Starting phenix.real_space_refine on Thu Jul 31 00:32:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vgq_31975/07_2025/7vgq_31975_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vgq_31975/07_2025/7vgq_31975.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vgq_31975/07_2025/7vgq_31975.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vgq_31975/07_2025/7vgq_31975.map" model { file = "/net/cci-nas-00/data/ceres_data/7vgq_31975/07_2025/7vgq_31975_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vgq_31975/07_2025/7vgq_31975_neut.cif" } resolution = 4.0 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= 0.001 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 96 5.16 5 C 8398 2.51 5 N 2202 2.21 5 O 2458 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13156 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 12749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1612, 12749 Classifications: {'peptide': 1612} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 46, 'TRANS': 1565} Chain breaks: 14 Unresolved non-hydrogen bonds: 178 Unresolved non-hydrogen angles: 223 Unresolved non-hydrogen dihedrals: 155 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 4, 'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 141 Chain: "B" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 405 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12817 SG CYS B 41 56.193 81.865 17.896 1.00 4.57 S ATOM 12823 SG CYS B 42 59.837 81.536 16.998 1.00 3.86 S ATOM 12957 SG CYS B 58 57.974 82.935 13.980 1.00 12.05 S ATOM 12982 SG CYS B 61 56.989 79.384 15.195 1.00 8.30 S ATOM 13072 SG CYS B 72 47.604 82.865 20.009 1.00 13.30 S ATOM 13096 SG CYS B 75 46.615 86.667 22.432 1.00 11.61 S Time building chain proxies: 8.22, per 1000 atoms: 0.62 Number of scatterers: 13156 At special positions: 0 Unit cell: (115.2, 118.4, 126.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 96 16.00 O 2458 8.00 N 2202 7.00 C 8398 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 60 " distance=2.03 Simple disulfide: pdb=" SG CYS A1650 " - pdb=" SG CYS A1664 " distance=2.03 Simple disulfide: pdb=" SG CYS A1691 " - pdb=" SG CYS A1776 " distance=2.04 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: 3.42 Conformation dependent library (CDL) restraints added in 1.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 101 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 42 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 41 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 58 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 61 " pdb=" ZN B 102 " pdb="ZN ZN B 102 " - pdb=" NE2 HIS B 55 " pdb="ZN ZN B 102 " - pdb=" SG CYS B 75 " pdb="ZN ZN B 102 " - pdb=" SG CYS B 72 " Number of angles added : 6 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3166 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 11 sheets defined 45.5% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.97 Creating SS restraints... Processing helix chain 'A' and resid 4 through 12 removed outlier: 4.189A pdb=" N LYS A 9 " --> pdb=" O VAL A 5 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLY A 10 " --> pdb=" O GLN A 6 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE A 12 " --> pdb=" O LEU A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 27 removed outlier: 3.917A pdb=" N LYS A 26 " --> pdb=" O PHE A 22 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL A 27 " --> pdb=" O ALA A 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 22 through 27' Processing helix chain 'A' and resid 34 through 39 removed outlier: 4.007A pdb=" N LEU A 39 " --> pdb=" O PRO A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 51 removed outlier: 3.574A pdb=" N SER A 48 " --> pdb=" O LYS A 44 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL A 50 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 57 Processing helix chain 'A' and resid 112 through 125 removed outlier: 4.852A pdb=" N ALA A 118 " --> pdb=" O LYS A 114 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER A 121 " --> pdb=" O LYS A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 131 Processing helix chain 'A' and resid 132 through 134 No H-bonds generated for 'chain 'A' and resid 132 through 134' Processing helix chain 'A' and resid 156 through 164 removed outlier: 3.673A pdb=" N ARG A 161 " --> pdb=" O ILE A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 175 removed outlier: 3.720A pdb=" N LEU A 175 " --> pdb=" O SER A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 192 Processing helix chain 'A' and resid 200 through 205 removed outlier: 3.624A pdb=" N LEU A 204 " --> pdb=" O LEU A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 223 removed outlier: 4.071A pdb=" N SER A 221 " --> pdb=" O ARG A 217 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE A 223 " --> pdb=" O ASN A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 250 removed outlier: 3.554A pdb=" N LYS A 241 " --> pdb=" O GLU A 237 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASP A 248 " --> pdb=" O MET A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 275 removed outlier: 4.860A pdb=" N SER A 271 " --> pdb=" O LEU A 267 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N SER A 272 " --> pdb=" O GLU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 289 removed outlier: 4.270A pdb=" N ASN A 288 " --> pdb=" O CYS A 284 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ASN A 289 " --> pdb=" O PRO A 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 284 through 289' Processing helix chain 'A' and resid 290 through 300 removed outlier: 3.826A pdb=" N ILE A 294 " --> pdb=" O LYS A 290 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE A 300 " --> pdb=" O TYR A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 339 removed outlier: 3.782A pdb=" N LYS A 336 " --> pdb=" O SER A 332 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLY A 339 " --> pdb=" O ASN A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 366 removed outlier: 4.531A pdb=" N LEU A 353 " --> pdb=" O THR A 349 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE A 364 " --> pdb=" O LEU A 360 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER A 365 " --> pdb=" O MET A 361 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLU A 366 " --> pdb=" O VAL A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 410 removed outlier: 3.513A pdb=" N ILE A 403 " --> pdb=" O ALA A 399 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG A 404 " --> pdb=" O ILE A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 451 removed outlier: 4.111A pdb=" N ILE A 447 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A 451 " --> pdb=" O ILE A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 478 removed outlier: 3.636A pdb=" N MET A 478 " --> pdb=" O PHE A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 499 removed outlier: 3.850A pdb=" N PHE A 487 " --> pdb=" O GLN A 483 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N THR A 489 " --> pdb=" O ARG A 485 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N SER A 492 " --> pdb=" O LYS A 488 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER A 496 " --> pdb=" O SER A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 578 removed outlier: 3.978A pdb=" N ARG A 577 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 595 removed outlier: 4.344A pdb=" N CYS A 592 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLU A 593 " --> pdb=" O ALA A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 599 Processing helix chain 'A' and resid 602 through 622 removed outlier: 3.564A pdb=" N ASP A 608 " --> pdb=" O GLY A 604 " (cutoff:3.500A) Proline residue: A 611 - end of helix removed outlier: 3.542A pdb=" N ARG A 614 " --> pdb=" O GLY A 610 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N LEU A 615 " --> pdb=" O PRO A 611 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A 616 " --> pdb=" O ILE A 612 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU A 621 " --> pdb=" O VAL A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 634 removed outlier: 4.406A pdb=" N LEU A 632 " --> pdb=" O ASN A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 644 Processing helix chain 'A' and resid 650 through 654 Processing helix chain 'A' and resid 671 through 679 removed outlier: 3.991A pdb=" N ARG A 677 " --> pdb=" O GLY A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 701 removed outlier: 3.733A pdb=" N ARG A 692 " --> pdb=" O PHE A 688 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A 699 " --> pdb=" O TYR A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 