Starting phenix.real_space_refine on Thu Jul 31 11:22:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6dnh_7112/07_2025/6dnh_7112.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dnh_7112/07_2025/6dnh_7112.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/6dnh_7112/07_2025/6dnh_7112.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dnh_7112/07_2025/6dnh_7112.map" model { file = "/net/cci-nas-00/data/ceres_data/6dnh_7112/07_2025/6dnh_7112.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dnh_7112/07_2025/6dnh_7112.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 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: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 P 7 5.49 5 S 89 5.16 5 C 8574 2.51 5 N 2338 2.21 5 O 2431 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13442 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 9337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1177, 9337 Classifications: {'peptide': 1177} Link IDs: {'PTRANS': 66, 'TRANS': 1110} Chain breaks: 12 Chain: "B" Number of atoms: 3035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3035 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 15, 'TRANS': 360} Chain: "C" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 917 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 6, 'TRANS': 110} Chain: "E" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 150 Classifications: {'RNA': 7} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 1, 'rna3p_pyr': 1} Link IDs: {'rna2p': 6} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12682 SG CYS C 41 65.500 35.700 17.405 1.00 39.96 S ATOM 12746 SG CYS C 49 69.488 33.242 16.962 1.00 39.96 S ATOM 12781 SG CYS C 55 68.567 33.935 21.043 1.00 39.96 S ATOM 12953 SG CYS C 76 53.386 24.077 22.615 1.00 69.54 S ATOM 13119 SG CYS C 96 33.280 21.341 18.350 1.00 39.93 S ATOM 13237 SG CYS C 110 33.552 24.825 20.217 1.00 37.40 S Time building chain proxies: 7.33, per 1000 atoms: 0.55 Number of scatterers: 13442 At special positions: 0 Unit cell: (87.74, 135.89, 102.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 S 89 16.00 P 7 15.00 O 2431 8.00 N 2338 7.00 C 8574 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 Time building additional restraints: 2.84 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" NE2 HIS C 59 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 49 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 41 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 55 " pdb=" ZN C 302 " pdb="ZN ZN C 302 " - pdb=" NE2 HIS C 86 " pdb="ZN ZN C 302 " - pdb=" SG CYS C 76 " pdb=" ZN C 303 " pdb="ZN ZN C 303 " - pdb=" NE2 HIS C 114 " pdb="ZN ZN C 303 " - pdb=" SG CYS C 110 " pdb="ZN ZN C 303 " - pdb=" SG CYS C 96 " Number of angles added : 3 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3120 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 32 sheets defined 7.5% alpha, 32.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.88 Creating SS restraints... Processing helix chain 'A' and resid 487 through 491 removed outlier: 3.616A pdb=" N GLN A 491 " --> pdb=" O GLU A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 509 Processing helix chain 'A' and resid 1153 through 1156 Processing helix chain 'A' and resid 1352 through 1369 removed outlier: 3.743A pdb=" N ARG A1358 " --> pdb=" O LYS A1354 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A1359 " --> pdb=" O THR A1355 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET A1361 " --> pdb=" O ARG A1357 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A1362 " --> pdb=" O ARG A1358 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA A1365 " --> pdb=" O MET A1361 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N THR A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1372 through 1376 Processing helix chain 'A' and resid 1403 through 1407 Processing helix chain 'A' and resid 1411 through 1423 removed outlier: 3.737A pdb=" N SER A1416 " --> pdb=" O THR A1412 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU A1417 " --> pdb=" O MET A1413 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU A1418 " --> pdb=" O GLU A1414 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA A1419 " --> pdb=" O ARG A1415 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1434 removed outlier: 3.820A pdb=" N ILE A1429 " --> pdb=" O THR A1425 " (cutoff:3.500A) Processing helix chain 'A' and resid 1434 through 1439 removed outlier: 3.508A pdb=" N VAL A1439 " --> pdb=" O GLU A1435 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 73 removed outlier: 3.659A pdb=" N LYS B 65 " --> pdb=" O PRO B 61 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ILE B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N TRP B 72 " --> pdb=" O GLU B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 92 removed outlier: 3.590A pdb=" N ASP B 91 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU B 92 " --> pdb=" O TYR B 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 88 through 92' Processing helix chain 'B' and resid 101 through 106 removed outlier: 3.544A pdb=" N ALA B 105 " --> pdb=" O PRO B 102 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL B 106 " --> pdb=" O MET B 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 19 Processing helix chain 'C' and resid 42 through 47 Processing helix chain 'C' and resid 70 through 74 removed outlier: 3.537A pdb=" N ARG C 73 " --> pdb=" O HIS C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 82 removed outlier: 3.855A pdb=" N GLN C 81 " --> pdb=" O LYS C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 101 removed outlier: 3.638A pdb=" N SER C 100 " --> pdb=" O CYS C 96 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1312 through 1315 removed outlier: 6.898A pdb=" N HIS A1334 " --> pdb=" O PRO A1350 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N ILE A1345 " --> pdb=" O ALA A 8 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS A 6 " --> pdb=" O LEU A1347 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 20 removed outlier: 6.641A pdb=" N ALA A 33 " --> pdb=" O GLU A 15 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N SER A 17 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL A 31 " --> pdb=" O SER A 17 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N TYR A 19 " --> pdb=" O ASN A 29 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ASN A 29 " --> pdb=" O TYR A 19 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLN A 37 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LEU A 38 " --> pdb=" O SER A 71 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N SER A 71 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL A 40 " --> pdb=" O ALA A 69 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 80 through 84 removed outlier: 3.612A pdb=" N LYS A 102 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LEU A 103 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LEU A 120 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL A 105 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 140 through 143 removed outlier: 3.716A pdb=" N ARG A 140 " --> pdb=" O LEU