_19114.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.019 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ARG:plan': 7, 'GLU:plan': 6, 'GLN:plan1': 4, 'ASP:plan': 9, 'HIS:plan': 1, 'TRP:plan': 2, 'PHE:plan': 4, 'ASN:plan1': 3} 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: {'ARG:plan': 7, 'GLU:plan': 6, 'GLN:plan1': 4, 'ASP:plan': 9, 'HIS:plan': 1, 'TRP:plan': 2, 'PHE:plan': 4, 'ASN:plan1': 3} 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: 9.56, per 1000 atoms: 0.44 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: 2.14 Conformation dependent library (CDL) restraints added in 1.8 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.52 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: 7.06 Time building geometry restraints manager: 2.81 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: 1.790 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 31.120 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.940 ------------------------------------------------------------------------------- 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 : 10.45 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (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 ARG 0.005 0.000 ARG A1324 TYR 0.012 0.001 TYR A 931 PHE 0.016 0.001 PHE A 238 TRP 0.049 0.001 TRP A 967 HIS 0.004 0.001 HIS A 569 Details of bonding type rmsd covalent geometry : bond 0.00374 (22422) covalent geometry : angle 0.73031 (30473) hydrogen bonds : bond 0.19549 ( 917) hydrogen bonds : angle 7.05529 ( 2725) link_BETA1-2 : bond 0.01056 ( 14) link_BETA1-2 : angle 2.92920 ( 42) link_BETA1-3 : bond 0.01226 ( 2) link_BETA1-3 : angle 1.54776 ( 6) *********************** 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 : 0.867 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: 0.3372 (mm) REVERT: A 232 PRO cc_start: 0.8523 (Cg_endo) cc_final: 0.8303 (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: 0.7223 (tmm) REVERT: A 467 VAL cc_start: 0.7893 (t) cc_final: 0.7225 (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: 0.7222 (tt) REVERT: A 582 MET cc_start: 0.6806 (ppp) cc_final: 0.6062 (ppp) REVERT: A 643 HIS cc_start: 0.7334 (t70) cc_final: 0.7056 (t70) REVERT: A 798 TRP cc_start: 0.7048 (t60) cc_final: 0.6842 (t-100) REVERT: A 800 MET cc_start: 0.4891 (mtm) cc_final: 0.4435 (tpt) REVERT: A 824 MET cc_start: 0.5377 (mtt) cc_final: 0.5117 (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: 0.4579 (tpp) REVERT: A 931 TYR cc_start: 0.6049 (m-10) cc_final: 0.5759 (m-10) REVERT: A 1750 ASP cc_start: 0.7783 (t0) cc_final: 0.7191 (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: 0.2667 (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: 0.6180 (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: 0.5390 (t) outliers start: 6 outliers final: 3 residues processed: 543 average time/residue: 0.2140 time to fit residues: 166.4663 Evaluate side-chains 255 residues out of total 2299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 252 time to evaluate : 0.844 ------------------------------------------------------------------------------- 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 197 optimal weight: 5.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.1980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.0170 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.0970 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 7.9990 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 ASN A 934 GLN A1053 GLN A1111 HIS A1362 GLN A1480 HIS ** A1516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1567 HIS 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.148470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.128806 restraints weight = 103853.239| |-----------------------------------------------------------------------------| r_work (start): 0.4295 rms_B_bonded: 5.69 r_work (final): 0.4295 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4295 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4295 r_free = 0.4295 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4294 r_free = 0.4294 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.4294 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6817 moved from start: 0.2722 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= 0.146 Angle : 0.745 13.779 30521 Z= 0.371 Chirality : 0.046 0.219 3406 Planarity : 0.006 0.139 3947 Dihedral : 12.388 113.980 3452 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.65 % Allowed : 8.70 % Favored : 90.65 % Rotamer: Outliers : 1.67 % Allowed : 10.58 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.10 (0.16), residues: 2776 helix: 0.80 (0.16), residues: 1149 sheet: 0.20 (0.30), residues: 330 loop : -2.52 (0.16), residues: 1297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 572 TYR 0.036 0.002 TYR A 139 PHE 0.030 0.002 PHE A2359 TRP 0.039 0.002 TRP A2785 HIS 0.014 0.001 HIS A1823 Details of bonding type rmsd covalent geometry : bond 0.00314 (22422) covalent geometry : angle 0.73706 (30473) hydrogen bonds : bond 0.04291 ( 917) hydrogen bonds : angle 5.22230 ( 2725) link_BETA1-2 : bond 0.00581 ( 14) link_BETA1-2 : angle 2.77881 ( 42) link_BETA1-3 : bond 0.00655 ( 2) link_BETA1-3 : angle 3.17906 ( 6) *********************** 