706 removed outlier: 3.869A pdb=" N LEU A 705 " --> pdb=" O LEU A 702 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE A 706 " --> pdb=" O CYS A 703 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 702 through 706' Processing helix chain 'A' and resid 716 through 730 removed outlier: 3.689A pdb=" N GLU A 726 " --> pdb=" O GLU A 722 " (cutoff:3.500A) Proline residue: A 727 - end of helix removed outlier: 3.751A pdb=" N LYS A 730 " --> pdb=" O GLU A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 760 removed outlier: 3.665A pdb=" N ILE A 751 " --> pdb=" O ASP A 747 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET A 752 " --> pdb=" O GLN A 748 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE A 760 " --> pdb=" O LEU A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 789 removed outlier: 3.691A pdb=" N ASN A 781 " --> pdb=" O LYS A 777 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TYR A 782 " --> pdb=" O GLU A 778 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N PHE A 787 " --> pdb=" O CYS A 783 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG A 789 " --> pdb=" O SER A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 852 removed outlier: 4.348A pdb=" N VAL A 841 " --> pdb=" O LYS A 837 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU A 850 " --> pdb=" O SER A 846 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG A 851 " --> pdb=" O SER A 847 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE A 852 " --> pdb=" O MET A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 874 removed outlier: 4.038A pdb=" N THR A 874 " --> pdb=" O LEU A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 894 removed outlier: 3.655A pdb=" N SER A 891 " --> pdb=" O GLN A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 920 removed outlier: 4.092A pdb=" N SER A 904 " --> pdb=" O GLU A 900 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU A 907 " --> pdb=" O GLU A 903 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA A 920 " --> pdb=" O LEU A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 960 Processing helix chain 'A' and resid 961 through 970 Processing helix chain 'A' and resid 971 through 975 Processing helix chain 'A' and resid 982 through 990 removed outlier: 3.663A pdb=" N ALA A 986 " --> pdb=" O GLU A 982 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS A 989 " --> pdb=" O ASP A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1021 removed outlier: 4.062A pdb=" N THR A1016 " --> pdb=" O LYS A1012 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER A1017 " --> pdb=" O ASN A1013 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER A1018 " --> pdb=" O LEU A1014 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU A1021 " --> pdb=" O SER A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1035 Processing helix chain 'A' and resid 1079 through 1083 Processing helix chain 'A' and resid 1090 through 1094 removed outlier: 3.999A pdb=" N ASN A1093 " --> pdb=" O ALA A1090 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU A1094 " --> pdb=" O LEU A1091 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1090 through 1094' Processing helix chain 'A' and resid 1135 through 1153 removed outlier: 3.670A pdb=" N LEU A1140 " --> pdb=" O LEU A1136 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LEU A1144 " --> pdb=" O LEU A1140 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N VAL A1145 " --> pdb=" O MET A1141 " (cutoff:3.500A) Processing helix chain 'A' and resid 1163 through 1179 removed outlier: 3.939A pdb=" N PHE A1167 " --> pdb=" O SER A1163 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N MET A1176 " --> pdb=" O CYS A1172 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN A1179 " --> pdb=" O LYS A1175 " (cutoff:3.500A) Processing helix chain 'A' and resid 1197 through 1206 removed outlier: 3.690A pdb=" N PHE A1201 " --> pdb=" O SER A1197 " (cutoff:3.500A) Processing helix chain 'A' and resid 1221 through 1226 Processing helix chain 'A' and resid 1227 through 1233 removed outlier: 3.729A pdb=" N HIS A1233 " --> pdb=" O LYS A1229 " (cutoff:3.500A) Processing helix chain 'A' and resid 1239 through 1244 removed outlier: 4.029A pdb=" N GLU A1244 " --> pdb=" O ILE A1240 " (cutoff:3.500A) Processing helix chain 'A' and resid 1265 through 1271 Processing helix chain 'A' and resid 1295 through 1299 Processing helix chain 'A' and resid 1301 through 1317 removed outlier: 3.743A pdb=" N THR A1306 " --> pdb=" O TYR A1302 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLU A1307 " --> pdb=" O GLY A1303 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU A1314 " --> pdb=" O LEU A1310 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASP A1315 " --> pdb=" O CYS A1311 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU A1316 " --> pdb=" O TYR A1312 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU A1317 " --> pdb=" O ALA A1313 " (cutoff:3.500A) Processing helix chain 'A' and resid 1351 through 1363 removed outlier: 3.694A pdb=" N ILE A1355 " --> pdb=" O TRP A1351 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE A1357 " --> pdb=" O GLU A1353 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE A1360 " --> pdb=" O CYS A1356 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER A1362 " --> pdb=" O HIS A1358 " (cutoff:3.500A) Processing helix chain 'A' and resid 1364 through 1366 No H-bonds generated for 'chain 'A' and resid 1364 through 1366' Processing helix chain 'A' and resid 1395 through 1405 removed outlier: 4.494A pdb=" N PHE A1399 " --> pdb=" O LEU A1395 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL A1400 " --> pdb=" O LEU A1396 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N SER A1401 " --> pdb=" O THR A1397 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N HIS A1405 " --> pdb=" O SER A1401 " (cutoff:3.500A) Processing helix chain 'A' and resid 1414 through 1427 removed outlier: 4.048A pdb=" N ILE A1419 " --> pdb=" O LEU A1415 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ASP A1420 " --> pdb=" O SER A1416 " (cutoff:3.500A) Processing helix chain 'A' and resid 1435 through 1449 removed outlier: 3.609A pdb=" N SER A1440 " --> pdb=" O VAL A1436 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LYS A1441 " --> pdb=" O ALA A1437 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG A1442 " --> pdb=" O ARG A1438 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ASN A1444 " --> pdb=" O SER A1440 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE A1447 " --> pdb=" O VAL A1443 " (cutoff:3.500A) Processing helix chain 'A' and resid 1472 through 1485 removed outlier: 3.703A pdb=" N ARG A1476 " --> pdb=" O SER A1472 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU A1477 " --> pdb=" O ARG A1473 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N GLN A1478 " --> pdb=" O GLY A1474 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG A1479 " --> pdb=" O TYR A1475 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA A1483 " --> pdb=" O ARG A1479 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE A1484 " --> pdb=" O LYS A1480 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N PHE A1485 " --> pdb=" O ILE A1481 " (cutoff:3.500A) Processing helix chain 'A' and resid 1491 through 1506 removed outlier: 4.048A pdb=" N ASN A1503 " --> pdb=" O ARG A1499 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASP A1504 " --> pdb=" O LYS A1500 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS A1506 " --> pdb=" O PHE A1502 " (cutoff:3.500A) Processing helix chain 'A' and resid 1515 through 1520 removed outlier: 4.313A pdb=" N GLY A1520 " --> pdb=" O ILE A1516 " (cutoff:3.500A) Processing helix chain 'A' and resid 1525 through 1535 removed outlier: 4.303A pdb=" N GLN A1532 " --> pdb=" O THR A1528 " (cutoff:3.500A) Processing helix chain 'A' and resid 1537 through 1545 removed outlier: 4.301A pdb=" N VAL A1541 " --> pdb=" O SER A1537 " (cutoff:3.500A) Processing helix chain 'A' and resid 1580 through 1590 removed outlier: 3.874A pdb=" N SER A1587 " --> pdb=" O LYS A1583 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS A1588 " --> pdb=" O THR A1584 " (cutoff:3.500A) Processing helix chain 'A' and resid 1613 through 1617 Processing helix chain 'A' and resid 1618 through 1622 Processing helix chain 'A' and resid 1640 through 1645 Processing helix chain 'A' and resid 1677 through 1693 removed outlier: 4.082A pdb=" N ASP A1681 " --> pdb=" O PRO A1677 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N CYS A1691 " --> pdb=" O LEU A1687 " (cutoff:3.500A) Processing helix chain 'A' and resid 1743 through 1750 removed