A 153 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 202 through 208 removed outlier: 5.937A pdb=" N ILE A 203 " --> pdb=" O GLU A 222 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLU A 222 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASP A 205 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE A 240 " --> pdb=" O SER A 257 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N SER A 257 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE A 255 " --> pdb=" O ALA A 242 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 265 through 270 removed outlier: 4.418A pdb=" N GLN A 267 " --> pdb=" O PHE A 281 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER A 285 " --> pdb=" O ALA A 282 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N GLY A 297 " --> pdb=" O ARG A 313 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 326 through 328 removed outlier: 6.792A pdb=" N THR A 348 " --> pdb=" O PHE A 360 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N PHE A 360 " --> pdb=" O THR A 348 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ILE A 350 " --> pdb=" O ARG A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 326 through 328 removed outlier: 4.685A pdb=" N ILE A 344 " --> pdb=" O ALA A 365 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 375 through 376 removed outlier: 3.566A pdb=" N LEU A 392 " --> pdb=" O LEU A 384 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N SER A 391 " --> pdb=" O SER A 468 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N SER A 468 " --> pdb=" O SER A 391 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU A 393 " --> pdb=" O CYS A 466 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 478 through 481 Processing sheet with id=AB2, first strand: chain 'A' and resid 522 through 526 removed outlier: 5.238A pdb=" N VAL A 523 " --> pdb=" O VAL A1000 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL A1000 " --> pdb=" O VAL A 523 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR A 525 " --> pdb=" O ILE A 998 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TYR A 989 " --> pdb=" O ARG A 997 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N SER A 974 " --> pdb=" O PHE A 990 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 534 through 539 removed outlier: 3.857A pdb=" N ASP A 534 " --> pdb=" O SER A 578 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER A 578 " --> pdb=" O ASP A 534 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 608 through 612 removed outlier: 3.591A pdb=" N PHE A 608 " --> pdb=" O VAL A 621 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR A 617 " --> pdb=" O ILE A 612 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 648 through 652 removed outlier: 3.820A pdb=" N GLN A 648 " --> pdb=" O MET A 659 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 695 through 702 removed outlier: 6.946A pdb=" N VAL A 788 " --> pdb=" O ILE A 696 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LEU A 698 " --> pdb=" O LEU A 786 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU A 786 " --> pdb=" O LEU A 698 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LEU A 700 " --> pdb=" O TRP A 784 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N TRP A 784 " --> pdb=" O LEU A 700 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N MET A 794 " --> pdb=" O LEU A 807 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LEU A 807 " --> pdb=" O MET A 794 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE A 796 " --> pdb=" O VAL A 805 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 846 through 854 removed outlier: 6.633A pdb=" N HIS A 866 " --> pdb=" O LYS A 847 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N VAL A 849 " --> pdb=" O LEU A 864 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LEU A 864 " --> pdb=" O VAL A 849 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LEU A 851 " --> pdb=" O TYR A 862 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N TYR A 862 " --> pdb=" O LEU A 851 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ALA A 853 " --> pdb=" O ARG A 860 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ARG A 860 " --> pdb=" O ALA A 853 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 865 " --> pdb=" O LEU A 872 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU A 872 " --> pdb=" O VAL A 865 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 877 through 878 Processing sheet with id=AB9, first strand: chain 'A' and resid 931 through 937 removed outlier: 5.705A pdb=" N TYR A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1024 through 1028 removed outlier: 3.661A pdb=" N TYR A1024 " --> pdb=" O ALA A1037 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1046 through 1047 Processing sheet with id=AC3, first strand: chain 'A' and resid 1098 through 1106 removed outlier: 6.745A pdb=" N GLY A1124 " --> pdb=" O THR A1101 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N MET A1103 " --> pdb=" O ALA A1122 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ALA A1122 " --> pdb=" O MET A1103 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N THR A1105 " --> pdb=" O TYR A1120 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N TYR A1120 " --> pdb=" O THR A1105 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N GLY A1137 " --> pdb=" O GLU A1167 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N GLU A1167 " --> pdb=" O GLY A1137 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ILE A1139 " --> pdb=" O GLU A1165 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLU A1165 " --> pdb=" O ILE A1139 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE A1141 " --> pdb=" O LEU A1163 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 1172 through 1177 removed outlier: 4.313A pdb=" N ALA A1174 " --> pdb=" O ALA A1185 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE A1190 " --> pdb=" O PHE A1205 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N PHE A1205 " --> pdb=" O ILE A1190 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU A1192 " --> pdb=" O MET A1203 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 1212 through 1217 removed outlier: 3.558A pdb=" N GLN A1214 " --> pdb=" O ALA A1225 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE A1231 " --> pdb=" O ARG A1248 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ARG A1248 " --> pdb=" O ILE A1231 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N LEU A1233 " --> pdb=" O VAL A1246 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN A1237 " --> pdb=" O THR A1242 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR A1242 " --> pdb=" O GLN A1237 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 1255 through 1258 removed outlier: 6.857A pdb=" N SER A1272 " --> pdb=" O TYR A1256 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N VAL A1258 " --> pdb=" O LEU A1270 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU A1270 " --> pdb=" O VAL A1258 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 1255 through 1258 removed outlier: 6.857A pdb=" N SER A1272 " --> pdb=" O TYR A1256 