Starting phenix.real_space_refine on Thu Jul 31 17:23:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6eoj_3908/07_2025/6eoj_3908.cif Found real_map, /net/cci-nas-00/data/ceres_data/6eoj_3908/07_2025/6eoj_3908.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6eoj_3908/07_2025/6eoj_3908.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6eoj_3908/07_2025/6eoj_3908.map" model { file = "/net/cci-nas-00/data/ceres_data/6eoj_3908/07_2025/6eoj_3908.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6eoj_3908/07_2025/6eoj_3908.cif" } resolution = 3.55 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.032 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 66 5.16 5 C 8747 2.51 5 N 2319 2.21 5 O 2554 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13688 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 9801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1233, 9801 Classifications: {'peptide': 1233} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 52, 'TRANS': 1180} Chain breaks: 8 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 788 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 82} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 3072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3072 Classifications: {'peptide': 383} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 19, 'TRANS': 363} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "D" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 25 Classifications: {'peptide': 5} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'UNK:plan-1': 5} Unresolved non-hydrogen planarities: 5 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 10352 SG CYS B 67 58.725 56.406 18.932 1.00100.70 S ATOM 10424 SG CYS B 75 55.446 56.386 18.299 1.00 99.83 S ATOM 10473 SG CYS B 81 57.496 53.730 16.587 1.00104.94 S ATOM 10088 SG CYS B 34 57.372 31.929 22.523 1.00162.41 S ATOM 10186 SG CYS B 46 54.315 29.542 20.976 1.00180.34 S ATOM 10229 SG CYS B 52 54.559 30.589 24.714 1.00164.23 S Time building chain proxies: 7.33, per 1000 atoms: 0.54 Number of scatterers: 13688 At special positions: 0 Unit cell: (96.6, 109.2, 127.4, 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 66 16.00 O 2554 8.00 N 2319 7.00 C 8747 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.82 Conformation dependent library (CDL) restraints added in 1.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 85 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 75 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 67 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 81 " pdb=" ZN B 302 " pdb="ZN ZN B 302 " - pdb=" NE2 HIS B 56 " pdb="ZN ZN B 302 " - pdb=" SG CYS B 46 " pdb="ZN ZN B 302 " - pdb=" SG CYS B 34 " pdb="ZN ZN B 302 " - pdb=" SG CYS B 52 " Number of angles added : 6 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3264 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 29 sheets defined 8.2% alpha, 33.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.82 Creating SS restraints... Processing helix chain 'A' and resid 105 through 111 Processing helix chain 'A' and resid 203 through 207 Processing helix chain 'A' and resid 697 through 702 removed outlier: 4.133A pdb=" N GLU A 701 " --> pdb=" O GLU A 697 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N MET A 702 " --> pdb=" O ILE A 698 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 697 through 702' Processing helix chain 'A' and resid 841 through 846 removed outlier: 4.301A pdb=" N SER A 846 " --> pdb=" O LYS A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 1203 through 1207 Processing helix chain 'A' and resid 1262 through 1280 removed outlier: 3.579A pdb=" N ARG A1267 " --> pdb=" O GLU A1263 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A1269 " --> pdb=" O LYS A1265 " (cutoff:3.500A) Processing helix chain 'A' and resid 1287 through 1292 Processing helix chain 'A' and resid 1310 through 1319 removed outlier: 4.008A pdb=" N ARG A1315 " --> pdb=" O ASN A1311 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N PHE A1316 " --> pdb=" O VAL A1312 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N CYS A1317 " --> pdb=" O ILE A1313 " (cutoff:3.500A) Processing helix chain 'A' and resid 1320 through 1327 Processing helix chain 