outlier: 3.706A pdb=" N LEU A1747 " --> pdb=" O ASN A1743 " (cutoff:3.500A) Processing helix chain 'A' and resid 1788 through 1793 removed outlier: 3.929A pdb=" N LEU A1793 " --> pdb=" O ILE A1789 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 67 removed outlier: 4.201A pdb=" N GLN B 63 " --> pdb=" O LEU B 59 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N THR B 64 " --> pdb=" O ARG B 60 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N MET B 65 " --> pdb=" O CYS B 61 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU B 66 " --> pdb=" O HIS B 62 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ARG B 67 " --> pdb=" O GLN B 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 59 through 67' Processing sheet with id=AA1, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.809A pdb=" N LEU A 98 " --> pdb=" O THR A 136 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 387 through 388 Processing sheet with id=AA3, first strand: chain 'A' and resid 457 through 459 Processing sheet with id=AA4, first strand: chain 'A' and resid 529 through 534 removed outlier: 3.742A pdb=" N TYR A 545 " --> pdb=" O TYR A 529 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N PHE A 533 " --> pdb=" O GLY A 541 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR A 558 " --> pdb=" O PHE A 542 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU A 559 " --> pdb=" O SER A 566 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N SER A 566 " --> pdb=" O LEU A 559 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 646 through 647 Processing sheet with id=AA6, first strand: chain 'A' and resid 1236 through 1237 removed outlier: 3.597A pdb=" N VAL A1236 " --> pdb=" O ILE A1284 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1323 through 1326 removed outlier: 3.976A pdb=" N ILE A1332 " --> pdb=" O TYR A1325 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1548 through 1549 removed outlier: 4.108A pdb=" N ARG A1548 " --> pdb=" O TYR A1663 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1630 through 1631 removed outlier: 3.524A pdb=" N VAL A1630 " --> pdb=" O LEU A1638 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1716 through 1718 Processing sheet with id=AB2, first strand: chain 'B' and resid 49 through 51 360 hydrogen bonds defined for protein. 1011 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: 4.56 Time building geometry restraints manager: 4.08 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: 3632 1.33 - 1.46: 2728 1.46 - 1.58: 6887 1.58 - 1.70: 0 1.70 - 1.82: 137 Bond restraints: 13384 Sorted by residual: bond pdb=" CA ASP A1470 " pdb=" CB ASP A1470 " ideal model delta sigma weight residual 1.531 1.432 0.099 3.28e-02 9.30e+02 9.13e+00 bond pdb=" CG LEU A 613 " pdb=" CD1 LEU A 613 " ideal model delta sigma weight residual 1.521 1.436 0.085 3.30e-02 9.18e+02 6.68e+00 bond pdb=" CB ASN A 698 " pdb=" CG ASN A 698 " ideal model delta sigma weight residual 1.516 1.453 0.063 2.50e-02 1.60e+03 6.44e+00 bond pdb=" N ILE A 396 " pdb=" CA ILE A 396 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.25e-02 6.40e+03 6.14e+00 bond pdb=" CG LEU A 696 " pdb=" CD2 LEU A 696 " ideal model delta sigma weight residual 1.521 1.441 0.080 3.30e-02 9.18e+02 5.89e+00 ... (remaining 13379 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.78: 17863 4.78 - 9.56: 176 9.56 - 14.33: 13 14.33 - 19.11: 0 19.11 - 23.89: 1 Bond angle restraints: 18053 Sorted by residual: angle pdb=" N ILE A 396 " pdb=" CA ILE A 396 " pdb=" C ILE A 396 " ideal model delta sigma weight residual 109.34 133.23 -23.89 2.08e+00 2.31e-01 1.32e+02 angle pdb=" N ILE A 958 " pdb=" CA ILE A 958 " pdb=" C ILE A 958 " ideal model delta sigma weight residual 110.62 100.04 10.58 1.02e+00 9.61e-01 1.08e+02 angle pdb=" C ASP A 971 " pdb=" N PRO A 972 " pdb=" CA PRO A 972 " ideal model delta sigma weight residual 119.28 128.18 -8.90 1.10e+00 8.26e-01 6.54e+01 angle pdb=" C LYS A 401 " pdb=" N LEU A 402 " pdb=" CA LEU A 402 " ideal model delta sigma weight residual 120.44 130.18 -9.74 1.30e+00 5.92e-01 5.61e+01 angle pdb=" N VAL A 962 " pdb=" CA VAL A 962 " pdb=" C VAL A 962 " ideal model delta sigma weight residual 110.62 116.55 -5.93 1.02e+00 9.61e-01 3.38e+01 ... (remaining 18048 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.43: 7462 16.43 - 32.87: 578 32.87 - 49.30: 96 49.30 - 65.73: 6 65.73 - 82.17: 7 Dihedral angle restraints: 8149 sinusoidal: 3285 harmonic: 4864 Sorted by residual: dihedral pdb=" CA LEU A1693 " pdb=" C LEU A1693 " pdb=" N GLY A1694 " pdb=" CA GLY A1694 " ideal model delta harmonic sigma weight residual 180.00 150.93 29.07 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA SER A1440 " pdb=" C SER A1440 " pdb=" N LYS A1441 " pdb=" CA LYS A1441 " ideal model delta harmonic sigma weight residual 180.00 151.78 28.22 0 5.00e+00 4.00e-02 3.19e+01 dihedral pdb=" CA HIS A1271 " pdb=" C HIS A1271 " pdb=" N GLN A1272 " pdb=" CA GLN A1272 " ideal model delta harmonic sigma weight residual 180.00 153.17 26.83 0 5.00e+00 4.00e-02 2.88e+01 ... (remaining 8146 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 1950 0.131 - 0.263: 114 0.263 - 0.394: 9 0.394 - 0.526: 1 0.526 - 0.657: 1 Chirality restraints: 2075 Sorted by residual: chirality pdb=" CA ILE A 396 " pdb=" N ILE A 396 " pdb=" C ILE A 396 " pdb=" CB ILE A 396 " both_signs ideal model delta sigma weight residual False 2.43 1.78 0.66 2.00e-01 2.50e+01 1.08e+01 chirality pdb=" CB ILE A1332 " pdb=" CA ILE A1332 " pdb=" CG1 ILE A1332 " pdb=" CG2 ILE A1332 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.45 2.00e-01 2.50e+01 4.98e+00 chirality pdb=" CA VAL A 389 " pdb=" N VAL A 389 " pdb=" C VAL A 389 " pdb=" CB VAL A 389 " both_signs ideal model delta sigma weight residual False 2.44 2.06 0.38 2.00e-01 2.50e+01 3.70e+00 ... (remaining 2072 not shown) Planarity restraints: 2279 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 395 " -0.019 2.00e-02 2.50e+03 3.76e-02 1.42e+01 pdb=" C ASP A 395 " 0.065 2.00e-02 2.50e+03 pdb=" O ASP A 395 " -0.024 2.00e-02 2.50e+03 pdb=" N ILE A 396 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 610 " -0.049 5.00e-02 4.00e+02 7.44e-02 8.87e+00 pdb=" N PRO A 611 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO A 611 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 611 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A1193 " -0.015 2.00e-02 2.50e+03 2.92e-02 8.51e+00 pdb=" C GLY A1193 " 0.050 2.00e-02 2.50e+03 pdb=" O GLY A1193 " -0.019 2.00e-02 2.50e+03 pdb=" N PRO A1194 " -0.017 2.00e-02 2.50e+03 ... (remaining 2276 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1902 2.75 - 3.29: 12364 3.29 - 3.82: 19643 3.82 - 4.36: 22158 4.36 - 4.90: 37373 Nonbonded interactions: 93440 Sorted by model distance: nonbonded pdb=" N SER A 479 " pdb=" OE2 GLU A 482 " model vdw 2.211 3.120 nonbonded pdb=" O ILE A 958 " pdb=" N ALA A 960 " model vdw 2.219 3.120 nonbonded pdb=" O LEU A 497 " pdb=" OG SER A 500 " model vdw 2.272 3.040 nonbonded pdb=" O LEU A1668 " pdb=" OG SER A1672 " model vdw 2.281 3.040 nonbonded pdb=" ND2 ASN A 788 " pdb=" OE1 GLU A1209 " model vdw 2.293 3.120 ... (remaining 93435 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 group one per residue 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: 0.100 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: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 36.770 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 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 : 0.010 0.402 13394 Z= 0.426 Angle : 1.283 23.888 18065 Z= 0.684 Chirality : 0.072 0.657 2075 Planarity : 0.008 0.074 2279 Dihedral : 12.164 82.167 4974 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.18 % Allowed : 13.87 % Favored : 85.94 % Rotamer: Outliers : 0.74 % Allowed : 7.53 % Favored : 91.73 % Cbeta Deviations : 0.13 % 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: -5.44 (0.15), residues: 1629 helix: -3.80 (0.12), residues: 708 sheet: -4.49 (0.38), residues: 77 loop : -3.38 (0.18), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.004 TRP B 43 HIS 0.014 0.003 HIS A1231 PHE 0.032 0.004 PHE A 852 TYR 0.031 0.004 TYR A 695 ARG 0.010 0.001 ARG A 691 Details of bonding type rmsd hydrogen bonds : bond 0.17907 ( 360) hydrogen bonds : angle 7.18949 ( 1011) metal coordination : bond 0.18121 ( 7) metal coordination : angle 10.57114 ( 6) SS BOND : bond 0.00487 ( 3) SS BOND : angle 1.59290 ( 6) covalent geometry : bond 0.00943 (13384) covalent geometry : angle 1.26875 (18053) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 302 time to evaluate : 1.