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N VAL A1258 " --> pdb=" O LEU A1270 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU A1270 " --> pdb=" O VAL A1258 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU A1278 " --> pdb=" O ASP A1301 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ASP A1301 " --> pdb=" O LEU A1278 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL A1280 " --> pdb=" O ARG A1299 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 109 through 113 removed outlier: 6.644A pdb=" N PHE B 401 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N THR B 113 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N SER B 399 " --> pdb=" O THR B 113 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS B 400 " --> pdb=" O SER B 392 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ILE B 389 " --> pdb=" O TRP B 383 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N TRP B 383 " --> pdb=" O ILE B 389 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N CYS B 391 " --> pdb=" O LEU B 381 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LEU B 381 " --> pdb=" O CYS B 391 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLY B 393 " --> pdb=" O TRP B 379 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 124 through 127 removed outlier: 3.517A pdb=" N VAL B 124 " --> pdb=" O GLY B 137 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR B 155 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 164 through 169 removed outlier: 3.799A pdb=" N ALA B 166 " --> pdb=" O ALA B 179 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N TYR B 184 " --> pdb=" O ASP B 180 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL B 185 " --> pdb=" O MET B 197 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N MET B 197 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N TYR B 187 " --> pdb=" O VAL B 195 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 205 through 210 removed outlier: 6.997A pdb=" N CYS B 220 " --> pdb=" O ARG B 206 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ALA B 208 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ALA B 218 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N PHE B 210 " --> pdb=" O LYS B 216 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LYS B 216 " --> pdb=" O PHE B 210 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG B 238 " --> pdb=" O ILE B 228 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ASP B 230 " --> pdb=" O GLU B 236 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N GLU B 236 " --> pdb=" O ASP B 230 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 250 through 252 Processing sheet with id=AD4, first strand: chain 'B' and resid 291 through 296 removed outlier: 3.569A pdb=" N CYS B 312 " --> pdb=" O PHE B 327 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 334 through 339 removed outlier: 3.846A pdb=" N ALA B 336 " --> pdb=" O GLY B 350 " (cutoff:3.500A) 339 hydrogen bonds defined for protein. 882 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: 5.54 Time building geometry restraints manager: 3.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3970 1.33 - 1.45: 2277 1.45 - 1.57: 7381 1.57 - 1.69: 13 1.69 - 1.81: 141 Bond restraints: 13782 Sorted by residual: bond pdb=" C ILE B 57 " pdb=" N ASP B 58 " ideal model delta sigma weight residual 1.331 1.404 -0.073 1.42e-02 4.96e+03 2.64e+01 bond pdb=" CB PHE B 210 " pdb=" CG PHE B 210 " ideal model delta sigma weight residual 1.502 1.443 0.059 2.30e-02 1.89e+03 6.50e+00 bond pdb=" N MET A 377 " pdb=" CA MET A 377 " ideal model delta sigma weight residual 1.457 1.427 0.031 1.29e-02 6.01e+03 5.63e+00 bond pdb=" CG LEU A1347 " pdb=" CD2 LEU A1347 " ideal model delta sigma weight residual 1.521 1.445 0.076 3.30e-02 9.18e+02 5.29e+00 bond pdb=" N ILE A 330 " pdb=" CA ILE A 330 " ideal model delta sigma weight residual 1.459 1.431 0.028 1.24e-02 6.50e+03 5.00e+00 ... (remaining 13777 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 17801 2.27 - 4.54: 787 4.54 - 6.80: 88 6.80 - 9.07: 27 9.07 - 11.34: 8 Bond angle restraints: 18711 Sorted by residual: angle pdb=" N CYS A 466 " pdb=" CA CYS A 466 " pdb=" C CYS A 466 " ideal model delta sigma weight residual 111.14 120.88 -9.74 1.08e+00 8.57e-01 8.13e+01 angle pdb=" N LEU A 200 " pdb=" CA LEU A 200 " pdb=" C LEU A 200 " ideal model delta sigma weight residual 111.07 119.88 -8.81 1.07e+00 8.73e-01 6.77e+01 angle pdb=" N SER B 266 " pdb=" CA SER B 266 " pdb=" C SER B 266 " ideal model delta sigma weight residual 111.28 118.10 -6.82 1.09e+00 8.42e-01 3.91e+01 angle pdb=" N ASP A1273 " pdb=" CA ASP A1273 " pdb=" C ASP A1273 " ideal model delta sigma weight residual 109.07 118.67 -9.60 1.61e+00 3.86e-01 3.55e+01 angle pdb=" C SER A 331 " pdb=" CA SER A 331 " pdb=" CB SER A 331 " ideal model delta sigma weight residual 116.63 109.83 6.80 1.16e+00 7.43e-01 3.44e+01 ... (remaining 18706 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.79: 7597 14.79 - 29.57: 496 29.57 - 44.35: 86 44.35 - 59.14: 13 59.14 - 73.92: 8 Dihedral angle restraints: 8200 sinusoidal: 3370 harmonic: 4830 Sorted by residual: dihedral pdb=" C ASP A 333 " pdb=" N ASP A 333 " pdb=" CA ASP A 333 " pdb=" CB ASP A 333 " ideal model delta harmonic sigma weight residual -122.60 -139.88 17.28 0 2.50e+00 1.60e-01 4.78e+01 dihedral pdb=" N ASP A 333 " pdb=" C ASP A 333 " pdb=" CA ASP A 333 " pdb=" CB ASP A 333 " ideal model delta harmonic sigma weight residual 122.80 139.11 -16.31 0 2.50e+00 1.60e-01 4.25e+01 dihedral pdb=" CA ASN B 100 " pdb=" C ASN B 100 " pdb=" N ASN B 101 " pdb=" CA ASN B 101 " ideal model delta harmonic sigma weight residual -180.00 -150.92 -29.08 0 5.00e+00 4.00e-02 3.38e+01 ... (remaining 8197 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.129: 1983 0.129 - 0.258: 89 0.258 - 0.386: 7 0.386 - 0.515: 0 0.515 - 0.644: 1 Chirality restraints: 2080 Sorted by residual: chirality pdb=" CA ASP A 333 " pdb=" N ASP A 333 " pdb=" C ASP A 333 " pdb=" CB ASP A 333 " both_signs ideal model delta sigma weight residual False 2.51 1.87 0.64 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" CA ILE A 330 " pdb=" N ILE A 330 " pdb=" C ILE A 330 " pdb=" CB ILE A 330 " both_signs ideal model delta sigma weight residual False 2.43 2.77 -0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" CA MET C 1 " pdb=" N MET C 1 " pdb=" C MET C 1 " pdb=" CB MET C 1 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.66e+00 ... (remaining 2077 not shown) Planarity restraints: 2362 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 465 " -0.023 2.00e-02 2.50e+03 4.57e-02 2.09e+01 pdb=" C VAL A 465 " 0.079 2.00e-02 2.50e+03 pdb=" O VAL A 465 " -0.030 2.00e-02 2.50e+03 pdb=" N CYS A 466 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1312 " 0.048 2.00e-02 2.50e+03 2.60e-02 1.70e+01 pdb=" CG TRP A1312 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 TRP A1312 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP A1312 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP A1312 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A1312 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A1312 " -0.017 