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 299 residues out of total 2299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 266 time to evaluate : 0.929 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: 0.3823 (mt) cc_final: 0.3074 (mm) REVERT: A 290 LYS cc_start: 0.8816 (mttp) cc_final: 0.8608 (mptt) REVERT: A 505 MET cc_start: 0.8015 (mmp) cc_final: 0.7739 (mmt) REVERT: A 598 LEU cc_start: 0.8323 (mt) cc_final: 0.8088 (mt) REVERT: A 643 HIS cc_start: 0.7845 (t70) cc_final: 0.7577 (t70) REVERT: A 931 TYR cc_start: 0.6151 (m-10) cc_final: 0.5833 (m-10) REVERT: A 1153 ASP cc_start: 0.4040 (m-30) cc_final: 0.2756 (m-30) REVERT: A 1244 MET cc_start: 0.7266 (mtt) cc_final: 0.7024 (mtt) REVERT: A 1398 TYR cc_start: 0.7272 (m-80) cc_final: 0.7066 (m-80) REVERT: A 1816 LYS cc_start: 0.8600 (mmtm) cc_final: 0.8158 (tmmt) REVERT: A 1822 ARG cc_start: 0.7687 (ttm-80) cc_final: 0.7005 (tpm170) REVERT: A 2273 ILE cc_start: 0.6512 (tt) cc_final: 0.6232 (tt) REVERT: A 2479 MET cc_start: 0.6383 (mmt) cc_final: 0.6083 (mmp) outliers start: 33 outliers final: 19 residues processed: 288 average time/residue: 0.1773 time to fit residues: 78.6348 Evaluate side-chains 229 residues out of total 2299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 210 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ARG 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 1143 ILE 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 1991 VAL Chi-restraints excluded: chain A residue 2082 ASN Chi-restraints excluded: chain A residue 2145 MET Chi-restraints excluded: chain A residue 2335 VAL Chi-restraints excluded: chain A residue 2414 LEU Chi-restraints excluded: chain A residue 2578 LEU 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 202 optimal weight: 2.9990 chunk 191 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 201 optimal weight: 5.9990 chunk 128 optimal weight: 0.0870 chunk 99 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 119 optimal weight: 0.9990 chunk 139 optimal weight: 9.9990 chunk 263 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 overall best weight: 1.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 595 ASN A 934 GLN 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.138831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.117844 restraints weight = 127327.794| |-----------------------------------------------------------------------------| r_work (start): 0.4127 rms_B_bonded: 6.26 r_work (final): 0.4127 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4127 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4127 r_free = 0.4127 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4127 r_free = 0.4127 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4127 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 22438 Z= 0.188 Angle : 0.769 13.996 30521 Z= 0.390 Chirality : 0.047 0.217 3406 Planarity : 0.006 0.091 3947 Dihedral : 9.831 124.049 3448 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.72 % Allowed : 8.23 % Favored : 91.05 % Rotamer: Outliers : 2.21 % Allowed : 12.87 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.12 (0.16), residues: 2776 helix: 0.65 (0.16), residues: 1184 sheet: 0.23 (0.30), residues: 332 loop : -2.49 (0.16), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1711 TYR 0.020 0.002 TYR A 331 PHE 0.022 0.002 PHE A2359 TRP 0.037 0.002 TRP A2785 HIS 0.011 0.002 HIS A 592 Details of bonding type rmsd covalent geometry : bond 0.00416 (22422) covalent geometry : angle 0.76092 (30473) hydrogen bonds : bond 0.04652 ( 917) hydrogen bonds : angle 4.87282 ( 2725) link_BETA1-2 : bond 0.00642 ( 14) link_BETA1-2 : angle 2.84943 ( 42) link_BETA1-3 : bond 0.00943 ( 2) link_BETA1-3 : angle 2.99846 ( 6) *********************** 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 273 residues out of total 2299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 228 time to evaluate : 0.870 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 591 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8278 (pp) REVERT: A 799 LYS cc_start: 0.8036 (pttp) cc_final: 0.7363 (ptpt) REVERT: A 911 MET cc_start: 0.6282 (tpp) cc_final: 0.5826 (tpt) REVERT: A 931 TYR cc_start: 0.6384 (m-10) cc_final: 0.5926 (m-10) REVERT: A 1822 ARG cc_start: 0.7631 (ttm-80) cc_final: 0.7059 (tpm170) REVERT: A 1979 GLU cc_start: 0.7588 (mm-30) cc_final: 0.7271 (pp20) REVERT: A 1994 VAL cc_start: 0.8354 (m) cc_final: 0.8126 (m) REVERT: A 2425 ASP cc_start: 0.7623 (m-30) cc_final: 0.7293 (p0) REVERT: A 2571 TRP cc_start: 0.7108 (m-10) cc_final: 0.6705 (m-10) outliers start: 45 outliers final: 25 residues processed: 258 average time/residue: 0.1617 time to fit residues: 65.9185 Evaluate side-chains 215 residues out of total 2299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 189 time to evaluate : 0.852 ------------------------------------------------------------------------------- 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 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 1143 ILE Chi-restraints excluded: chain A residue 1166 GLU Chi-restraints excluded: chain A residue 1408 LEU Chi-restraints excluded: chain A residue 1603 ILE 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 2082 ASN Chi-restraints excluded: chain A residue 2238 SER 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 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 257 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 93 optimal weight: 0.0970 chunk 33 optimal weight: 5.9990 chunk 233 optimal weight: 0.9990 chunk 231 optimal weight: 0.9990 chunk 127 optimal weight: 0.9980 chunk 277 optimal weight: 0.6980 chunk 188 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 HIS A 595 ASN A 934 GLN A1206 ASN A1480 HIS ** A1516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2527 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.139571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.119677 restraints weight = 102893.708| |-----------------------------------------------------------------------------| r_work (start): 0.4162 rms_B_bonded: 5.39 r_work (final): 0.4162 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4161 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4161 r_free = 0.4161 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4161 r_free = 0.4161 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4161 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.4215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 22438 Z= 0.133 Angle : 0.706 12.611 30521 Z= 0.350 Chirality : 0.044 0.206 3406 Planarity : 0.005 0.087 3947 Dihedral : 9.150 118.946 3444 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.72 % Allowed : 7.76 % Favored : 91.52 % Rotamer: Outliers : 1.94 % Allowed : 14.22 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.16), residues: 2776 helix: 0.76 (0.16), residues: 1181 sheet: 0.15 (0.30), residues: 333 loop : -2.45 (0.16), residues: 1262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1412 TYR 0.021 0.001 TYR A 331 PHE 0.025 0.001 PHE A2359 TRP 0.034 0.001 TRP A2785 HIS 0.009 0.001 HIS A1480 Details of bonding type rmsd covalent geometry : bond 0.00287 (22422) covalent geometry : angle 0.69662 (30473) hydrogen bonds : bond 0.03873 ( 917) hydrogen bonds : angle 4.61350 ( 2725) link_BETA1-2 : bond 0.00595 ( 14) link_BETA1-2 : angle 2.91744 ( 42) link_BETA1-3 : bond 0.00919 ( 2) link_BETA1-3 : angle 3.61297 ( 6) *********************** 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 244 residues out of total 2299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 205 time to evaluate : 0.886 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 582 MET cc_start: 0.6475 (tmm) cc_final: 0.5970 (tmm) REVERT: A 591 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8434 (pp) REVERT: A 592 HIS cc_start: 0.5680 (m-70) cc_final: 0.4894 (m-70) REVERT: A 911 MET cc_start: 0.6213 (tpp) cc_final: 0.5018 (tpt) REVERT: A 1244 MET cc_start: 0.7486 (mtt) cc_final: 0.7248 (mtt) REVERT: A 1822 ARG cc_start: 0.7605 (ttm-80) cc_final: 0.6990 (tpm170) REVERT: A 1956 ARG cc_start: 0.6942 (mmm160) cc_final: 0.6713 (mmm160) REVERT: A 1979 GLU cc_start: 0.7459 (mm-30) cc_final: 0.7220 (pp20) REVERT: A 1994 VAL cc_start: 0.8298 (m) cc_final: 0.8075 (m) REVERT: A 2195 LEU cc_start: 0.7528 (OUTLIER) cc_final: 0.7160 (mt) outliers start: 39 outliers final: 31 residues processed: 233 average time/residue: 0.1554 time to fit residues: 59.6565 Evaluate side-chains 222 residues out of total 2299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 189 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 621 MET Chi-restraints excluded: chain A residue 630 MET Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 934 GLN Chi-restraints excluded: chain A residue 1048 VAL Chi-restraints excluded: chain A residue 1143 ILE 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 1648 SER 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 2195 LEU Chi-restraints excluded: chain A residue 2236 ASP 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 2578 LEU Chi-restraints excluded: chain A residue 2687 THR 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 18 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 189 optimal weight: 7.9990 chunk 180 optimal weight: 0.0980 chunk 11 optimal weight: 0.9990 chunk 69 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 chunk 179 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 chunk 105 optimal weight: 0.8980 chunk 270 optimal weight: 8.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1209 HIS A1243 ASN A1353 GLN A1480 HIS A1516 GLN A1585 GLN ** A1658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2056 ASN ** A2104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2351 GLN A2365 ASN ** 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.129829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.110651 restraints weight = 114946.927| |-----------------------------------------------------------------------------| r_work (start): 0.4013 rms_B_bonded: 5.22 r_work (final): 0.4013 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4011 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4011 r_free = 0.4011 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4011 r_free = 0.4011 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4011 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.5406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 22438 Z= 0.227 Angle : 0.815 11.496 30521 Z= 0.419 Chirality : 0.049 