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 ASP cc_start: 0.7045 (p0) cc_final: 0.6457 (p0) REVERT: A 361 MET cc_start: 0.7348 (ttp) cc_final: 0.7130 (ttm) REVERT: A 387 MET cc_start: 0.6529 (ttt) cc_final: 0.5872 (ttt) REVERT: A 394 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8078 (tm) REVERT: A 543 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.7431 (tt) REVERT: A 900 GLU cc_start: 0.5549 (mt-10) cc_final: 0.4643 (tp30) REVERT: A 989 LYS cc_start: 0.4295 (tmtt) cc_final: 0.3959 (tmtt) REVERT: A 1156 MET cc_start: 0.8253 (mmt) cc_final: 0.7907 (mmt) REVERT: A 1226 SER cc_start: 0.8504 (m) cc_final: 0.7619 (t) REVERT: A 1318 TYR cc_start: 0.7636 (m-80) cc_final: 0.7233 (m-10) REVERT: A 1489 LYS cc_start: 0.7766 (mtpt) cc_final: 0.7225 (ttmm) REVERT: A 1548 ARG cc_start: 0.6797 (mmt90) cc_final: 0.6581 (mmt-90) REVERT: A 1647 ILE cc_start: 0.8353 (tt) cc_final: 0.8113 (mm) outliers start: 11 outliers final: 2 residues processed: 309 average time/residue: 0.3030 time to fit residues: 135.0951 Evaluate side-chains 202 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 198 time to evaluate : 1.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 971 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 5.9990 chunk 125 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 129 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 96 optimal weight: 10.0000 chunk 149 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A 63 ASN A 369 GLN A 384 GLN A 390 ASN A 412 ASN A 499 ASN A 522 ASN A 629 GLN ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 781 ASN A1111 ASN A1114 ASN A1206 GLN A1296 HIS A1358 HIS A1405 HIS A1665 ASN A1689 ASN ** A1711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1712 ASN ** A1714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.188303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.155353 restraints weight = 17601.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.155567 restraints weight = 28763.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.156501 restraints weight = 25113.317| |-----------------------------------------------------------------------------| r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13394 Z= 0.115 Angle : 0.675 10.201 18065 Z= 0.351 Chirality : 0.043 0.206 2075 Planarity : 0.005 0.054 2279 Dihedral : 6.563 52.233 1777 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.78 % Favored : 91.10 % Rotamer: Outliers : 3.43 % Allowed : 11.02 % Favored : 85.55 % 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: -4.37 (0.17), residues: 1629 helix: -2.67 (0.16), residues: 709 sheet: -3.51 (0.52), residues: 66 loop : -3.10 (0.19), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 116 HIS 0.004 0.001 HIS A1812 PHE 0.029 0.001 PHE A 223 TYR 0.021 0.001 TYR A 782 ARG 0.005 0.001 ARG A 392 Details of bonding type rmsd hydrogen bonds : bond 0.03393 ( 360) hydrogen bonds : angle 4.73888 ( 1011) metal coordination : bond 0.00634 ( 7) metal coordination : angle 4.03563 ( 6) SS BOND : bond 0.00263 ( 3) SS BOND : angle 0.64410 ( 6) covalent geometry : bond 0.00248 (13384) covalent geometry : angle 0.67155 (18053) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 238 time to evaluate : 1.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LYS cc_start: 0.7206 (tptp) cc_final: 0.6925 (tptp) REVERT: A 100 LEU cc_start: 0.8558 (mp) cc_final: 0.8355 (mp) REVERT: A 191 LEU cc_start: 0.8747 (mm) cc_final: 0.8368 (mm) REVERT: A 223 PHE cc_start: 0.7885 (m-80) cc_final: 0.7455 (m-80) REVERT: A 244 MET cc_start: 0.7908 (ttm) cc_final: 0.7521 (tpp) REVERT: A 261 THR cc_start: 0.6380 (p) cc_final: 0.6019 (p) REVERT: A 280 ASP cc_start: 0.7717 (p0) cc_final: 0.7421 (p0) REVERT: A 458 MET cc_start: 0.7612 (tmm) cc_final: 0.7205 (tmm) REVERT: A 585 ASP cc_start: 0.7530 (t0) cc_final: 0.7250 (t0) REVERT: A 591 MET cc_start: 0.8923 (ttp) cc_final: 0.8672 (ptm) REVERT: A 726 GLU cc_start: 0.8320 (mm-30) cc_final: 0.7872 (mm-30) REVERT: A 914 VAL cc_start: 0.8820 (t) cc_final: 0.8496 (p) REVERT: A 989 LYS cc_start: 0.5484 (tmtt) cc_final: 0.4506 (tmtt) REVERT: A 1156 MET cc_start: 0.8325 (mmt) cc_final: 0.7830 (mmt) REVERT: A 1174 MET cc_start: 0.7970 (ttp) cc_final: 0.7699 (mtt) REVERT: A 1274 MET cc_start: 0.7501 (mmt) cc_final: 0.7117 (mmp) REVERT: A 1285 MET cc_start: 0.7416 (ttm) cc_final: 0.7031 (mtp) REVERT: A 1490 GLU cc_start: 0.8327 (tp30) cc_final: 0.8059 (tp30) REVERT: A 1621 PHE cc_start: 0.8329 (t80) cc_final: 0.8121 (t80) REVERT: A 1688 THR cc_start: 0.8225 (OUTLIER) cc_final: 0.7992 (m) REVERT: A 1774 ASP cc_start: 0.8021 (t70) cc_final: 0.7790 (m-30) REVERT: A 1782 MET cc_start: 0.4689 (ppp) cc_final: 0.4268 (ptt) outliers start: 51 outliers final: 19 residues processed: 280 average time/residue: 0.2450 time to fit residues: 101.6623 Evaluate side-chains 215 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 195 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 757 LYS Chi-restraints excluded: chain A residue 763 SER Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 1087 THR Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1280 ILE Chi-restraints excluded: chain A residue 1298 THR Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1324 SER Chi-restraints excluded: chain A residue 1375 ILE Chi-restraints excluded: chain A residue 1465 VAL Chi-restraints excluded: chain A residue 1688 THR Chi-restraints excluded: chain A residue 1712 ASN Chi-restraints excluded: chain A residue 1808 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 94 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 chunk 57 optimal weight: 9.9990 chunk 58 optimal weight: 0.7980 chunk 35 optimal weight: 9.9990 chunk 154 optimal weight: 9.9990 chunk 128 optimal weight: 6.9990 chunk 146 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 chunk 34 optimal weight: 0.0000 chunk 3 optimal weight: 30.0000 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 GLN ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1358 HIS ** A1711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1712 ASN ** A1714 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 = 0.4015 r_free = 0.4015 target = 0.182094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.151138 restraints weight = 18007.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.151495 restraints weight = 34996.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.152746 restraints weight = 25811.223| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13394 Z= 0.185 Angle : 0.708 11.476 18065 Z= 0.366 Chirality : 0.046 0.186 2075 Planarity : 0.004 0.049 2279 Dihedral : 6.241 57.645 1772 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.11 % Favored : 88.83 % Rotamer: Outliers : 5.17 % Allowed : 12.43 % Favored : 82.39 % 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: -3.91 (0.18), residues: 1629 helix: -2.13 (0.17), residues: 707 sheet: -3.32 (0.47), residues: 84 loop : -2.97 (0.20), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 116 HIS 0.006 0.001 HIS A1231 PHE 0.028 0.002 PHE A 731 TYR 0.017 0.002 TYR A 695 ARG 0.005 0.001 ARG A 376 Details of bonding type rmsd hydrogen bonds : bond 0.03606 ( 360) hydrogen bonds : angle 4.70266 ( 1011) metal coordination : bond 0.00609 ( 7) metal coordination : angle 3.04720 ( 6) SS BOND : bond 0.00305 ( 3) SS BOND : angle 0.68173 ( 6) covalent geometry : bond 0.00440 (13384) covalent geometry : angle 0.70618 (18053) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 198 time to evaluate : 1.