'A' and resid 1335 through 1348 removed outlier: 3.830A pdb=" N ASP A1342 " --> pdb=" O GLU A1338 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASN A1345 " --> pdb=" O ARG A1341 " (cutoff:3.500A) Processing helix chain 'A' and resid 1349 through 1355 removed outlier: 3.708A pdb=" N SER A1352 " --> pdb=" O SER A1349 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 22 removed outlier: 3.569A pdb=" N GLN B 21 " --> pdb=" O PRO B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 52 removed outlier: 4.268A pdb=" N LEU B 51 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N CYS B 52 " --> pdb=" O GLY B 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 48 through 52' Processing helix chain 'B' and resid 67 through 72 Processing helix chain 'D' and resid 35 through 46 Processing helix chain 'D' and resid 58 through 65 removed outlier: 3.534A pdb=" N ILE D 63 " --> pdb=" O SER D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 71 Processing helix chain 'D' and resid 75 through 79 Processing sheet with id=A, first strand: chain 'A' and resid 14 through 18 removed outlier: 6.315A pdb=" N ARG A 41 " --> pdb=" O LEU A 50 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N LEU A 50 " --> pdb=" O ARG A 41 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N THR A 43 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU A 48 " --> pdb=" O THR A 43 " (cutoff:3.500A) Processing sheet with id=B, first strand: chain 'A' and resid 60 through 66 removed outlier: 6.578A pdb=" N CYS A 79 " --> pdb=" O THR A 61 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ILE A 63 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU A 77 " --> pdb=" O ILE A 63 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N LEU A 65 " --> pdb=" O CYS A 75 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N CYS A 75 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LYS A 84 " --> pdb=" O THR A 80 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER A 101 " --> pdb=" O ILE A 87 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LYS A 89 " --> pdb=" O THR A 99 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N THR A 99 " --> pdb=" O LYS A 89 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ASN A 91 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ILE A 97 " --> pdb=" O ASN A 91 " (cutoff:3.500A) Processing sheet with id=C, first strand: chain 'A' and resid 122 through 126 removed outlier: 3.792A pdb=" N ASP A 126 " --> pdb=" O CYS A 131 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N CYS A 131 " --> pdb=" O ASP A 126 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N SER A 130 " --> pdb=" O PHE A 145 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ILE A 139 " --> pdb=" O ASN A 136 " (cutoff:3.500A) Processing sheet with id=D, first strand: chain 'A' and resid 213 through 219 removed outlier: 5.451A pdb=" N ILE A 213 " --> pdb=" O GLN A 232 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N GLN A 232 " --> pdb=" O ILE A 213 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN A 217 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N THR A 226 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N THR A 248 " --> pdb=" O LYS A 275 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N LYS A 275 " --> pdb=" O THR A 248 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N TYR A 250 " --> pdb=" O PHE A 273 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N PHE A 273 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ILE A 252 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU A 267 " --> pdb=" O ASN A 256 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN A 258 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing sheet with id=E, first strand: chain 'A' and resid 283 through 287 removed outlier: 4.482A pdb=" N GLU A 298 " --> pdb=" O GLY A 295 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N SER A 310 " --> pdb=" O PHE A 301 " (cutoff:3.500A) removed outlier: 12.811A pdb=" N THR A 311 " --> pdb=" O SER A 331 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N SER A 331 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ASN A 329 " --> pdb=" O LEU A 313 " (cutoff:3.500A) removed outlier: 12.703A pdb=" N ASN A 315 " --> pdb=" O