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1312 " 0.009 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1312 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A1312 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 252 " -0.024 2.00e-02 2.50e+03 1.94e-02 9.45e+00 pdb=" CG TRP B 252 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP B 252 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP B 252 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 252 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP B 252 " 0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP B 252 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 252 " -0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 252 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 252 " 0.001 2.00e-02 2.50e+03 ... (remaining 2359 not shown) Histogram of nonbonded interaction distances: 1.26 - 1.99: 4 1.99 - 2.71: 801 2.71 - 3.44: 17251 3.44 - 4.17: 32020 4.17 - 4.90: 57167 Nonbonded interactions: 107243 Sorted by model distance: nonbonded pdb=" OE2 GLU A 630 " pdb=" CB LEU A 635 " model vdw 1.258 3.440 nonbonded pdb=" O LEU A 628 " pdb=" CD2 LEU A 629 " model vdw 1.320 3.460 nonbonded pdb=" O ASP A1273 " pdb=" N ASP A1275 " model vdw 1.877 3.120 nonbonded pdb=" ND2 ASN A 202 " pdb=" OE1 GLN A 225 " model vdw 1.906 3.120 nonbonded pdb=" OE2 GLU A 630 " pdb=" CG LEU A 635 " model vdw 2.010 3.470 ... (remaining 107238 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.360 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: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 34.140 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 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 : 0.013 0.537 13791 Z= 0.509 Angle : 1.091 15.561 18714 Z= 0.611 Chirality : 0.065 0.644 2080 Planarity : 0.008 0.062 2362 Dihedral : 10.644 73.923 5080 Min Nonbonded Distance : 1.258 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.48 % Favored : 91.22 % Rotamer: Outliers : 1.10 % Allowed : 1.99 % Favored : 96.91 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.04 (0.17), residues: 1640 helix: -4.77 (0.17), residues: 104 sheet: -2.46 (0.18), residues: 633 loop : -2.58 (0.18), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.005 TRP A1312 HIS 0.017 0.003 HIS A 9 PHE 0.043 0.004 PHE A1074 TYR 0.041 0.004 TYR A 2 ARG 0.012 0.001 ARG B 404 Details of bonding type rmsd hydrogen bonds : bond 0.26444 ( 330) hydrogen bonds : angle 10.70328 ( 882) metal coordination : bond 0.32223 ( 9) metal coordination : angle 12.79988 ( 3) covalent geometry : bond 0.00962 (13782) covalent geometry : angle 1.07858 (18711) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 350 time to evaluate : 1.423 Fit side-chains revert: symmetry clash REVERT: A 79 MET cc_start: 0.7931 (mmp) cc_final: 0.7679 (mmt) REVERT: A 1210 LEU cc_start: 0.8037 (mp) cc_final: 0.7703 (mt) REVERT: A 1253 LEU cc_start: 0.9079 (tp) cc_final: 0.8697 (tp) REVERT: B 292 MET cc_start: 0.7821 (mmm) cc_final: 0.7616 (mmt) REVERT: B 335 THR cc_start: 0.8280 (p) cc_final: 0.8072 (p) outliers start: 16 outliers final: 8 residues processed: 363 average time/residue: 0.3084 time to fit residues: 152.7285 Evaluate side-chains 191 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 183 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 1118 LYS Chi-restraints excluded: chain A residue 1176 CYS Chi-restraints excluded: chain A residue 1206 ILE Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1316 CYS Chi-restraints excluded: chain B residue 265 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 10.0000 chunk 125 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 129 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 29 ASN A 516 GLN ** A 620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 636 HIS A 648 GLN A 783 HIS A 869 GLN A1309 ASN A1332 ASN B 60 ASN B 189 GLN B 235 HIS B 297 ASN B 310 HIS B 325 GLN B 405 ASN B 416 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.123700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.101717 restraints weight = 20395.393| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.49 r_work: 0.3078 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 13791 Z= 0.162 Angle : 0.689 8.378 18714 Z= 0.359 Chirality : 0.047 0.186 2080 Planarity : 0.005 0.070 2362 Dihedral : 8.058 73.256 1911 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.26 % Favored : 92.62 % Rotamer: Outliers : 2.20 % Allowed : 8.18 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.33 (0.18), residues: 1640 helix: -3.50 (0.34), residues: 105 sheet: -1.85 (0.19), residues: 626 loop : -2.33 (0.18), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 252 HIS 0.006 0.001 HIS A 680 PHE 0.015 0.002 PHE B 217 TYR 0.017 0.002 TYR A1256 ARG 0.006 0.001 ARG B 112 Details of bonding type rmsd hydrogen bonds : bond 0.04396 ( 330) hydrogen bonds : angle 7.15974 ( 882) metal coordination : bond 0.01559 ( 9) metal coordination : angle 5.95801 ( 3) covalent geometry : bond 0.00369 (13782) covalent geometry : angle 0.68484 (18711) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 227 time to evaluate : 2.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 MET cc_start: 0.9142 (mmp) cc_final: 0.8814 (mmt) REVERT: A 162 LEU cc_start: 0.8854 (mt) cc_final: 0.8566 (tp) REVERT: A 216 THR cc_start: 0.9198 (m) cc_final: 0.8857 (p) REVERT: A 492 ASN cc_start: 0.8287 (m-40) cc_final: 0.7679 (p0) REVERT: A 653 ASP cc_start: 0.8212 (m-30) cc_final: 0.7987 (t0) REVERT: A 798 GLN cc_start: 0.8201 (tm-30) cc_final: 0.7881 (tm-30) REVERT: A 1118 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8108 (tptp) REVERT: A 1143 ASP cc_start: 0.8686 (t0) cc_final: 0.8404 (t0) REVERT: A 1176 CYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8524 (t) REVERT: A 1291 PHE cc_start: 0.7621 (m-10) cc_final: 0.7366 (m-10) REVERT: B 265 ASP cc_start: 0.8600 (OUTLIER) cc_final: 0.8008 (p0) REVERT: B 297 ASN cc_start: 0.8473 (OUTLIER) cc_final: 0.8256 (t0) REVERT: B 412 ARG cc_start: 0.6455 (tpt170) cc_final: 0.5916 (tpt170) outliers start: 32 outliers final: 14 residues processed: 248 average time/residue: 0.3159 time to fit residues: 116.3980 Evaluate side-chains 195 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 177 time to evaluate : 2.