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LYS cc_start: 0.7241 (tptp) cc_final: 0.6977 (tptp) REVERT: A 146 ASN cc_start: 0.7921 (p0) cc_final: 0.7557 (p0) REVERT: A 191 LEU cc_start: 0.8794 (mm) cc_final: 0.8547 (mt) REVERT: A 227 LYS cc_start: 0.8244 (mmtm) cc_final: 0.7752 (mmtp) REVERT: A 280 ASP cc_start: 0.7724 (p0) cc_final: 0.7221 (p0) REVERT: A 543 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7045 (tt) REVERT: A 591 MET cc_start: 0.8969 (ttp) cc_final: 0.8666 (ptm) REVERT: A 651 LEU cc_start: 0.6887 (OUTLIER) cc_final: 0.6453 (pt) REVERT: A 914 VAL cc_start: 0.8915 (t) cc_final: 0.8594 (p) REVERT: A 989 LYS cc_start: 0.5189 (tmtt) cc_final: 0.4420 (tmtt) REVERT: A 1156 MET cc_start: 0.8444 (mmt) cc_final: 0.7906 (mmt) REVERT: A 1427 ILE cc_start: 0.8155 (tt) cc_final: 0.7935 (tt) REVERT: A 1490 GLU cc_start: 0.8442 (tp30) cc_final: 0.8169 (tp30) REVERT: A 1538 GLU cc_start: 0.7521 (pm20) cc_final: 0.7073 (pp20) REVERT: A 1586 GLN cc_start: 0.7191 (pp30) cc_final: 0.6965 (pp30) REVERT: A 1625 MET cc_start: 0.7937 (ttt) cc_final: 0.7547 (ttt) REVERT: A 1688 THR cc_start: 0.8409 (OUTLIER) cc_final: 0.8165 (m) REVERT: B 54 ASP cc_start: 0.7825 (m-30) cc_final: 0.7523 (m-30) outliers start: 77 outliers final: 48 residues processed: 256 average time/residue: 0.2581 time to fit residues: 100.1692 Evaluate side-chains 240 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 189 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 554 CYS Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 701 TYR Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 757 LYS Chi-restraints excluded: chain A residue 763 SER Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 980 TYR Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1087 THR Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1202 LEU Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain A residue 1280 ILE Chi-restraints excluded: chain A residue 1298 THR Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1324 SER Chi-restraints excluded: chain A residue 1375 ILE Chi-restraints excluded: chain A residue 1450 SER Chi-restraints excluded: chain A residue 1460 ILE Chi-restraints excluded: chain A residue 1465 VAL Chi-restraints excluded: chain A residue 1486 TYR Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain A residue 1545 LEU Chi-restraints excluded: chain A residue 1554 SER Chi-restraints excluded: chain A residue 1561 VAL Chi-restraints excluded: chain A residue 1688 THR Chi-restraints excluded: chain A residue 1700 THR Chi-restraints excluded: chain A residue 1808 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 74 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 129 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 0 optimal weight: 50.0000 chunk 20 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1358 HIS ** A1366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.184044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.152600 restraints weight = 17730.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.151408 restraints weight = 34572.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.152566 restraints weight = 31428.973| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13394 Z= 0.133 Angle : 0.643 11.207 18065 Z= 0.329 Chirality : 0.043 0.176 2075 Planarity : 0.004 0.044 2279 Dihedral : 5.620 27.183 1770 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.15 % Favored : 90.79 % Rotamer: Outliers : 4.84 % Allowed : 14.05 % Favored : 81.12 % 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: -3.52 (0.19), residues: 1629 helix: -1.75 (0.18), residues: 714 sheet: -3.14 (0.49), residues: 82 loop : -2.83 (0.20), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1192 HIS 0.004 0.001 HIS A1189 PHE 0.030 0.002 PHE A 731 TYR 0.012 0.001 TYR A 782 ARG 0.003 0.000 ARG A 376 Details of bonding type rmsd hydrogen bonds : bond 0.02987 ( 360) hydrogen bonds : angle 4.35965 ( 1011) metal coordination : bond 0.00529 ( 7) metal coordination : angle 3.23165 ( 6) SS BOND : bond 0.00277 ( 3) SS BOND : angle 0.50998 ( 6) covalent geometry : bond 0.00311 (13384) covalent geometry : angle 0.64048 (18053) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 200 time to evaluate : 1.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LYS cc_start: 0.6987 (tptp) cc_final: 0.6524 (tptp) REVERT: A 146 ASN cc_start: 0.7752 (p0) cc_final: 0.7479 (p0) REVERT: A 227 LYS cc_start: 0.8291 (mmtm) cc_final: 0.8050 (mmtp) REVERT: A 280 ASP cc_start: 0.7889 (p0) cc_final: 0.7437 (p0) REVERT: A 543 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7486 (mt) REVERT: A 651 LEU cc_start: 0.6665 (OUTLIER) cc_final: 0.6214 (pt) REVERT: A 863 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6752 (tp30) REVERT: A 914 VAL cc_start: 0.8835 (t) cc_final: 0.8501 (p) REVERT: A 989 LYS cc_start: 0.5185 (tmtt) cc_final: 0.4415 (tmtt) REVERT: A 1100 ASP cc_start: 0.7706 (t0) cc_final: 0.7341 (t0) REVERT: A 1156 MET cc_start: 0.8229 (mmt) cc_final: 0.7686 (mmt) REVERT: A 1490 GLU cc_start: 0.8598 (tp30) cc_final: 0.8278 (tp30) REVERT: A 1530 PHE cc_start: 0.7804 (OUTLIER) cc_final: 0.7076 (t80) REVERT: A 1538 GLU cc_start: 0.7718 (pm20) cc_final: 0.7454 (pp20) REVERT: A 1548 ARG cc_start: 0.7116 (mmt90) cc_final: 0.6113 (mtt90) REVERT: A 1774 ASP cc_start: 0.8031 (t70) cc_final: 0.7733 (m-30) REVERT: B 76 TRP cc_start: 0.7802 (m-90) cc_final: 0.7568 (m-90) outliers start: 72 outliers final: 42 residues processed: 255 average time/residue: 0.2280 time to fit residues: 87.6673 Evaluate side-chains 237 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 191 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 554 CYS Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 701 TYR Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 763 SER Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 863 GLU Chi-restraints excluded: chain A residue 980 TYR Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1087 THR Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1202 LEU Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain A residue 1242 VAL Chi-restraints excluded: chain A residue 1280 ILE Chi-restraints excluded: chain A residue 1298 THR Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1324 SER Chi-restraints excluded: chain A residue 1375 ILE Chi-restraints excluded: chain A residue 1421 THR Chi-restraints excluded: chain A residue 1450 SER Chi-restraints excluded: chain A residue 1460 ILE Chi-restraints excluded: chain A residue 1465 VAL Chi-restraints excluded: chain A residue 1486 TYR Chi-restraints excluded: chain A residue 1530 PHE Chi-restraints excluded: chain A residue 1545 LEU Chi-restraints excluded: chain A residue 1554 SER Chi-restraints excluded: chain A residue 1561 VAL Chi-restraints excluded: chain A residue 1808 CYS Chi-restraints excluded: chain B residue 74 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 96 optimal weight: 0.0770 chunk 36 optimal weight: 5.9990 chunk 154 optimal weight: 10.0000 chunk 85 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 76 optimal weight: 0.0040 chunk 139 optimal weight: 20.0000 chunk 20 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 45 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 overall best weight: 0.9752 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1358 HIS ** A1366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1714 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.184770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.151465 restraints weight = 17739.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.151010 restraints weight = 32195.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.152061 restraints weight = 29378.267| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13394 Z= 0.105 Angle : 0.606 8.947 18065 Z= 0.309 Chirality : 0.042 0.171 2075 Planarity : 0.004 0.041 2279 Dihedral : 5.153 26.845 1770 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.78 % Favored : 91.16 % Rotamer: Outliers : 4.44 % Allowed : 16.13 % Favored : 79.44 % 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: -3.08 (0.20), residues: 1629 helix: -1.32 (0.19), residues: 715 sheet: -2.59 (0.57), residues: 68 loop : -2.72 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1192 HIS 0.005 0.001 HIS A1358 PHE 0.029 0.001 PHE A 43 TYR 0.013 0.001 TYR A 184 ARG 0.004 0.000 ARG A 437 Details of bonding type rmsd hydrogen bonds : bond 0.02594 ( 360) hydrogen bonds : angle 4.07768 ( 1011) metal coordination : bond 0.00403 ( 7) metal coordination : angle 3.05492 ( 6) SS BOND : bond 0.00310 ( 3) SS BOND : angle 0.44027 ( 6) covalent geometry : bond 0.00236 (13384) covalent geometry : angle 0.60403 (18053) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 220 time to evaluate : 1.