ILE A 327 " (cutoff:3.500A) removed outlier: 15.173A pdb=" N ILE A 327 " --> pdb=" O ASN A 315 " (cutoff:3.500A) Processing sheet with id=F, first strand: chain 'A' and resid 343 through 347 removed outlier: 4.403A pdb=" N THR A 343 " --> pdb=" O MET A 366 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLU A 361 " --> pdb=" O MET A 377 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N MET A 377 " --> pdb=" O GLU A 361 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LEU A 363 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN A 371 " --> pdb=" O ASP A 367 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ILE A 372 " --> pdb=" O LYS A 391 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LYS A 391 " --> pdb=" O ILE A 372 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N TYR A 374 " --> pdb=" O ILE A 389 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ILE A 389 " --> pdb=" O TYR A 374 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLN A 376 " --> pdb=" O PHE A 387 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N PHE A 387 " --> pdb=" O GLN A 376 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU A 378 " --> pdb=" O ILE A 385 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE A 385 " --> pdb=" O GLU A 378 " (cutoff:3.500A) Processing sheet with id=G, first strand: chain 'A' and resid 407 through 410 removed outlier: 6.741A pdb=" N ARG A 435 " --> pdb=" O LEU A 501 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N LEU A 501 " --> pdb=" O ARG A 435 " (cutoff:3.500A) Processing sheet with id=H, first strand: chain 'A' and resid 511 through 517 removed outlier: 6.456A pdb=" N THR A 542 " --> pdb=" O THR A 512 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LEU A 514 " --> pdb=" O VAL A 540 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N VAL A 540 " --> pdb=" O LEU A 514 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N VAL A 516 " --> pdb=" O SER A 538 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N SER A 538 " --> pdb=" O VAL A 516 " (cutoff:3.500A) Processing sheet with id=I, first strand: chain 'A' and resid 561 through 567 removed outlier: 3.786A pdb=" N LEU A 564 " --> pdb=" O VAL A 913 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ASN A 910 " --> pdb=" O ASP A 906 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP A 906 " --> pdb=" O ASN A 910 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER A 901 " --> pdb=" O TRP A 897 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N SER A 893 " --> pdb=" O VAL A 905 " (cutoff:3.500A) Processing sheet with id=J, first strand: chain 'A' and resid 584 through 590 removed outlier: 3.662A pdb=" N ARG A 595 " --> pdb=" O ASP A 590 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ILE A 598 " --> pdb=" O LYS A 606 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ASN A 604 " --> pdb=" O GLU A 600 " (cutoff:3.500A) Processing sheet with id=K, first strand: chain 'A' and resid 619 through 626 Processing sheet with id=L, first strand: chain 'A' and resid 658 through 664 removed outlier: 4.475A pdb=" N ASP A 676 " --> pdb=" O VAL A 672 " (cutoff:3.500A) Processing sheet with id=M, first strand: chain 'A' and resid 704 through 712 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 704 through 712 current: chain 'A' and resid 740 through 744 removed outlier: 4.314A pdb=" N ILE A 741 " --> pdb=" O LEU A 755 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N TYR A 766 " --> pdb=" O ASN A 756 " (cutoff:3.500A) Processing sheet with id=N, first strand: chain 'A' and resid 782 through 791 removed outlier: 5.129A pdb=" N GLU A 797 " --> pdb=" O LYS A 813 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU A 807 " --> pdb=" O THR A 803 " (cutoff:3.500A) Processing sheet with id=O, first strand: chain 'A' and resid 850 through 855 removed outlier: 3.934A pdb=" N ILE A 850 " --> pdb=" O THR A 866 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N SER A 861 " --> pdb=" O LYS A 875 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LYS A 875 " --> pdb=" O SER A 861 " (cutoff:3.500A) Processing sheet with id=P, first strand: chain 'A' and resid 943 through 950 removed outlier: 6.086A pdb=" N LEU A 944 " --> pdb=" O CYS A 961 