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 782 THR Chi-restraints excluded: chain A residue 856 SER Chi-restraints excluded: chain A residue 880 ASP Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 1118 LYS Chi-restraints excluded: chain A residue 1176 CYS Chi-restraints excluded: chain A residue 1312 TRP Chi-restraints excluded: chain A residue 1316 CYS Chi-restraints excluded: chain B residue 210 PHE Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 297 ASN Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 60 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 3 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 84 optimal weight: 8.9990 chunk 101 optimal weight: 6.9990 chunk 69 optimal weight: 7.9990 chunk 159 optimal weight: 6.9990 chunk 155 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 291 GLN A 620 GLN ** A1209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 ASN B 189 GLN B 235 HIS B 301 ASN B 343 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.115967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.093903 restraints weight = 20902.951| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.45 r_work: 0.2955 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.079 13791 Z= 0.343 Angle : 0.790 8.959 18714 Z= 0.405 Chirality : 0.050 0.166 2080 Planarity : 0.006 0.076 2362 Dihedral : 7.907 73.243 1907 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.02 % Favored : 90.85 % Rotamer: Outliers : 2.82 % Allowed : 11.41 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.19), residues: 1640 helix: -2.79 (0.41), residues: 103 sheet: -1.65 (0.19), residues: 651 loop : -2.16 (0.19), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A1312 HIS 0.010 0.002 HIS A1099 PHE 0.030 0.003 PHE B 210 TYR 0.025 0.002 TYR A 345 ARG 0.006 0.001 ARG A1298 Details of bonding type rmsd hydrogen bonds : bond 0.04400 ( 330) hydrogen bonds : angle 6.57201 ( 882) metal coordination : bond 0.01482 ( 9) metal coordination : angle 6.67744 ( 3) covalent geometry : bond 0.00814 (13782) covalent geometry : angle 0.78550 (18711) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 168 time to evaluate : 2.334 Fit side-chains REVERT: A 79 MET cc_start: 0.9158 (mmp) cc_final: 0.8913 (mmt) REVERT: A 492 ASN cc_start: 0.8328 (m-40) cc_final: 0.7552 (p0) REVERT: A 592 ILE cc_start: 0.8327 (OUTLIER) cc_final: 0.7767 (tp) REVERT: A 1056 GLU cc_start: 0.7673 (mp0) cc_final: 0.7068 (mp0) REVERT: A 1118 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.7949 (tptp) REVERT: A 1288 LYS cc_start: 0.8312 (tppt) cc_final: 0.7916 (tppt) REVERT: B 46 LYS cc_start: 0.8467 (mmtm) cc_final: 0.8262 (mmtp) REVERT: B 49 ARG cc_start: 0.8176 (mmt180) cc_final: 0.7726 (mmm-85) REVERT: B 265 ASP cc_start: 0.8551 (OUTLIER) cc_final: 0.8040 (p0) outliers start: 41 outliers final: 26 residues processed: 195 average time/residue: 0.3289 time to fit residues: 97.0216 Evaluate side-chains 191 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 162 time to evaluate : 2.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 782 THR Chi-restraints excluded: chain A residue 856 SER Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 969 ASP Chi-restraints excluded: chain A residue 1118 LYS Chi-restraints excluded: chain A residue 1199 GLU Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1312 TRP Chi-restraints excluded: chain A residue 1316 CYS Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 189 GLN Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 210 PHE Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 307 SER Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 377 MET Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 60 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 161 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 150 optimal weight: 9.9990 chunk 57 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN A 680 HIS ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1334 HIS B 152 ASN B 235 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.119092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.097564 restraints weight = 20520.545| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.38 r_work: 0.3011 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13791 Z= 0.184 Angle : 0.642 7.625 18714 Z= 0.331 Chirality : 0.046 0.170 2080 Planarity : 0.005 0.079 2362 Dihedral : 7.427 73.201 1906 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.80 % Favored : 92.07 % Rotamer: Outliers : 2.75 % Allowed : 12.99 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.19), residues: 1640 helix: -2.26 (0.46), residues: 103 sheet: -1.47 (0.19), residues: 637 loop : -2.00 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A1312 HIS 0.005 0.001 HIS B 243 PHE 0.017 0.002 PHE B 210 TYR 0.013 0.001 TYR A 345 ARG 0.003 0.000 ARG B 133 Details of bonding type rmsd hydrogen bonds : bond 0.03464 ( 330) hydrogen bonds : angle 6.20148 ( 882) metal coordination : bond 0.01020 ( 9) metal coordination : angle 5.60537 ( 3) covalent geometry : bond 0.00438 (13782) covalent geometry : angle 0.63769 (18711) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 172 time to evaluate : 1.469 Fit side-chains REVERT: A 79 MET cc_start: 0.9131 (mmp) cc_final: 0.8911 (mmt) REVERT: A 162 LEU cc_start: 0.8851 (mt) cc_final: 0.8508 (tp) REVERT: A 492 ASN cc_start: 0.8210 (m-40) cc_final: 0.7552 (p0) REVERT: A 592 ILE cc_start: 0.8488 (OUTLIER) cc_final: 0.7998 (tp) REVERT: A 1056 GLU cc_start: 0.7722 (mp0) cc_final: 0.7033 (mp0) REVERT: A 1118 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.7929 (tptp) REVERT: A 1288 LYS cc_start: 0.8277 (tppt) cc_final: 0.7874 (tppt) REVERT: B 49 ARG cc_start: 0.8187 (mmt180) cc_final: 0.7642 (mmm-85) REVERT: B 142 GLU cc_start: 0.8764 (mm-30) cc_final: 0.8505 (mm-30) outliers start: 40 outliers final: 24 residues processed: 199 average time/residue: 0.2491 time to fit residues: 74.5324 Evaluate side-chains 188 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 162 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 782 THR Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 969 ASP Chi-restraints excluded: chain A residue 990 PHE Chi-restraints excluded: chain A residue 1103 MET Chi-restraints excluded: chain A residue 1118 LYS Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1273 ASP Chi-restraints excluded: chain A residue 1312 TRP Chi-restraints excluded: chain A residue 1316 CYS Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 210 PHE Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 89 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 152 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 99 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 140 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 66 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 151 optimal weight: 0.9980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1077 GLN ** A1237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 HIS B 297 ASN ** B 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.119791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.097997 restraints weight = 20716.677| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.48 r_work: 0.3013 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13791 Z= 0.169 Angle : 0.610 7.104 18714 Z= 0.314 Chirality : 0.045 0.158 2080 Planarity : 0.005 0.077 2362 Dihedral : 6.931 73.289 1904 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.66 % Favored : 91.22 % Rotamer: Outliers : 3.30 % Allowed : 12.65 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.20), residues: 1640 helix: -1.86 (0.49), residues: 103 sheet: -1.14 (0.19), residues: 631 loop : -1.97 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1312 HIS 0.005 0.001 HIS A1385 PHE 0.014 0.002 PHE A 975 TYR 0.012 0.001 TYR A 345 ARG 0.003 0.000 ARG A 520 Details of bonding type rmsd hydrogen bonds : bond 0.03197 ( 330) hydrogen bonds : angle 5.85084 ( 882) metal