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LYS cc_start: 0.6930 (tptp) cc_final: 0.6500 (tptp) REVERT: A 146 ASN cc_start: 0.7594 (p0) cc_final: 0.7380 (p0) REVERT: A 222 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8599 (mt) REVERT: A 227 LYS cc_start: 0.8347 (mmtm) cc_final: 0.8000 (mmtp) REVERT: A 353 LEU cc_start: 0.7088 (OUTLIER) cc_final: 0.6747 (pp) REVERT: A 543 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7675 (mt) REVERT: A 651 LEU cc_start: 0.6682 (OUTLIER) cc_final: 0.6172 (pt) REVERT: A 914 VAL cc_start: 0.8740 (t) cc_final: 0.8407 (p) REVERT: A 989 LYS cc_start: 0.5509 (tmtt) cc_final: 0.4756 (tmtt) REVERT: A 1100 ASP cc_start: 0.7633 (t0) cc_final: 0.7044 (t0) REVERT: A 1156 MET cc_start: 0.8158 (mmt) cc_final: 0.7713 (mmt) REVERT: A 1359 GLU cc_start: 0.7941 (tm-30) cc_final: 0.7655 (tm-30) REVERT: A 1490 GLU cc_start: 0.8654 (tp30) cc_final: 0.8290 (tp30) REVERT: A 1530 PHE cc_start: 0.7781 (OUTLIER) cc_final: 0.7083 (t80) REVERT: A 1774 ASP cc_start: 0.8035 (t70) cc_final: 0.7758 (m-30) REVERT: B 34 TYR cc_start: 0.6710 (m-80) cc_final: 0.6419 (m-10) outliers start: 66 outliers final: 42 residues processed: 270 average time/residue: 0.2158 time to fit residues: 88.6216 Evaluate side-chains 243 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 196 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 554 CYS Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 701 TYR Chi-restraints excluded: chain A residue 703 CYS Chi-restraints excluded: chain A residue 763 SER Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 980 TYR Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1087 THR Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1202 LEU Chi-restraints excluded: chain A residue 1242 VAL Chi-restraints excluded: chain A residue 1280 ILE Chi-restraints excluded: chain A residue 1288 LEU Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1324 SER Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1375 ILE Chi-restraints excluded: chain A residue 1450 SER Chi-restraints excluded: chain A residue 1455 THR Chi-restraints excluded: chain A residue 1460 ILE Chi-restraints excluded: chain A residue 1465 VAL Chi-restraints excluded: chain A residue 1486 TYR Chi-restraints excluded: chain A residue 1530 PHE Chi-restraints excluded: chain A residue 1545 LEU Chi-restraints excluded: chain A residue 1554 SER Chi-restraints excluded: chain A residue 1578 VAL Chi-restraints excluded: chain B residue 74 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 120 optimal weight: 8.9990 chunk 15 optimal weight: 0.5980 chunk 109 optimal weight: 0.0970 chunk 84 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 64 optimal weight: 0.3980 chunk 20 optimal weight: 0.3980 chunk 69 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1358 HIS ** A1366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1714 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.188086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.154187 restraints weight = 17871.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.153389 restraints weight = 31344.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.154832 restraints weight = 31001.564| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13394 Z= 0.098 Angle : 0.597 8.738 18065 Z= 0.300 Chirality : 0.041 0.194 2075 Planarity : 0.003 0.040 2279 Dihedral : 4.794 25.416 1770 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.55 % Favored : 92.39 % Rotamer: Outliers : 3.76 % Allowed : 18.08 % Favored : 78.16 % 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: -2.79 (0.20), residues: 1629 helix: -1.00 (0.19), residues: 717 sheet: -2.43 (0.57), residues: 70 loop : -2.64 (0.20), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 155 HIS 0.006 0.001 HIS A1358 PHE 0.031 0.001 PHE A 731 TYR 0.011 0.001 TYR A 214 ARG 0.008 0.000 ARG A 392 Details of bonding type rmsd hydrogen bonds : bond 0.02323 ( 360) hydrogen bonds : angle 3.87421 ( 1011) metal coordination : bond 0.00357 ( 7) metal coordination : angle 3.11739 ( 6) SS BOND : bond 0.00270 ( 3) SS BOND : angle 0.39188 ( 6) covalent geometry : bond 0.00211 (13384) covalent geometry : angle 0.59442 (18053) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 216 time to evaluate : 1.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LYS cc_start: 0.6811 (tptp) cc_final: 0.6543 (tptp) REVERT: A 227 LYS cc_start: 0.8335 (mmtm) cc_final: 0.7889 (mmtp) REVERT: A 296 TYR cc_start: 0.8372 (t80) cc_final: 0.8164 (t80) REVERT: A 353 LEU cc_start: 0.7052 (OUTLIER) cc_final: 0.6751 (pp) REVERT: A 624 PRO cc_start: 0.8525 (Cg_endo) cc_final: 0.8287 (Cg_exo) REVERT: A 651 LEU cc_start: 0.6403 (OUTLIER) cc_final: 0.5857 (pt) REVERT: A 798 LEU cc_start: 0.6831 (OUTLIER) cc_final: 0.6231 (tt) REVERT: A 909 LYS cc_start: 0.8117 (ttmt) cc_final: 0.7892 (ttmt) REVERT: A 914 VAL cc_start: 0.8725 (t) cc_final: 0.8433 (p) REVERT: A 989 LYS cc_start: 0.5509 (tmtt) cc_final: 0.4802 (tmtt) REVERT: A 1100 ASP cc_start: 0.7274 (t0) cc_final: 0.6954 (t0) REVERT: A 1156 MET cc_start: 0.8079 (mmt) cc_final: 0.7763 (mmt) REVERT: A 1274 MET cc_start: 0.6524 (mmt) cc_final: 0.6272 (mmp) REVERT: A 1359 GLU cc_start: 0.8011 (tm-30) cc_final: 0.7706 (tm-30) REVERT: A 1461 GLU cc_start: 0.7877 (pm20) cc_final: 0.7203 (pm20) REVERT: A 1467 ASP cc_start: 0.7343 (p0) cc_final: 0.7095 (p0) REVERT: A 1490 GLU cc_start: 0.8717 (tp30) cc_final: 0.8373 (tp30) REVERT: A 1502 PHE cc_start: 0.8307 (t80) cc_final: 0.8088 (t80) REVERT: A 1530 PHE cc_start: 0.7828 (OUTLIER) cc_final: 0.7103 (t80) REVERT: B 34 TYR cc_start: 0.6733 (m-80) cc_final: 0.6490 (m-10) outliers start: 56 outliers final: 39 residues processed: 254 average time/residue: 0.2327 time to fit residues: 89.1264 Evaluate side-chains 243 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 200 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 554 CYS Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 701 TYR Chi-restraints excluded: chain A residue 703 CYS Chi-restraints excluded: chain A residue 763 SER Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1087 THR Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1176 MET Chi-restraints excluded: chain A residue 1242 VAL Chi-restraints excluded: chain A residue 1288 LEU Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1375 ILE Chi-restraints excluded: chain A residue 1450 SER Chi-restraints excluded: chain A residue 1455 THR Chi-restraints excluded: chain A residue 1460 ILE Chi-restraints excluded: chain A residue 1465 VAL Chi-restraints excluded: chain A residue 1486 TYR Chi-restraints excluded: chain A residue 1530 PHE Chi-restraints excluded: chain A residue 1545 LEU Chi-restraints excluded: chain A residue 1578 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 158 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 0 optimal weight: 50.0000 chunk 153 optimal weight: 2.9990 chunk 154 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 164 optimal weight: 20.0000 chunk 141 optimal weight: 4.9990 chunk 156 optimal weight: 6.9990 chunk 3 optimal weight: 0.4980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1358 HIS ** A1366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1726 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.185710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.154684 restraints weight = 17892.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.154345 restraints weight = 34210.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.155332 restraints weight = 30936.471| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13394 Z= 0.123 Angle : 0.608 8.426 18065 Z= 0.309 Chirality : 0.042 0.164 2075 Planarity : 0.003 0.040 2279 Dihedral : 4.831 26.512 1770 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.53 % Favored : 91.41 % Rotamer: Outliers : 3.97 % Allowed : 18.35 % Favored : 77.69 % 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: -2.57 (0.20), residues: 1629 helix: -0.78 (0.20), residues: 706 sheet: -2.52 (0.53), residues: 78 loop : -2.49 (0.21), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 116 HIS 0.004 0.001 HIS A1358 PHE 0.031 0.001 PHE A 731 TYR 0.015 0.001 TYR A 184 ARG 0.007 0.000 ARG A 392 Details of bonding type rmsd hydrogen bonds : bond 0.02574 ( 360) hydrogen bonds : angle 3.92988 ( 1011) metal coordination : bond 0.00460 ( 7) metal coordination : angle 2.71876 ( 6) SS BOND : bond 0.00289 ( 3) SS BOND : angle 0.48316 ( 6) covalent geometry : bond 0.00288 (13384) covalent geometry : angle 0.60616 (18053) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 201 time to evaluate : 2.