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N CYS A 961 " --> pdb=" O LEU A 944 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N LYS A 946 " --> pdb=" O SER A 959 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SER A 959 " --> pdb=" O LYS A 946 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL A 964 " --> pdb=" O GLY A 988 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N SER A 991 " --> pdb=" O PHE A1009 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE A1009 " --> pdb=" O SER A 991 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ASN A 997 " --> pdb=" O VAL A1003 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL A1003 " --> pdb=" O ASN A 997 " (cutoff:3.500A) Processing sheet with id=Q, first strand: chain 'A' and resid 1013 through 1021 removed outlier: 7.250A pdb=" N GLY A1039 " --> pdb=" O ASN A1016 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N MET A1018 " --> pdb=" O ILE A1037 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE A1037 " --> pdb=" O MET A1018 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N SER A1020 " --> pdb=" O TYR A1035 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N TYR A1035 " --> pdb=" O SER A1020 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N GLU A1034 " --> pdb=" O VAL A1059 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N VAL A1059 " --> pdb=" O GLU A1034 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N THR A1051 " --> pdb=" O ASN A1042 " (cutoff:3.500A) Processing sheet with id=R, first strand: chain 'A' and resid 1087 through 1093 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1087 through 1093 current: chain 'A' and resid 1104 through 1111 removed outlier: 5.953A pdb=" N ASP A1109 " --> pdb=" O PRO A1118 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N GLN A1111 " --> pdb=" O VAL A1116 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N VAL A1116 " --> pdb=" O GLN A1111 " (cutoff:3.500A) Processing sheet with id=S, first strand: chain 'A' and resid 1128 through 1134 No H-bonds generated for sheet with id=S Processing sheet with id=T, first strand: chain 'A' and resid 1172 through 1179 removed outlier: 3.979A pdb=" N SER A1173 " --> pdb=" O THR A1188 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N MET A1183 " --> pdb=" O TYR A1199 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ASN A1193 " --> pdb=" O ASP A1189 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ARG A1192 " --> pdb=" O LEU A1220 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LYS A1198 " --> pdb=" O HIS A1214 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N HIS A1214 " --> pdb=" O LYS A1198 " (cutoff:3.500A) Processing sheet with id=U, first strand: chain 'A' and resid 1224 through 1232 No H-bonds generated for sheet with id=U Processing sheet with id=V, first strand: chain 'D' and resid 83 through 88 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 83 through 88 current: chain 'D' and resid 364 through 369 Processing sheet with id=W, first strand: chain 'D' and resid 96 through 101 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 96 through 101 current: chain 'D' and resid 107 through 112 removed outlier: 5.706A pdb=" N PHE D 117 " --> pdb=" O MET D 131 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N LEU D 119 " --> pdb=" O THR D 129 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N THR D 129 " --> pdb=" O LEU D 119 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASN D 121 " --> pdb=" O PHE D 127 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N PHE D 127 " --> pdb=" O ASN D 121 " (cutoff:3.500A) Processing sheet with id=X, first strand: chain 'D' and resid 138 through 144 removed outlier: 5.289A pdb=" N THR D 140 " --> pdb=" O GLY D 153 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N TRP D 149 " --> pdb=" O SER D 144 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LYS D 160 " --> pdb=" O SER D 152 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N MET D 158 " --> pdb=" O ASP D 154 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS D 170 " --> pdb=" O ILE D 161 " (cutoff:3.500A) Processing sheet with id=Y, first strand: chain 'D' and resid 179 through 186 removed outlier: 3.865A pdb=" N ASP D 182 " --> pdb=" O CYS D 195 