0.287 3406 Planarity : 0.006 0.069 3947 Dihedral : 9.189 114.217 3444 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.72 % Allowed : 9.60 % Favored : 89.68 % Rotamer: Outliers : 2.25 % Allowed : 15.71 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.41 (0.16), residues: 2776 helix: 0.36 (0.15), residues: 1193 sheet: 0.13 (0.30), residues: 332 loop : -2.63 (0.16), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 933 TYR 0.030 0.003 TYR A 764 PHE 0.039 0.002 PHE A1747 TRP 0.032 0.003 TRP A2747 HIS 0.010 0.002 HIS A1480 Details of bonding type rmsd covalent geometry : bond 0.00515 (22422) covalent geometry : angle 0.80639 (30473) hydrogen bonds : bond 0.05209 ( 917) hydrogen bonds : angle 4.86060 ( 2725) link_BETA1-2 : bond 0.00591 ( 14) link_BETA1-2 : angle 3.02368 ( 42) link_BETA1-3 : bond 0.00842 ( 2) link_BETA1-3 : angle 3.23419 ( 6) *********************** 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 252 residues out of total 2299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 206 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 HIS cc_start: 0.6793 (m-70) cc_final: 0.6571 (m-70) REVERT: A 389 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7886 (mm) REVERT: A 685 PHE cc_start: 0.8127 (OUTLIER) cc_final: 0.7890 (m-80) REVERT: A 1086 TRP cc_start: 0.8410 (m100) cc_final: 0.8002 (m100) REVERT: A 1822 ARG cc_start: 0.7768 (ttm-80) cc_final: 0.7013 (tpm170) REVERT: A 1841 GLN cc_start: 0.8289 (tt0) cc_final: 0.8039 (tt0) REVERT: A 1979 GLU cc_start: 0.7620 (mm-30) cc_final: 0.7379 (pp20) REVERT: A 1994 VAL cc_start: 0.8076 (m) cc_final: 0.7850 (m) REVERT: A 2195 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.7278 (mt) REVERT: A 2620 TRP cc_start: 0.7284 (t-100) cc_final: 0.6904 (t-100) outliers start: 46 outliers final: 30 residues processed: 238 average time/residue: 0.1556 time to fit residues: 59.7676 Evaluate side-chains 215 residues out of total 2299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 182 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 255 TRP 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 598 LEU Chi-restraints excluded: chain A residue 630 MET Chi-restraints excluded: chain A residue 685 PHE 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 1476 ASN Chi-restraints excluded: chain A residue 1603 ILE Chi-restraints excluded: chain A residue 1686 VAL Chi-restraints excluded: chain A residue 1814 VAL 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 2195 LEU 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 2433 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 152 optimal weight: 3.9990 chunk 164 optimal weight: 3.9990 chunk 126 optimal weight: 0.9980 chunk 139 optimal weight: 5.9990 chunk 187 optimal weight: 4.9990 chunk 218 optimal weight: 2.9990 chunk 222 optimal weight: 4.9990 chunk 85 optimal weight: 9.9990 chunk 54 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 119 optimal weight: 5.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 934 GLN A1243 ASN A1430 GLN A1480 HIS A1658 HIS ** A2412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2454 ASN A2681 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.128487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.107845 restraints weight = 125661.026| |-----------------------------------------------------------------------------| r_work (start): 0.3974 rms_B_bonded: 5.93 r_work (final): 0.3974 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3974 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3974 r_free = 0.3974 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3974 r_free = 0.3974 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3974 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.6005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 22438 Z= 0.201 Angle : 0.773 11.530 30521 Z= 0.394 Chirality : 0.047 0.194 3406 Planarity : 0.005 0.069 3947 Dihedral : 9.001 105.091 3444 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.69 % Allowed : 9.03 % Favored : 90.29 % Rotamer: Outliers : 1.98 % Allowed : 16.65 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.42 (0.16), residues: 2776 helix: 0.39 (0.15), residues: 1186 sheet: 0.01 (0.30), residues: 348 loop : -2.66 (0.16), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A2305 TYR 0.019 0.002 TYR A 73 PHE 0.032 0.002 PHE A1747 TRP 0.037 0.002 TRP A2785 HIS 0.007 0.001 HIS A1950 Details of bonding type rmsd covalent geometry : bond 0.00457 (22422) covalent geometry : angle 0.76442 (30473) hydrogen bonds : bond 0.04709 ( 917) hydrogen bonds : angle 4.77412 ( 2725) link_BETA1-2 : bond 0.00585 ( 14) link_BETA1-2 : angle 2.91635 ( 42) link_BETA1-3 : bond 0.01057 ( 2) link_BETA1-3 : angle 3.13096 ( 6) *********************** 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 233 residues out of total 2299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 193 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.6672 (mmt) cc_final: 0.6456 (mmp) REVERT: A 44 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.8514 (mtm-85) REVERT: A 505 MET cc_start: 0.8164 (mmt) cc_final: 0.7804 (mmt) REVERT: A 591 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8536 (pp) REVERT: A 598 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8356 (tt) REVERT: A 1086 TRP cc_start: 0.8311 (m100) cc_final: 0.7879 (m100) REVERT: A 1476 ASN cc_start: 0.7873 (OUTLIER) cc_final: 0.7631 (p0) REVERT: A 1822 ARG cc_start: 0.7724 (ttm-80) cc_final: 0.7250 (tpm170) REVERT: A 1953 GLU cc_start: 0.7289 (pt0) cc_final: 0.6561 (tm-30) REVERT: A 1979 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7507 (pp20) REVERT: A 2620 TRP cc_start: 0.7574 (t-100) cc_final: 0.6768 (t-100) outliers start: 40 outliers final: 29 residues processed: 224 average time/residue: 0.1626 time to fit residues: 57.9459 Evaluate side-chains 203 residues out of total 2299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 170 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG 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 491 VAL Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 598 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 1476 ASN 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 1731 ILE 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 2238 SER 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 2453 ILE Chi-restraints excluded: chain A residue 2457 VAL Chi-restraints excluded: chain A residue 2479 MET Chi-restraints excluded: chain A residue 2643 LEU Chi-restraints excluded: chain A residue 2687 THR Chi-restraints excluded: chain A residue 2691 LEU Chi-restraints excluded: chain A residue 2712 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 73 optimal weight: 4.9990 chunk 38 optimal weight: 0.0370 chunk 69 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 chunk 26 optimal weight: 0.7980 chunk 168 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 238 optimal weight: 0.6980 chunk 226 optimal weight: 10.0000 chunk 244 optimal weight: 6.9990 overall best weight: 0.9062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1476 ASN A1480 HIS A1585 GLN A1658 HIS ** A2225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2427 GLN A2527 ASN A2700 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.130596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.110851 restraints weight = 111491.619| |-----------------------------------------------------------------------------| r_work (start): 0.4017 rms_B_bonded: 5.51 r_work (final): 0.4017 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4018 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4018 r_free = 0.4018 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4018 r_free = 0.4018 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4018 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.6083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 22438 Z= 0.134 Angle : 0.709 11.822 30521 Z= 0.356 Chirality : 0.044 0.189 3406 Planarity : 0.005 0.080 3947 Dihedral : 8.690 102.347 3444 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.69 % Allowed : 9.06 % Favored : 90.25 % Rotamer: Outliers : 1.71 % Allowed : 17.19 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.18 (0.16), residues: 2776 helix: 0.65 (0.16), residues: 1185 sheet: 0.09 (0.30), residues: 349 loop : -2.58 (0.16), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1956 TYR 0.038 0.001 TYR A 764 PHE 0.027 0.001 PHE A1747 TRP 0.029 0.002 TRP A2785 HIS 0.006 0.001 HIS A1823 Details of bonding type rmsd covalent geometry : bond 0.00291 (22422) covalent geometry : angle 0.70088 (30473) hydrogen bonds : bond 0.04055 ( 917) hydrogen bonds : angle 4.52113 ( 2725) link_BETA1-2 : bond 0.00598 ( 14) link_BETA1-2 : angle 2.79245 ( 42) link_BETA1-3 : bond 0.01047 ( 2) link_BETA1-3 : angle 3.11092 ( 6) *********************** 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 218 residues out of total 2299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 184 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 LEU cc_start: 0.8956 (tp) cc_final: 0.8576 (tp) REVERT: A 297 ASP cc_start: 0.7142 (m-30) cc_final: 0.6822 (m-30) REVERT: A 386 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7633 (mt-10) REVERT: A 591 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8515 (pp) REVERT: A 598 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8352 (tt) REVERT: A 1086 TRP cc_start: 0.8223 (m100) cc_final: 0.7812 (m100) REVERT: A 1657 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8301 (pt0) REVERT: A 1822 ARG cc_start: 0.7821 (ttm-80) cc_final: 0.6783 (tpm170) REVERT: A 1979 GLU cc_start: 0.7747 (mm-30) cc_final: 0.7544 (pp20) REVERT: A 2362 MET cc_start: 0.5864 (ptm) cc_final: 0.5613 (ttp) REVERT: A 2620 TRP cc_start: 0.7410 (t-100) cc_final: 0.6890 (t-100) REVERT: A 2785 TRP cc_start: 0.5783 (m-10) cc_final: 0.5161 (m100) outliers start: 34 outliers final: 21 residues processed: 207 average time/residue: 0.1633 time to fit residues: 54.2575 Evaluate side-chains 199 residues out of total 2299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 175 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 491 VAL Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 598 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 1603 ILE Chi-restraints excluded: chain A residue 1657 GLU Chi-restraints excluded: chain A residue 1686 VAL Chi-restraints excluded: chain A residue 1731 ILE Chi-restraints excluded: chain A residue 1814 VAL Chi-restraints excluded: chain A residue 1976 