coordination : bond 0.01016 ( 9) metal coordination : angle 5.54494 ( 3) covalent geometry : bond 0.00403 (13782) covalent geometry : angle 0.60569 (18711) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 175 time to evaluate : 2.305 Fit side-chains revert: symmetry clash REVERT: A 79 MET cc_start: 0.9151 (mmp) cc_final: 0.8928 (mmt) REVERT: A 162 LEU cc_start: 0.8831 (mt) cc_final: 0.8467 (tp) REVERT: A 492 ASN cc_start: 0.8226 (m-40) cc_final: 0.7580 (p0) REVERT: A 592 ILE cc_start: 0.8478 (OUTLIER) cc_final: 0.8008 (tp) REVERT: A 608 PHE cc_start: 0.8315 (t80) cc_final: 0.8039 (t80) REVERT: A 798 GLN cc_start: 0.8038 (tm-30) cc_final: 0.7806 (tm-30) REVERT: A 953 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8634 (tt) REVERT: A 1056 GLU cc_start: 0.7634 (mp0) cc_final: 0.7016 (mp0) REVERT: A 1118 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7794 (tptp) REVERT: A 1288 LYS cc_start: 0.8261 (tppt) cc_final: 0.7900 (tppt) REVERT: A 1291 PHE cc_start: 0.8047 (m-10) cc_final: 0.7841 (m-10) REVERT: B 79 MET cc_start: 0.8942 (ttt) cc_final: 0.8727 (ttt) REVERT: B 142 GLU cc_start: 0.8740 (mm-30) cc_final: 0.8497 (mm-30) REVERT: B 297 ASN cc_start: 0.8914 (OUTLIER) cc_final: 0.8666 (t0) outliers start: 48 outliers final: 30 residues processed: 207 average time/residue: 0.3089 time to fit residues: 98.8471 Evaluate side-chains 197 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 163 time to evaluate : 2.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 782 THR Chi-restraints excluded: chain A residue 856 SER Chi-restraints excluded: chain A residue 880 ASP Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 969 ASP Chi-restraints excluded: chain A residue 990 PHE Chi-restraints excluded: chain A residue 999 SER Chi-restraints excluded: chain A residue 1118 LYS Chi-restraints excluded: chain A residue 1199 GLU Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1273 ASP Chi-restraints excluded: chain A residue 1312 TRP Chi-restraints excluded: chain A residue 1316 CYS Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 210 PHE Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 297 ASN Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 89 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 109 optimal weight: 1.9990 chunk 38 optimal weight: 0.0770 chunk 108 optimal weight: 4.9990 chunk 151 optimal weight: 2.9990 chunk 103 optimal weight: 0.4980 chunk 82 optimal weight: 6.9990 chunk 133 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 149 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 overall best weight: 1.7144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 HIS B 299 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.121026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.099073 restraints weight = 20884.947| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.51 r_work: 0.3028 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13791 Z= 0.143 Angle : 0.591 9.552 18714 Z= 0.303 Chirality : 0.045 0.166 2080 Planarity : 0.004 0.074 2362 Dihedral : 6.676 73.266 1904 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.20 % Favored : 92.68 % Rotamer: Outliers : 2.68 % Allowed : 14.16 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.20), residues: 1640 helix: -1.63 (0.51), residues: 103 sheet: -0.89 (0.20), residues: 620 loop : -1.87 (0.20), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1312 HIS 0.006 0.001 HIS A1385 PHE 0.014 0.001 PHE A 975 TYR 0.009 0.001 TYR A 345 ARG 0.007 0.000 ARG B 133 Details of bonding type rmsd hydrogen bonds : bond 0.02999 ( 330) hydrogen bonds : angle 5.70507 ( 882) metal coordination : bond 0.00909 ( 9) metal coordination : angle 4.72550 ( 3) covalent geometry : bond 0.00342 (13782) covalent geometry : angle 0.58823 (18711) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 174 time to evaluate : 1.432 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.9169 (ptp) cc_final: 0.8952 (ptp) REVERT: A 79 MET cc_start: 0.9161 (mmp) cc_final: 0.8933 (mmt) REVERT: A 162 LEU cc_start: 0.8802 (mt) cc_final: 0.8442 (tp) REVERT: A 492 ASN cc_start: 0.8173 (m-40) cc_final: 0.7581 (p0) REVERT: A 608 PHE cc_start: 0.8330 (t80) cc_final: 0.8073 (t80) REVERT: A 798 GLN cc_start: 0.7963 (tm-30) cc_final: 0.7729 (tm-30) REVERT: A 887 ASN cc_start: 0.8191 (m-40) cc_final: 0.7931 (p0) REVERT: A 932 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.8350 (mtp85) REVERT: A 953 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8639 (tt) REVERT: A 1056 GLU cc_start: 0.7558 (mp0) cc_final: 0.6969 (mp0) REVERT: A 1118 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7694 (tptp) REVERT: A 1288 LYS cc_start: 0.8153 (tppt) cc_final: 0.7830 (tppt) REVERT: B 142 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8544 (mm-30) outliers start: 39 outliers final: 29 residues processed: 200 average time/residue: 0.2349 time to fit residues: 70.5365 Evaluate side-chains 197 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 165 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 782 THR Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 932 ARG Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 990 PHE Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1118 LYS Chi-restraints excluded: chain A residue 1199 GLU Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1261 MET Chi-restraints excluded: chain A residue 1273 ASP Chi-restraints excluded: chain A residue 1312 TRP Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 210 PHE Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 89 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 96 optimal weight: 1.9990 chunk 84 optimal weight: 8.9990 chunk 155 optimal weight: 8.9990 chunk 30 optimal weight: 4.9990 chunk 104 optimal weight: 9.9990 chunk 108 optimal weight: 6.9990 chunk 102 optimal weight: 4.9990 chunk 63 optimal weight: 7.9990 chunk 162 optimal weight: 5.9990 chunk 149 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.115329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.094259 restraints weight = 21199.697| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.32 r_work: 0.2971 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 13791 Z= 0.313 Angle : 0.726 10.273 18714 Z= 0.370 Chirality : 0.049 0.164 2080 Planarity : 0.005 0.069 2362 Dihedral : 7.143 73.186 1903 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.27 % Favored : 90.61 % Rotamer: Outliers : 3.71 % Allowed : 14.02 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.20), residues: 1640 helix: -1.62 (0.51), residues: 98 sheet: -1.10 (0.19), residues: 654 loop : -1.87 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A1312 HIS 0.008 0.002 HIS B 384 PHE 0.022 0.002 PHE B 210 TYR 0.020 0.002 TYR C 97 ARG 0.006 0.001 ARG B 133 Details of bonding type rmsd hydrogen bonds : bond 0.03651 ( 330) hydrogen bonds : angle 6.00850 ( 882) metal coordination : bond 0.01465 ( 9) metal coordination : angle 6.35287 ( 3) covalent geometry : bond 0.00745 (13782) covalent geometry : angle 0.72149 (18711) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 163 time to evaluate : 1.432 Fit side-chains revert: symmetry clash REVERT: A 162 LEU cc_start: 0.8836 (mt) cc_final: 0.8478 (tp) REVERT: A 324 CYS cc_start: 0.8505 (m) cc_final: 0.8169 (t) REVERT: A 492 ASN cc_start: 0.8208 (m-40) cc_final: 0.7503 (p0) REVERT: A 592 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8076 (tp) REVERT: A 702 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.7456 (ptt180) REVERT: A 932 ARG cc_start: 0.8970 (OUTLIER) cc_final: 0.8417 (mtp85) REVERT: A 953 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8598 (tt) REVERT: A 1056 GLU cc_start: 0.7738 (mp0) cc_final: 0.7176 (mp0) REVERT: A 1118 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.7911 (tptp) REVERT: A 1288 LYS cc_start: 0.8218 (tppt) cc_final: 0.8018 (tppt) REVERT: A 1332 ASN cc_start: 0.8769 (OUTLIER) cc_final: 0.8524 (t0) REVERT: B 142 GLU cc_start: 0.8871 (mm-30) cc_final: 0.8624 (mm-30) outliers start: 54 outliers final: 43 residues processed: 201 average time/residue: 0.2541 time to fit residues: 76.2218 Evaluate side-chains 207 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 158 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 702 ARG Chi-restraints excluded: chain A residue 782 THR Chi-restraints excluded: chain A residue 856 SER Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 932 ARG Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 969 ASP Chi-restraints excluded: chain A residue 999 SER Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1039 SER Chi-restraints excluded: chain A residue 1118 LYS Chi-restraints excluded: chain A residue 1199 GLU Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1261 MET Chi-restraints excluded: chain A residue 1273 ASP Chi-restraints excluded: chain A residue 1312 TRP Chi-restraints excluded: chain A residue 1332 ASN Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 210 PHE Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 377 MET Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 89 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 129 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 140 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 111 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 chunk 100 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 80 optimal weight: 8.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.118202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.097469 restraints weight = 21034.289| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.29 r_work: 0.3027 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13791 Z= 0.180 Angle : 0.625 8.982 18714 Z= 0.320 Chirality : 0.045 0.157 2080 Planarity : 0.005 0.070 2362 Dihedral : 6.823 73.209 1903 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.05 % Favored : 91.83 % Rotamer: Outliers : 3.51 % Allowed : 14.43 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.20), residues: 1640 helix: -1.65 (0.50), residues: 103 sheet: -0.97 (0.20), residues: 642 loop : -1.83 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A1312 HIS 0.007 0.001 HIS B 243 PHE 0.022 0.002 PHE A 608 TYR 0.019 0.001 TYR C 97 ARG 0.005 0.000 ARG B 133 Details of bonding type rmsd hydrogen bonds : bond 0.03109 ( 330) hydrogen bonds : angle 5.81402 ( 882) metal coordination : bond 0.01049 ( 9) metal coordination : angle 5.08782 ( 3) covalent geometry : bond 0.00429 (13782) covalent geometry : angle 0.62132 (18711) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 168 time to evaluate : 1.462 Fit side-chains revert: symmetry clash REVERT: A 162 LEU cc_start: 0.8801 (mt) cc_final: 0.8485 (tp) REVERT: A 324 CYS cc_start: 0.8451 (m) cc_final: 0.8237 (t) REVERT: A 492 ASN cc_start: 0.8199 (m-40) cc_final: 0.7562 (p0) REVERT: A 592 ILE cc_start: 0.8531 (OUTLIER) cc_final: 0.8067 (tp) REVERT: A 798 GLN cc_start: 0.8040 (tm-30) cc_final: 0.7825 (tm-30) REVERT: A 932 ARG cc_start: 0.8979 (OUTLIER) cc_final: 0.8434 (mtp85) REVERT: A 953 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8678 (tt) REVERT: A 1056 GLU cc_start: 0.7684 (mp0) cc_final: 0.7106 (mp0) REVERT: A 1118 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.7815 (tptp) REVERT: A 1332 ASN cc_start: 0.8756 (OUTLIER) cc_final: 0.8436 (t0) REVERT: B 46 LYS cc_start: 0.8462 (mmtp) cc_final: 0.8234 (mmtp) REVERT: B 142 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8559 (mm-30) REVERT: C 64 LYS cc_start: 0.7074 (OUTLIER) cc_final: 0.6853 (mttt) outliers start: 51 outliers final: 38 residues processed: 206 average time/residue: 0.2363 time to fit residues: 73.1421 Evaluate side-chains 209 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 165 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLN Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 782 THR Chi-restraints excluded: chain A residue 856 SER Chi-restraints excluded: chain A residue 880 ASP Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 932 ARG Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 999 SER Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1118 LYS Chi-restraints excluded: chain A residue 1199 GLU Chi-restraints excluded: chain A residue 1206 ILE Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1273 ASP Chi-restraints excluded: chain A residue 1312 TRP Chi-restraints excluded: chain A residue 1332 ASN Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 210 PHE Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 89 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 120 optimal weight: 0.5980 chunk 121 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 43 optimal weight: 0.0030 chunk 80 optimal weight: 8.9990 chunk 142 optimal weight: 9.9990 chunk 55 optimal weight: 8.9990 overall best weight: 1.0394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 HIS B 360 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.122293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.101008 restraints weight = 20496.325| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.42 r_work: 0.3060 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13791 Z= 0.115 Angle : 0.574 7.876 18714 Z= 0.295 Chirality : 0.044 0.160 2080 Planarity : 0.004 0.071 2362 Dihedral : 6.387 73.276 1903 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.80 % Favored : 92.13 % Rotamer: Outliers : 2.89 % Allowed : 15.33 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.20), residues: 1640 helix: -1.37 (0.52), residues: 103 sheet: -0.71 (0.21), residues: 607 loop : -1.71 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 72 HIS 0.006 0.001 HIS A1385 PHE 0.021 0.001 PHE A 608 TYR 0.024 0.001 TYR C 97 ARG 0.005 0.000 ARG B 133 Details of bonding type rmsd hydrogen bonds : bond 0.02774 ( 330) hydrogen bonds : angle 5.53606 ( 882) metal coordination : bond 0.00690 ( 9) metal coordination : angle 3.63904 ( 3) covalent geometry : bond 0.00273 (13782) covalent geometry : angle 0.57230 (18711) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 189 time to evaluate : 1.534 Fit side-chains revert: symmetry clash REVERT: A 124 GLU cc_start: 0.7783 (pm20) cc_final: 0.7557 (pm20) REVERT: A 162 LEU cc_start: 0.8769 (mt) cc_final: 0.8430 (tp) REVERT: A 216 THR cc_start: 0.9062 (m) cc_final: 