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LYS D 191 " --> pdb=" O SER D 186 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N SER D 196 " --> pdb=" O ILE D 200 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ILE D 200 " --> pdb=" O SER D 196 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LEU D 201 " --> pdb=" O VAL D 214 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N VAL D 214 " --> pdb=" O LEU D 201 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ILE D 203 " --> pdb=" O GLU D 212 " (cutoff:3.500A) Processing sheet with id=Z, first strand: chain 'D' and resid 222 through 227 removed outlier: 3.537A pdb=" N LYS D 244 " --> pdb=" O SER D 236 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N LEU D 242 " --> pdb=" O ILE D 257 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE D 257 " --> pdb=" O LEU D 242 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N LYS D 244 " --> pdb=" O SER D 255 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N SER D 255 " --> pdb=" O LYS D 244 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N TRP D 246 " --> pdb=" O CYS D 253 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N CYS D 253 " --> pdb=" O TRP D 246 " (cutoff:3.500A) Processing sheet with id=AA, first strand: chain 'D' and resid 264 through 269 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 264 through 269 current: chain 'D' and resid 276 through 281 removed outlier: 5.423A pdb=" N SER D 285 " --> pdb=" O SER D 281 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL D 288 " --> pdb=" O MET D 299 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N MET D 299 " --> pdb=" O VAL D 288 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ASP D 290 " --> pdb=" O GLU D 297 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N GLU D 297 " --> pdb=" O ASP D 290 " (cutoff:3.500A) Processing sheet with id=AB, first strand: chain 'D' and resid 309 through 312 Processing sheet with id=AC, first strand: chain 'D' and resid 328 through 332 No H-bonds generated for sheet with id=AC 328 hydrogen bonds defined for protein. 900 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.08 Time building geometry restraints manager: 3.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4343 1.34 - 1.46: 2053 1.46 - 1.58: 7479 1.58 - 1.70: 0 1.70 - 1.81: 107 Bond restraints: 13982 Sorted by residual: bond pdb=" N PRO A 510 " pdb=" CA PRO A 510 " ideal model delta sigma weight residual 1.474 1.446 0.028 7.40e-03 1.83e+04 1.44e+01 bond pdb=" CA ASP A 665 " pdb=" C ASP A 665 " ideal model delta sigma weight residual 1.523 1.552 -0.028 1.00e-02 1.00e+04 8.07e+00 bond pdb=" CA VAL A 777 " pdb=" CB VAL A 777 " ideal model delta sigma weight residual 1.540 1.565 -0.026 9.00e-03 1.23e+04 8.03e+00 bond pdb=" CA ILE A 782 " pdb=" CB ILE A 782 " ideal model delta sigma weight residual 1.532 1.563 -0.031 1.08e-02 8.57e+03 8.00e+00 bond pdb=" N LEU A 246 " pdb=" CA LEU A 246 " ideal model delta sigma weight residual 1.458 1.478 -0.020 7.40e-03 1.83e+04 7.44e+00 ... (remaining 13977 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 17171 2.16 - 4.33: 1557 4.33 - 6.49: 170 6.49 - 8.66: 32 8.66 - 10.82: 7 Bond angle restraints: 18937 Sorted by residual: angle pdb=" C PRO D 67 " pdb=" N PRO D 68 " pdb=" CA PRO D 68 " ideal model delta sigma weight residual 119.84 127.25 -7.41 1.25e+00 6.40e-01 3.51e+01 angle pdb=" N VAL A1178 " pdb=" CA VAL A1178 " pdb=" C VAL A1178 " ideal model delta sigma weight residual 111.81 116.85 -5.04 8.60e-01 1.35e+00 3.43e+01 angle pdb=" C THR D 102 " pdb=" N PRO D 103 " pdb=" CA PRO D 103 " ideal model delta sigma weight residual 119.84 126.88 -7.04 1.25e+00 6.40e-01 3.17e+01 angle pdb=" N TYR D 44 " pdb=" CA TYR D 44 " pdb=" C TYR D 44 " ideal model delta sigma weight residual 112.13 105.06 7.07 1.37e+00 5.33e-01 2.67e+01 angle pdb=" N MET D 158 " pdb=" CA MET D 158 " pdb=" C MET D 158 " ideal model delta sigma weight residual 110.50 117.60 -7.10 1.41e+00 5.03e-01 2.54e+01 ... (remaining 18932 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.62: 7231 16.62 - 33.23: 920 33.23 - 49.85: 212 49.85 - 66.47: 84 66.47 - 83.08: 15 Dihedral angle restraints: 8462 sinusoidal: 3431 harmonic: 5031 Sorted by residual: dihedral pdb=" CA GLU A1155 " pdb=" C GLU A1155 " pdb=" N PRO A1156 " pdb=" CA PRO A1156 " ideal model delta harmonic sigma weight residual 180.00 152.57 27.43 0 5.00e+00 4.00e-02 3.01e+01 dihedral pdb=" C THR A 414 " pdb=" N THR A 414 " pdb=" CA THR A 414 " pdb=" CB THR A 414 " ideal model delta harmonic sigma weight residual -122.00 -134.53 12.53 0 2.50e+00 1.60e-01 2.51e+01 dihedral pdb=" C ASN A 221 " pdb=" N ASN A 221 " pdb=" CA ASN A 221 " pdb=" CB ASN A 221 " ideal model delta harmonic sigma weight residual -122.60 -133.87 11.27 0 2.50e+00 1.60e-01 2.03e+01 ... (remaining 8459 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 1551 0.085 - 0.170: 453 0.170 - 0.254: 113 0.254 - 0.339: 21 0.339 - 0.424: 6 Chirality restraints: 2144 Sorted by residual: chirality pdb=" CA ASN A 221 " pdb=" N ASN A 221 " pdb=" C ASN A 221 " pdb=" CB ASN A 221 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.50e+00 chirality pdb=" CA THR A 414 " pdb=" N THR A 414 " pdb=" C THR A 414 " pdb=" CB THR A 414 " both_signs ideal model delta sigma weight residual False 2.53 2.11 0.42 2.00e-01 2.50e+01 4.43e+00 chirality pdb=" CA LYS A 926 " pdb=" N LYS A 926 " pdb=" C LYS A 926 " pdb=" CB LYS A 926 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.76e+00 ... (remaining 2141 not shown) Planarity restraints: 2412 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 509 " 0.042 5.00e-02 4.00e+02 6.43e-02 6.61e+00 pdb=" N PRO A 510 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 510 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 510 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 665 " 0.042 5.00e-02 4.00e+02 6.29e-02 6.33e+00 pdb=" N PRO A 666 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 666 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 666 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A1155 " -0.037 5.00e-02 4.00e+02 5.67e-02 5.14e+00 pdb=" N PRO A1156 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO A1156 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A1156 " -0.032 5.00e-02 4.00e+02 ... (remaining 2409 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.00: 6239 3.00 - 3.48: 14845 3.48 - 3.95: 25357 3.95 - 4.43: 27926 4.43 - 4.90: 46268 Nonbonded interactions: 120635 Sorted by model distance: nonbonded pdb=" O THR A 34 " pdb=" N ILE A 60 " model vdw 2.526 3.120 nonbonded pdb=" OG SER A1088 " pdb=" OG SER A1100 " model vdw 2.529 3.040 nonbonded pdb=" OH TYR A1266 " pdb=" O PRO A1306 " model vdw 2.530 3.040 nonbonded pdb=" O PRO A1231 " pdb=" OG SER A1352 " model vdw 2.532 3.040 nonbonded pdb=" O MET D 66 " pdb=" NH1 ARG D 379 " model vdw 2.541 3.120 ... (remaining 120630 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.240 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: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 36.050 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 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 : 0.007 0.048 13990 Z= 0.475 Angle : 1.339 20.954 18943 Z= 0.819 Chirality : 0.089 0.424 2144 Planarity : 0.005 0.064 2412 Dihedral : 16.646 83.085 5198 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 1.66 % Allowed : 10.14 % Favored : 88.20 % Rotamer: Outliers : 4.80 % Allowed : 13.67 % Favored : 81.53 % Cbeta Deviations : 0.43 % 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: -3.75 (0.17), residues: 1686 helix: -3.58 (0.29), residues: 101 sheet: -2.16 (0.19), residues: 530 loop : -2.66 (0.16), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 101 HIS 0.007 0.001 HIS A1221 PHE 0.016 0.002 PHE D 269 TYR 0.017 0.002 TYR A1184 ARG 0.003 0.001 ARG D 47 Details of bonding type rmsd hydrogen bonds : bond 0.22372 ( 328) hydrogen bonds : angle 11.43333 ( 900) metal coordination : bond 0.02540 ( 8) metal coordination : angle 10.79165 ( 6) covalent geometry : bond 0.00709 (13982) covalent geometry : angle 1.32569 (18937) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 505 time to evaluate : 1.