MET Chi-restraints excluded: chain A residue 1991 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 2433 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 270 optimal weight: 4.9990 chunk 162 optimal weight: 2.9990 chunk 163 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 chunk 225 optimal weight: 1.9990 chunk 250 optimal weight: 0.9990 chunk 260 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 9 optimal weight: 0.0970 chunk 166 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 878 GLN A1480 HIS ** A2225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2700 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.131344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.111519 restraints weight = 111314.739| |-----------------------------------------------------------------------------| r_work (start): 0.4035 rms_B_bonded: 5.34 r_work (final): 0.4035 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4034 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4034 r_free = 0.4034 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4034 r_free = 0.4034 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4034 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.6174 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= 0.129 Angle : 0.706 12.579 30521 Z= 0.351 Chirality : 0.044 0.237 3406 Planarity : 0.005 0.067 3947 Dihedral : 8.433 102.276 3444 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.65 % Allowed : 8.74 % Favored : 90.61 % Rotamer: Outliers : 1.71 % Allowed : 17.73 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.10 (0.16), residues: 2776 helix: 0.78 (0.16), residues: 1178 sheet: 0.03 (0.30), residues: 347 loop : -2.55 (0.16), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1956 TYR 0.017 0.001 TYR A 331 PHE 0.036 0.001 PHE A 251 TRP 0.024 0.001 TRP A 936 HIS 0.008 0.001 HIS A 592 Details of bonding type rmsd covalent geometry : bond 0.00280 (22422) covalent geometry : angle 0.69814 (30473) hydrogen bonds : bond 0.03789 ( 917) hydrogen bonds : angle 4.39388 ( 2725) link_BETA1-2 : bond 0.00566 ( 14) link_BETA1-2 : angle 2.73763 ( 42) link_BETA1-3 : bond 0.01026 ( 2) link_BETA1-3 : angle 3.19165 ( 6) *********************** 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 217 residues out of total 2299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 183 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 ASP cc_start: 0.7153 (m-30) cc_final: 0.6889 (m-30) REVERT: A 386 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7586 (mt-10) REVERT: A 591 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8570 (pp) REVERT: A 598 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8360 (tt) REVERT: A 878 GLN cc_start: 0.7793 (OUTLIER) cc_final: 0.6647 (tp40) REVERT: A 1086 TRP cc_start: 0.8325 (m100) cc_final: 0.7963 (m100) REVERT: A 1657 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8237 (pt0) REVERT: A 1822 ARG cc_start: 0.7709 (ttm-80) cc_final: 0.7081 (tpm170) REVERT: A 1979 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7527 (pp20) REVERT: A 2362 MET cc_start: 0.5958 (ptm) cc_final: 0.5644 (ttp) REVERT: A 2620 TRP cc_start: 0.7163 (t-100) cc_final: 0.6755 (t-100) REVERT: A 2785 TRP cc_start: 0.6009 (m-10) cc_final: 0.5539 (m100) outliers start: 34 outliers final: 21 residues processed: 207 average time/residue: 0.1605 time to fit residues: 53.6544 Evaluate side-chains 200 residues out of total 2299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 175 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 VAL 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 598 LEU Chi-restraints excluded: chain A residue 630 MET Chi-restraints excluded: chain A residue 878 GLN Chi-restraints excluded: chain A residue 893 MET Chi-restraints excluded: chain A residue 1166 GLU Chi-restraints excluded: chain A residue 1408 LEU Chi-restraints excluded: chain A residue 1603 ILE Chi-restraints excluded: chain A residue 1657 GLU Chi-restraints excluded: chain A residue 1686 VAL Chi-restraints excluded: chain A residue 1731 ILE Chi-restraints excluded: chain A residue 1814 VAL Chi-restraints excluded: chain A residue 1823 HIS Chi-restraints excluded: chain A residue 1976 MET Chi-restraints excluded: chain A residue 1991 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 2457 VAL Chi-restraints excluded: chain A residue 2687 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 64 optimal weight: 6.9990 chunk 126 optimal weight: 0.2980 chunk 191 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 230 optimal weight: 5.9990 chunk 251 optimal weight: 0.8980 chunk 123 optimal weight: 0.8980 chunk 214 optimal weight: 0.7980 chunk 255 optimal weight: 6.9990 chunk 86 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 878 GLN A1430 GLN A1480 HIS ** A2080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2412 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 = 0.4346 r_free = 0.4346 target = 0.132142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.110960 restraints weight = 138534.199| |-----------------------------------------------------------------------------| r_work (start): 0.4018 rms_B_bonded: 6.18 r_work (final): 0.4018 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4016 