0.8800 (p) REVERT: A 492 ASN cc_start: 0.8148 (m-40) cc_final: 0.7635 (p0) REVERT: A 592 ILE cc_start: 0.8438 (OUTLIER) cc_final: 0.8029 (tt) REVERT: A 798 GLN cc_start: 0.7935 (tm-30) cc_final: 0.7706 (tm-30) REVERT: A 932 ARG cc_start: 0.8918 (OUTLIER) cc_final: 0.8358 (mtp85) REVERT: A 953 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8654 (tt) REVERT: A 1056 GLU cc_start: 0.7613 (mp0) cc_final: 0.6960 (mp0) REVERT: A 1118 LYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7480 (tptp) REVERT: A 1288 LYS cc_start: 0.8336 (tppt) cc_final: 0.7991 (tppt) REVERT: A 1332 ASN cc_start: 0.8737 (OUTLIER) cc_final: 0.8396 (t0) REVERT: B 142 GLU cc_start: 0.8770 (mm-30) cc_final: 0.8557 (mm-30) REVERT: C 54 MET cc_start: 0.7981 (ttm) cc_final: 0.7493 (tpt) outliers start: 42 outliers final: 34 residues processed: 217 average time/residue: 0.2389 time to fit residues: 77.9225 Evaluate side-chains 217 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 178 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 856 SER Chi-restraints excluded: chain A residue 880 ASP Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 932 ARG Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 969 ASP Chi-restraints excluded: chain A residue 990 PHE Chi-restraints excluded: chain A residue 999 SER Chi-restraints excluded: chain A residue 1039 SER Chi-restraints excluded: chain A residue 1118 LYS Chi-restraints excluded: chain A residue 1199 GLU Chi-restraints excluded: chain A residue 1206 ILE Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1273 ASP Chi-restraints excluded: chain A residue 1312 TRP Chi-restraints excluded: chain A residue 1332 ASN Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 210 PHE Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 89 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 125 optimal weight: 4.9990 chunk 99 optimal weight: 0.0870 chunk 63 optimal weight: 7.9990 chunk 91 optimal weight: 0.0980 chunk 109 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 156 optimal weight: 7.9990 chunk 128 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 overall best weight: 1.3962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 HIS C 22 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.121931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.100374 restraints weight = 20631.668| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.47 r_work: 0.3049 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13791 Z= 0.129 Angle : 0.585 9.318 18714 Z= 0.299 Chirality : 0.044 0.156 2080 Planarity : 0.004 0.070 2362 Dihedral : 6.305 73.285 1903 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.38 % Favored : 92.56 % Rotamer: Outliers : 2.82 % Allowed : 15.60 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.21), residues: 1640 helix: -1.20 (0.52), residues: 103 sheet: -0.61 (0.21), residues: 599 loop : -1.65 (0.20), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1312 HIS 0.006 0.001 HIS A1385 PHE 0.020 0.001 PHE A 608 TYR 0.022 0.001 TYR C 97 ARG 0.004 0.000 ARG B 133 Details of bonding type rmsd hydrogen bonds : bond 0.02790 ( 330) hydrogen bonds : angle 5.47628 ( 882) metal coordination : bond 0.00783 ( 9) metal coordination : angle 4.11667 ( 3) covalent geometry : bond 0.00307 (13782) covalent geometry : angle 0.58233 (18711) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 182 time to evaluate : 1.445 Fit side-chains revert: symmetry clash REVERT: A 124 GLU cc_start: 0.7804 (pm20) cc_final: 0.7596 (pm20) REVERT: A 162 LEU cc_start: 0.8727 (mt) cc_final: 0.8438 (tp) REVERT: A 216 THR cc_start: 0.9077 (m) cc_final: 0.8811 (p) REVERT: A 492 ASN cc_start: 0.8166 (m-40) cc_final: 0.7669 (p0) REVERT: A 592 ILE cc_start: 0.8413 (OUTLIER) cc_final: 0.7931 (tp) REVERT: A 617 TYR cc_start: 0.7345 (m-80) cc_final: 0.7095 (m-80) REVERT: A 798 GLN cc_start: 0.7954 (tm-30) cc_final: 0.7728 (tm-30) REVERT: A 932 ARG cc_start: 0.8907 (OUTLIER) cc_final: 0.8351 (mtp85) REVERT: A 953 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8550 (tt) REVERT: A 1056 GLU cc_start: 0.7564 (mp0) cc_final: 0.6898 (mp0) REVERT: A 1118 LYS cc_start: 0.8055 (OUTLIER) cc_final: 0.7455 (tptp) REVERT: A 1288 LYS cc_start: 0.8270 (tppt) cc_final: 0.7774 (tppt) REVERT: A 1332 ASN cc_start: 0.8781 (OUTLIER) cc_final: 0.8436 (t0) REVERT: A 1430 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8711 (mt) REVERT: B 142 GLU cc_start: 0.8771 (mm-30) cc_final: 0.8540 (mm-30) REVERT: C 54 MET cc_start: 0.8009 (ttm) cc_final: 0.7499 (tpt) outliers start: 41 outliers final: 31 residues processed: 212 average time/residue: 0.2310 time to fit residues: 74.1786 Evaluate side-chains 208 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 171 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 856 SER Chi-restraints excluded: chain A residue 880 ASP Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 932 ARG Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 990 PHE Chi-restraints excluded: chain A residue 999 SER Chi-restraints excluded: chain A residue 1039 SER Chi-restraints excluded: chain A residue 1118 LYS Chi-restraints excluded: chain A residue 1199 GLU Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1273 ASP Chi-restraints excluded: chain A residue 1312 TRP Chi-restraints excluded: chain A residue 1332 ASN Chi-restraints excluded: chain A residue 1430 LEU Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 210 PHE Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 60 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 29 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 151 optimal weight: 0.6980 chunk 133 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 156 optimal weight: 10.0000 chunk 150 optimal weight: 10.0000 chunk 148 optimal weight: 2.9990 chunk 127 optimal weight: 5.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 HIS C 22 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.118522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.097189 restraints weight = 20772.741| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.42 r_work: 0.3011 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13791 Z= 0.204 Angle : 0.639 10.541 18714 Z= 0.326 Chirality : 0.046 0.160 2080 Planarity : 0.004 0.063 2362 Dihedral : 6.520 73.242 1903 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.72 % Favored : 91.22 % Rotamer: Outliers : 3.02 % Allowed : 15.40 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.21), residues: 1640 helix: -1.09 (0.53), residues: 98 sheet: -0.75 (0.20), residues: 639 loop : -1.63 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A1312 HIS 0.005 0.001 HIS A1385 PHE 0.021 0.002 PHE A 608 TYR 0.023 0.001 TYR C 97 ARG 0.006 0.000 ARG B 308 Details of bonding type rmsd hydrogen bonds : bond 0.03127 ( 330) hydrogen bonds : angle 5.61642 ( 882) metal coordination : bond 0.01039 ( 9) metal coordination : angle 4.84076 ( 3) covalent geometry : bond 0.00487 (13782) covalent geometry : angle 0.63652 (18711) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6369.92 seconds wall clock time: 113 minutes 53.22 seconds (6833.22 seconds total)