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LYS cc_start: 0.6855 (tptp) cc_final: 0.6588 (tptp) REVERT: A 227 LYS cc_start: 0.8325 (mmtm) cc_final: 0.7841 (mmtp) REVERT: A 353 LEU cc_start: 0.7155 (OUTLIER) cc_final: 0.6875 (pp) REVERT: A 543 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7518 (mt) REVERT: A 651 LEU cc_start: 0.6754 (OUTLIER) cc_final: 0.6244 (pt) REVERT: A 914 VAL cc_start: 0.8749 (t) cc_final: 0.8446 (p) REVERT: A 989 LYS cc_start: 0.5277 (tmtt) cc_final: 0.4609 (tmtt) REVERT: A 1037 PHE cc_start: 0.8326 (m-10) cc_final: 0.7411 (m-10) REVERT: A 1100 ASP cc_start: 0.7173 (t0) cc_final: 0.6922 (t0) REVERT: A 1156 MET cc_start: 0.8154 (mmt) cc_final: 0.7817 (mmt) REVERT: A 1274 MET cc_start: 0.6529 (mmt) cc_final: 0.6308 (mmp) REVERT: A 1359 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7746 (tm-30) REVERT: A 1461 GLU cc_start: 0.7735 (pm20) cc_final: 0.7320 (pm20) REVERT: A 1490 GLU cc_start: 0.8673 (tp30) cc_final: 0.8340 (tp30) REVERT: A 1538 GLU cc_start: 0.7528 (pm20) cc_final: 0.7046 (pp20) REVERT: B 34 TYR cc_start: 0.6827 (m-80) cc_final: 0.6562 (m-10) outliers start: 59 outliers final: 41 residues processed: 246 average time/residue: 0.2356 time to fit residues: 87.6891 Evaluate side-chains 239 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 195 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 554 CYS Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 701 TYR Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 980 TYR Chi-restraints excluded: chain A residue 1087 THR Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1176 MET Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain A residue 1242 VAL Chi-restraints excluded: chain A residue 1270 PHE Chi-restraints excluded: chain A residue 1288 LEU Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1324 SER Chi-restraints excluded: chain A residue 1375 ILE Chi-restraints excluded: chain A residue 1450 SER Chi-restraints excluded: chain A residue 1455 THR Chi-restraints excluded: chain A residue 1460 ILE Chi-restraints excluded: chain A residue 1465 VAL Chi-restraints excluded: chain A residue 1486 TYR Chi-restraints excluded: chain A residue 1545 LEU Chi-restraints excluded: chain A residue 1578 VAL Chi-restraints excluded: chain A residue 1581 LEU Chi-restraints excluded: chain B residue 47 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 130 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 86 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 75 optimal weight: 7.9990 chunk 109 optimal weight: 1.9990 chunk 92 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1358 HIS ** A1366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1714 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.186668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.155948 restraints weight = 17824.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.155825 restraints weight = 32605.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.157142 restraints weight = 26548.412| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13394 Z= 0.112 Angle : 0.605 8.226 18065 Z= 0.305 Chirality : 0.042 0.188 2075 Planarity : 0.003 0.041 2279 Dihedral : 4.725 25.847 1770 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.10 % Favored : 91.84 % Rotamer: Outliers : 3.97 % Allowed : 18.88 % Favored : 77.15 % 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: -2.51 (0.20), residues: 1629 helix: -0.75 (0.20), residues: 717 sheet: -2.47 (0.53), residues: 78 loop : -2.46 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1192 HIS 0.005 0.001 HIS A1358 PHE 0.032 0.001 PHE A 731 TYR 0.013 0.001 TYR A 782 ARG 0.006 0.000 ARG A 392 Details of bonding type rmsd hydrogen bonds : bond 0.02489 ( 360) hydrogen bonds : angle 3.89522 ( 1011) metal coordination : bond 0.00418 ( 7) metal coordination : angle 2.95700 ( 6) SS BOND : bond 0.00338 ( 3) SS BOND : angle 0.38014 ( 6) covalent geometry : bond 0.00260 (13384) covalent geometry : angle 0.60304 (18053) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 200 time to evaluate : 1.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LYS cc_start: 0.6914 (tptp) cc_final: 0.6576 (tptp) REVERT: A 227 LYS cc_start: 0.8257 (mmtm) cc_final: 0.7703 (mmtp) REVERT: A 353 LEU cc_start: 0.7153 (OUTLIER) cc_final: 0.6813 (pp) REVERT: A 413 TRP cc_start: 0.8050 (t60) cc_final: 0.7849 (t60) REVERT: A 543 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7554 (mt) REVERT: A 600 ASP cc_start: 0.7465 (m-30) cc_final: 0.6947 (p0) REVERT: A 651 LEU cc_start: 0.6583 (OUTLIER) cc_final: 0.6079 (pt) REVERT: A 714 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8200 (tt) REVERT: A 726 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7331 (tt0) REVERT: A 798 LEU cc_start: 0.6878 (OUTLIER) cc_final: 0.6346 (tt) REVERT: A 914 VAL cc_start: 0.8691 (t) cc_final: 0.8371 (p) REVERT: A 989 LYS cc_start: 0.5632 (tmtt) cc_final: 0.4842 (tmtt) REVERT: A 1037 PHE cc_start: 0.8289 (m-10) cc_final: 0.7377 (m-10) REVERT: A 1100 ASP cc_start: 0.7109 (t0) cc_final: 0.6830 (t0) REVERT: A 1156 MET cc_start: 0.8085 (mmt) cc_final: 0.7794 (mmt) REVERT: A 1359 GLU cc_start: 0.8136 (tm-30) cc_final: 0.7721 (tm-30) REVERT: A 1461 GLU cc_start: 0.7612 (pm20) cc_final: 0.7309 (pm20) REVERT: A 1490 GLU cc_start: 0.8683 (tp30) cc_final: 0.8346 (tp30) REVERT: A 1538 GLU cc_start: 0.7560 (pm20) cc_final: 0.7228 (pp20) REVERT: A 1715 PHE cc_start: 0.6480 (t80) cc_final: 0.6103 (t80) REVERT: B 34 TYR cc_start: 0.6767 (m-80) cc_final: 0.6505 (m-10) outliers start: 59 outliers final: 45 residues processed: 243 average time/residue: 0.2227 time to fit residues: 82.3556 Evaluate side-chains 247 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 197 time to evaluate : 1.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 554 CYS Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 701 TYR Chi-restraints excluded: chain A residue 703 CYS Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 980 TYR Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1087 THR Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1176 MET Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain A residue 1242 VAL Chi-restraints excluded: chain A residue 1288 LEU Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1324 SER Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1375 ILE Chi-restraints excluded: chain A residue 1450 SER Chi-restraints excluded: chain A residue 1455 THR Chi-restraints excluded: chain A residue 1460 ILE Chi-restraints excluded: chain A residue 1465 VAL Chi-restraints excluded: chain A residue 1486 TYR Chi-restraints excluded: chain A residue 1545 LEU Chi-restraints excluded: chain A residue 1561 VAL Chi-restraints excluded: chain A residue 1578 VAL Chi-restraints excluded: chain A residue 1625 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 36 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 96 optimal weight: 20.0000 chunk 45 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 161 optimal weight: 0.6980 chunk 144 optimal weight: 0.0980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1128 ASN A1358 HIS ** A1366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1714 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.182010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.156048 restraints weight = 17638.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.154863 restraints weight = 35456.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.156099 restraints weight = 31987.343| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13394 Z= 0.138 Angle : 0.632 8.118 18065 Z= 0.320 Chirality : 0.043 0.181 2075 Planarity : 0.004 0.040 2279 Dihedral : 4.840 26.955 1770 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.15 % Favored : 90.79 % Rotamer: Outliers : 4.23 % Allowed : 18.88 % Favored : 76.88 % 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 (0.21), residues: 1629 helix: -0.68 (0.20), residues: 713 sheet: -2.13 (0.55), residues: 80 loop : -2.49 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1192 HIS 0.004 0.001 HIS A1358 PHE 0.032 0.002 PHE A 731 TYR 0.019 0.001 TYR A 782 ARG 0.005 0.000 ARG A 392 Details of bonding type rmsd hydrogen bonds : bond 0.02746 ( 360) hydrogen bonds : angle 3.99139 ( 1011) metal coordination : bond 0.00519 ( 7) metal coordination : angle 2.74056 ( 6) SS BOND : bond 0.00318 ( 3) SS BOND : angle 0.47457 ( 6) covalent geometry : bond 0.00330 (13384) covalent geometry : angle 0.63063 (18053) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 195 time to evaluate : 1.