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4016 r_free = 0.4016 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4016 r_free = 0.4016 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4016 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.6260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 22438 Z= 0.127 Angle : 0.706 12.052 30521 Z= 0.349 Chirality : 0.043 0.194 3406 Planarity : 0.005 0.065 3947 Dihedral : 8.128 101.887 3444 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.61 % Allowed : 9.03 % Favored : 90.36 % Rotamer: Outliers : 1.49 % Allowed : 17.96 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.16), residues: 2776 helix: 0.81 (0.16), residues: 1181 sheet: 0.27 (0.31), residues: 332 loop : -2.54 (0.16), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1377 TYR 0.038 0.001 TYR A 764 PHE 0.024 0.001 PHE A1747 TRP 0.022 0.001 TRP A 936 HIS 0.014 0.001 HIS A 592 Details of bonding type rmsd covalent geometry : bond 0.00278 (22422) covalent geometry : angle 0.69716 (30473) hydrogen bonds : bond 0.03714 ( 917) hydrogen bonds : angle 4.34575 ( 2725) link_BETA1-2 : bond 0.00552 ( 14) link_BETA1-2 : angle 2.69295 ( 42) link_BETA1-3 : bond 0.01001 ( 2) link_BETA1-3 : angle 3.59498 ( 6) *********************** 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 211 residues out of total 2299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 182 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 PHE cc_start: 0.6967 (t80) cc_final: 0.6697 (t80) REVERT: A 297 ASP cc_start: 0.7184 (m-30) cc_final: 0.6912 (m-30) REVERT: A 386 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7626 (mt-10) REVERT: A 503 GLU cc_start: 0.8126 (tm-30) cc_final: 0.7883 (tm-30) REVERT: A 591 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8598 (pp) REVERT: A 596 MET cc_start: 0.8625 (mtm) cc_final: 0.7685 (mpp) REVERT: A 799 LYS cc_start: 0.7843 (pttp) cc_final: 0.7318 (ptpt) REVERT: A 878 GLN cc_start: 0.7763 (OUTLIER) cc_final: 0.6673 (tp40) REVERT: A 1086 TRP cc_start: 0.8293 (m100) cc_final: 0.7961 (m100) REVERT: A 1289 LEU cc_start: 0.7001 (tp) cc_final: 0.6767 (tt) REVERT: A 1657 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8290 (pt0) REVERT: A 1822 ARG cc_start: 0.7485 (ttm-80) cc_final: 0.6931 (tpm170) REVERT: A 1979 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7653 (pp20) REVERT: A 2362 MET cc_start: 0.6166 (ptm) cc_final: 0.5935 (ttp) REVERT: A 2620 TRP cc_start: 0.7200 (t-100) cc_final: 0.6822 (t-100) REVERT: A 2766 LEU cc_start: 0.7931 (mm) cc_final: 0.6168 (tt) REVERT: A 2785 TRP cc_start: 0.6138 (m-10) cc_final: 0.5698 (m100) outliers start: 29 outliers final: 23 residues processed: 203 average time/residue: 0.1575 time to fit residues: 51.0625 Evaluate side-chains 197 residues out of total 2299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 171 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 347 VAL 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 598 LEU Chi-restraints excluded: chain A residue 630 MET Chi-restraints excluded: chain A residue 878 GLN Chi-restraints excluded: chain A residue 893 MET Chi-restraints excluded: chain A residue 1166 GLU Chi-restraints excluded: chain A residue 1408 LEU Chi-restraints excluded: chain A residue 1603 ILE Chi-restraints excluded: chain A residue 1648 SER Chi-restraints excluded: chain A residue 1657 GLU Chi-restraints excluded: chain A residue 1686 VAL Chi-restraints excluded: chain A residue 1814 VAL Chi-restraints excluded: chain A residue 1823 HIS Chi-restraints excluded: chain A residue 1976 MET Chi-restraints excluded: chain A residue 1991 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 2457 VAL 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 224 optimal weight: 5.9990 chunk 47 optimal weight: 0.0010 chunk 147 optimal weight: 1.9990 chunk 222 optimal weight: 6.9990 chunk 142 optimal weight: 1.9990 chunk 126 optimal weight: 0.0970 chunk 242 optimal weight: 7.9990 chunk 110 optimal weight: 1.9990 chunk 153 optimal weight: 7.9990 chunk 231 optimal weight: 6.9990 chunk 112 optimal weight: 4.9990 overall best weight: 1.2190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 592 HIS A 878 GLN A1480 HIS A1733 HIS ** A2080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2412 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 = 0.4334 r_free = 0.4334 target = 0.131092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.111627 restraints weight = 97345.553| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 4.94 r_work (final): 0.4027 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4027 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4027 r_free = 0.4027 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4027 r_free = 0.4027 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4027 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.6441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 22438 Z= 0.138 Angle : 0.718 12.050 30521 Z= 0.357 Chirality : 0.044 0.195 3406 Planarity : 0.005 0.065 3947 Dihedral : 7.878 101.391 3444 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.72 % Allowed : 8.81 % Favored : 90.47 % Rotamer: Outliers : 1.62 % Allowed : 17.87 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.16), residues: 2776 helix: 0.82 (0.16), residues: 1183 sheet: 0.14 (0.31), residues: 342 loop : -2.52 (0.16), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A2305 TYR 0.037 0.001 TYR A 764 PHE 0.024 0.001 PHE A1747 TRP 0.023 0.001 TRP A 936 HIS 0.012 0.001 HIS A 592 Details of bonding type rmsd covalent geometry : bond 0.00308 (22422) covalent geometry : angle 0.70895 (30473) hydrogen bonds : bond 0.03790 ( 917) hydrogen bonds : angle 4.34458 ( 2725) link_BETA1-2 : bond 0.00540 ( 14) link_BETA1-2 : angle 2.69563 ( 42) link_BETA1-3 : bond 0.00838 ( 2) link_BETA1-3 : angle 3.89947 ( 6) ********************** 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 207 residues out of total 2299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 175 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.8361 (mtm180) REVERT: A 251 PHE cc_start: 0.6953 (t80) cc_final: 0.6683 (t80) REVERT: A 297 ASP cc_start: 0.7242 (m-30) cc_final: 0.6975 (m-30) REVERT: A 386 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7714 (mt-10) REVERT: A 435 MET cc_start: 0.6719 (ptp) cc_final: 0.6461 (ttp) REVERT: A 503 GLU cc_start: 0.8027 (tm-30) cc_final: 0.7774 (tm-30) REVERT: A 591 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8577 (pp) REVERT: A 596 MET cc_start: 0.8673 (mtm) cc_final: 0.7825 (mpp) REVERT: A 598 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8378 (tt) REVERT: A 876 ASN cc_start: 0.8130 (m-40) cc_final: 0.7685 (t0) REVERT: A 878 GLN cc_start: 0.7796 (OUTLIER) cc_final: 0.6721 (tp40) REVERT: A 1086 TRP cc_start: 0.8319 (m100) cc_final: 0.8010 (m100) REVERT: A 1657 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8232 (pt0) REVERT: A 1822 ARG cc_start: 0.7470 (ttm-80) cc_final: 0.6887 (tpm170) REVERT: A 1979 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7610 (pp20) REVERT: A 2620 TRP cc_start: 0.7307 (t-100) cc_final: 0.6975 (t-100) REVERT: A 2785 TRP cc_start: 0.6049 (m-10) cc_final: 0.5643 (m100) outliers start: 32 outliers final: 24 residues processed: 198 average time/residue: 0.1569 time to fit residues: 49.5516 Evaluate side-chains 199 residues out of total 2299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 170 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 347 VAL 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 598 LEU Chi-restraints excluded: chain A residue 630 MET Chi-restraints excluded: chain A residue 878 GLN Chi-restraints excluded: chain A residue 893 MET Chi-restraints excluded: chain A residue 1166 GLU Chi-restraints excluded: chain A residue 1408 LEU Chi-restraints excluded: chain A residue 1603 ILE Chi-restraints excluded: chain A residue 1648 SER Chi-restraints excluded: chain A residue 1657 GLU Chi-restraints excluded: chain A residue 1686 VAL Chi-restraints excluded: chain A residue 1814 VAL Chi-restraints excluded: chain A residue 1823 HIS 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 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 2457 VAL Chi-restraints excluded: chain A residue 2687 THR Chi-restraints excluded: chain A residue 2712 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 203 optimal weight: 2.9990 chunk 251 optimal weight: 0.9990 chunk 231 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 255 optimal weight: 8.9990 chunk 7 optimal weight: 5.9990 chunk 171 optimal weight: 6.9990 chunk 127 optimal weight: 0.0770 chunk 233 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 128 optimal weight: 7.9990 overall best weight: 1.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1480 HIS ** A2225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2412 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 = 0.4298 r_free = 0.4298 target = 0.128873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.109309 restraints weight = 117948.376| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 5.42 r_work (final): 0.3990 ------------------------------------------------------------------------------- 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 = 0.35 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 = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3991 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.6671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 22438 Z= 0.161 Angle : 0.737 12.370 30521 Z= 0.371 Chirality : 0.045 0.200 3406 Planarity : 0.005 0.064 3947 Dihedral : 7.851 100.704 3444 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.69 % Allowed : 9.24 % Favored : 90.07 % Rotamer: Outliers : 1.40 % Allowed : 18.18 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.16), residues: 2776 helix: 0.75 (0.16), residues: 1188 sheet: 0.14 (0.30), residues: 346 loop : -2.53 (0.16), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A2305 TYR 0.037 0.002 TYR A 764 PHE 0.025 0.002 PHE A1747 TRP 0.020 0.002 TRP A1122 HIS 0.005 0.001 HIS A1823 Details of bonding type rmsd covalent geometry : bond 0.00364 (22422) covalent geometry : angle 0.72920 (30473) hydrogen bonds : bond 0.04149 ( 917) hydrogen bonds : angle 4.43430 ( 2725) link_BETA1-2 : bond 0.00532 ( 14) link_BETA1-2 : angle 2.73293 ( 42) link_BETA1-3 : bond 0.00966 ( 2) link_BETA1-3 : angle 3.63622 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4800.35 seconds wall clock time: 83 minutes 24.49 seconds (5004.49 seconds total)