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LYS cc_start: 0.7003 (tptp) cc_final: 0.6731 (tptp) REVERT: A 96 LYS cc_start: 0.7563 (mmtt) cc_final: 0.6889 (ttmm) REVERT: A 227 LYS cc_start: 0.8113 (mmtm) cc_final: 0.7546 (mmtp) REVERT: A 353 LEU cc_start: 0.7346 (OUTLIER) cc_final: 0.6994 (pp) REVERT: A 413 TRP cc_start: 0.8046 (t60) cc_final: 0.7838 (t60) REVERT: A 543 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7733 (mt) REVERT: A 600 ASP cc_start: 0.6933 (m-30) cc_final: 0.6672 (p0) REVERT: A 651 LEU cc_start: 0.6916 (OUTLIER) cc_final: 0.6454 (pt) REVERT: A 714 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8364 (tt) REVERT: A 726 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7303 (tt0) REVERT: A 896 THR cc_start: 0.8583 (OUTLIER) cc_final: 0.8141 (t) REVERT: A 914 VAL cc_start: 0.8784 (t) cc_final: 0.8417 (p) REVERT: A 989 LYS cc_start: 0.5265 (tmtt) cc_final: 0.4531 (tmtt) REVERT: A 1037 PHE cc_start: 0.8373 (m-10) cc_final: 0.7407 (m-10) REVERT: A 1100 ASP cc_start: 0.6993 (t0) cc_final: 0.6788 (t0) REVERT: A 1156 MET cc_start: 0.8106 (mmt) cc_final: 0.7858 (mmt) REVERT: A 1274 MET cc_start: 0.6992 (mmp) cc_final: 0.6551 (mmt) REVERT: A 1359 GLU cc_start: 0.8026 (tm-30) cc_final: 0.7677 (tm-30) REVERT: A 1490 GLU cc_start: 0.8437 (tp30) cc_final: 0.8136 (tp30) REVERT: A 1715 PHE cc_start: 0.6525 (t80) cc_final: 0.6198 (t80) REVERT: B 34 TYR cc_start: 0.6856 (m-80) cc_final: 0.6581 (m-10) outliers start: 63 outliers final: 49 residues processed: 243 average time/residue: 0.2365 time to fit residues: 87.6035 Evaluate side-chains 244 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 190 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 554 CYS Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 701 TYR Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 763 SER Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 980 TYR Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1087 THR Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1176 MET Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain A residue 1242 VAL Chi-restraints excluded: chain A residue 1288 LEU Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1324 SER Chi-restraints excluded: chain A residue 1358 HIS Chi-restraints excluded: chain A residue 1375 ILE Chi-restraints excluded: chain A residue 1450 SER Chi-restraints excluded: chain A residue 1455 THR Chi-restraints excluded: chain A residue 1460 ILE Chi-restraints excluded: chain A residue 1465 VAL Chi-restraints excluded: chain A residue 1486 TYR Chi-restraints excluded: chain A residue 1545 LEU Chi-restraints excluded: chain A residue 1561 VAL Chi-restraints excluded: chain A residue 1578 VAL Chi-restraints excluded: chain A residue 1581 LEU Chi-restraints excluded: chain A residue 1625 MET Chi-restraints excluded: chain B residue 47 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 40 optimal weight: 10.0000 chunk 156 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 112 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 chunk 121 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 139 optimal weight: 9.9990 chunk 29 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1358 HIS ** A1366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1714 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.187560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.156377 restraints weight = 17651.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.154795 restraints weight = 33033.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.156342 restraints weight = 28589.324| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.3952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13394 Z= 0.104 Angle : 0.612 8.534 18065 Z= 0.307 Chirality : 0.042 0.194 2075 Planarity : 0.003 0.042 2279 Dihedral : 4.639 25.591 1770 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.67 % Favored : 92.27 % Rotamer: Outliers : 3.70 % Allowed : 19.49 % Favored : 76.81 % 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: -2.33 (0.21), residues: 1629 helix: -0.62 (0.20), residues: 718 sheet: -2.18 (0.59), residues: 70 loop : -2.37 (0.21), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1192 HIS 0.014 0.001 HIS A1358 PHE 0.033 0.001 PHE A 731 TYR 0.015 0.001 TYR A 782 ARG 0.006 0.000 ARG A 392 Details of bonding type rmsd hydrogen bonds : bond 0.02383 ( 360) hydrogen bonds : angle 3.83072 ( 1011) metal coordination : bond 0.00370 ( 7) metal coordination : angle 2.89341 ( 6) SS BOND : bond 0.00259 ( 3) SS BOND : angle 0.35823 ( 6) covalent geometry : bond 0.00238 (13384) covalent geometry : angle 0.61027 (18053) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 204 time to evaluate : 1.545 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 LYS cc_start: 0.7942 (mmtm) cc_final: 0.7470 (mmtm) REVERT: A 92 LYS cc_start: 0.6928 (tptp) cc_final: 0.6546 (tptp) REVERT: A 96 LYS cc_start: 0.7228 (mmtt) cc_final: 0.6699 (ttmm) REVERT: A 146 ASN cc_start: 0.8419 (p0) cc_final: 0.8144 (p0) REVERT: A 148 ASN cc_start: 0.7643 (t0) cc_final: 0.7278 (m-40) REVERT: A 227 LYS cc_start: 0.8130 (mmtm) cc_final: 0.7555 (mmtp) REVERT: A 353 LEU cc_start: 0.7149 (OUTLIER) cc_final: 0.6852 (pp) REVERT: A 413 TRP cc_start: 0.8095 (t60) cc_final: 0.7884 (t60) REVERT: A 543 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7719 (mt) REVERT: A 600 ASP cc_start: 0.7333 (m-30) cc_final: 0.6944 (p0) REVERT: A 651 LEU cc_start: 0.6600 (OUTLIER) cc_final: 0.6115 (pt) REVERT: A 714 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8183 (tt) REVERT: A 726 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7414 (tt0) REVERT: A 896 THR cc_start: 0.8537 (OUTLIER) cc_final: 0.8093 (t) REVERT: A 909 LYS cc_start: 0.8298 (ttmt) cc_final: 0.8072 (ttmt) REVERT: A 914 VAL cc_start: 0.8774 (t) cc_final: 0.8475 (p) REVERT: A 989 LYS cc_start: 0.5588 (tmtt) cc_final: 0.4812 (tmtt) REVERT: A 1037 PHE cc_start: 0.8243 (m-10) cc_final: 0.7980 (m-10) REVERT: A 1100 ASP cc_start: 0.7059 (t0) cc_final: 0.6821 (t0) REVERT: A 1156 MET cc_start: 0.8090 (mmt) cc_final: 0.7806 (mmt) REVERT: A 1274 MET cc_start: 0.7377 (mmp) cc_final: 0.6730 (mmt) REVERT: A 1359 GLU cc_start: 0.8232 (tm-30) cc_final: 0.7783 (tm-30) REVERT: A 1490 GLU cc_start: 0.8546 (tp30) cc_final: 0.8251 (tp30) REVERT: A 1548 ARG cc_start: 0.7589 (mmt-90) cc_final: 0.7216 (mmt-90) REVERT: A 1715 PHE cc_start: 0.6385 (t80) cc_final: 0.5974 (t80) REVERT: B 34 TYR cc_start: 0.6786 (m-80) cc_final: 0.6581 (m-10) outliers start: 55 outliers final: 45 residues processed: 244 average time/residue: 0.2316 time to fit residues: 85.8416 Evaluate side-chains 249 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 199 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 554 CYS Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 701 TYR Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 763 SER Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 980 TYR Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1087 THR Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1176 MET Chi-restraints excluded: chain A residue 1202 LEU Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain A residue 1242 VAL Chi-restraints excluded: chain A residue 1288 LEU Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1324 SER Chi-restraints excluded: chain A residue 1450 SER Chi-restraints excluded: chain A residue 1455 THR Chi-restraints excluded: chain A residue 1460 ILE Chi-restraints excluded: chain A residue 1465 VAL Chi-restraints excluded: chain A residue 1486 TYR Chi-restraints excluded: chain A residue 1545 LEU Chi-restraints excluded: chain A residue 1561 VAL Chi-restraints excluded: chain A residue 1578 VAL Chi-restraints excluded: chain A residue 1625 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 152 optimal weight: 8.9990 chunk 40 optimal weight: 6.9990 chunk 80 optimal weight: 0.9980 chunk 155 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 chunk 100 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 chunk 106 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 overall best weight: 4.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 704 HIS A1358 HIS ** A1551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.176233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.152986 restraints weight = 17860.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.152003 restraints weight = 38449.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.152690 restraints weight = 32064.340| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 13394 Z= 0.247 Angle : 0.763 7.738 18065 Z= 0.389 Chirality : 0.049 0.239 2075 Planarity : 0.004 0.042 2279 Dihedral : 5.442 29.652 1770 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.87 % Favored : 89.07 % Rotamer: Outliers : 3.97 % Allowed : 19.62 % Favored : 76.41 % 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: -2.57 (0.20), residues: 1629 helix: -0.85 (0.19), residues: 708 sheet: -2.48 (0.51), residues: 92 loop : -2.42 (0.21), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A1192 HIS 0.008 0.002 HIS A 472 PHE 0.035 0.003 PHE A 731 TYR 0.024 0.002 TYR A 695 ARG 0.005 0.001 ARG A 392 Details of bonding type rmsd hydrogen bonds : bond 0.03692 ( 360) hydrogen bonds : angle 4.53796 ( 1011) metal coordination : bond 0.00918 ( 7) metal coordination : angle 2.57452 ( 6) SS BOND : bond 0.00378 ( 3) SS BOND : angle 0.70506 ( 6) covalent geometry : bond 0.00597 (13384) covalent geometry : angle 0.76136 (18053) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3816.32 seconds wall clock time: 67 minutes 17.98 seconds (4037.98 seconds total)