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LEU cc_start: 0.8501 (mp) cc_final: 0.8221 (mt) REVERT: A 44 ARG cc_start: 0.6933 (mtt180) cc_final: 0.6732 (tpt170) REVERT: A 55 LYS cc_start: 0.8422 (tttt) cc_final: 0.7648 (ttpt) REVERT: A 75 CYS cc_start: 0.8654 (m) cc_final: 0.8037 (m) REVERT: A 79 CYS cc_start: 0.8513 (m) cc_final: 0.8215 (m) REVERT: A 92 THR cc_start: 0.8985 (m) cc_final: 0.8686 (p) REVERT: A 110 LYS cc_start: 0.7948 (mtmt) cc_final: 0.7688 (mttm) REVERT: A 115 VAL cc_start: 0.8603 (p) cc_final: 0.8321 (p) REVERT: A 129 SER cc_start: 0.8185 (m) cc_final: 0.7524 (p) REVERT: A 201 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8461 (pp) REVERT: A 205 GLU cc_start: 0.7666 (tt0) cc_final: 0.7328 (tp30) REVERT: A 215 ASP cc_start: 0.8580 (t0) cc_final: 0.8350 (t0) REVERT: A 265 LYS cc_start: 0.7858 (mttt) cc_final: 0.7649 (ttpt) REVERT: A 341 ASN cc_start: 0.8437 (p0) cc_final: 0.8127 (t0) REVERT: A 366 MET cc_start: 0.8916 (mtp) cc_final: 0.8676 (mtp) REVERT: A 372 ILE cc_start: 0.8728 (OUTLIER) cc_final: 0.8312 (mm) REVERT: A 411 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.7961 (pp) REVERT: A 507 ASN cc_start: 0.8822 (t0) cc_final: 0.8567 (t0) REVERT: A 512 THR cc_start: 0.8543 (m) cc_final: 0.8117 (m) REVERT: A 527 LYS cc_start: 0.7553 (mmtp) cc_final: 0.6937 (mmtm) REVERT: A 536 GLU cc_start: 0.8619 (tm-30) cc_final: 0.7950 (tt0) REVERT: A 539 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8890 (pt) REVERT: A 542 THR cc_start: 0.9197 (OUTLIER) cc_final: 0.8614 (p) REVERT: A 545 ASN cc_start: 0.8478 (t0) cc_final: 0.8255 (t0) REVERT: A 550 HIS cc_start: 0.9058 (p-80) cc_final: 0.8797 (p90) REVERT: A 564 LEU cc_start: 0.7750 (tp) cc_final: 0.7091 (mp) REVERT: A 614 ARG cc_start: 0.6794 (tpt90) cc_final: 0.6522 (tpt90) REVERT: A 629 LYS cc_start: 0.7446 (mtpp) cc_final: 0.6738 (mttp) REVERT: A 643 ASP cc_start: 0.6660 (t70) cc_final: 0.6375 (t0) REVERT: A 647 ARG cc_start: 0.6376 (ptt-90) cc_final: 0.5911 (ptm160) REVERT: A 653 LYS cc_start: 0.8414 (pttp) cc_final: 0.7673 (tptp) REVERT: A 655 ASP cc_start: 0.6599 (t70) cc_final: 0.6249 (t70) REVERT: A 657 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7427 (tt0) REVERT: A 659 ILE cc_start: 0.8665 (tp) cc_final: 0.8355 (pt) REVERT: A 681 GLU cc_start: 0.7215 (tt0) cc_final: 0.6984 (tp30) REVERT: A 688 ARG cc_start: 0.6722 (tpt170) cc_final: 0.6384 (mmm-85) REVERT: A 713 ASN cc_start: 0.8227 (p0) cc_final: 0.7399 (p0) REVERT: A 714 MET cc_start: 0.7775 (ptm) cc_final: 0.7474 (ptt) REVERT: A 724 LYS cc_start: 0.7161 (tptm) cc_final: 0.6882 (tttt) REVERT: A 728 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.6862 (pm20) REVERT: A 736 THR cc_start: 0.8749 (OUTLIER) cc_final: 0.8456 (m) REVERT: A 753 PHE cc_start: 0.8501 (m-80) cc_final: 0.8089 (m-10) REVERT: A 760 GLN cc_start: 0.6490 (pt0) cc_final: 0.6036 (pm20) REVERT: A 782 ILE cc_start: 0.9190 (OUTLIER) cc_final: 0.8852 (mt) REVERT: A 786 MET cc_start: 0.7447 (ptp) cc_final: 0.6883 (ptp) REVERT: A 807 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.7974 (tt0) REVERT: A 817 ARG cc_start: 0.7126 (ttm-80) cc_final: 0.6870 (mtp85) REVERT: A 818 ARG cc_start: 0.7888 (mtm-85) cc_final: 0.7669 (mtt90) REVERT: A 824 ASN cc_start: 0.6735 (OUTLIER) cc_final: 0.6491 (p0) REVERT: A 828 ASN cc_start: 0.7437 (m-40) cc_final: 0.7172 (m110) REVERT: A 933 LYS cc_start: 0.8074 (ptpt) cc_final: 0.7783 (mtmm) REVERT: A 939 ASP cc_start: 0.7351 (p0) cc_final: 0.7075 (p0) REVERT: A 942 LYS cc_start: 0.7683 (pttm) cc_final: 0.7433 (ptpp) REVERT: A 965 PRO cc_start: 0.9069 (Cg_endo) cc_final: 0.8829 (Cg_endo) REVERT: A 996 ILE cc_start: 0.8563 (OUTLIER) cc_final: 0.8334 (pt) REVERT: A 1002 LYS cc_start: 0.8747 (mtmt) cc_final: 0.8096 (mmtt) REVERT: A 1011 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8517 (mtpp) REVERT: A 1017 GLU cc_start: 0.7691 (mt-10) cc_final: 0.6424 (tt0) REVERT: A 1019 ARG cc_start: 0.8241 (mtt-85) cc_final: 0.7233 (mtt-85) REVERT: A 1081 GLU cc_start: 0.8096 (tt0) cc_final: 0.7637 (tp30) REVERT: A 1083 VAL cc_start: 0.7311 (m) cc_final: 0.6998 (p) REVERT: A 1144 MET cc_start: 0.8711 (ptm) cc_final: 0.8255 (ppp) REVERT: A 1160 ILE cc_start: 0.8687 (tp) cc_final: 0.8475 (tp) REVERT: A 1164 ARG cc_start: 0.8020 (mtt90) cc_final: 0.7474 (mtp-110) REVERT: A 1168 LYS cc_start: 0.8566 (pttp) cc_final: 0.8045 (mtmm) REVERT: A 1172 MET cc_start: 0.8803 (tpt) cc_final: 0.8532 (tpp) REVERT: A 1177 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8217 (pp) REVERT: A 1189 ASP cc_start: 0.8201 (m-30) cc_final: 0.7792 (m-30) REVERT: A 1226 CYS cc_start: 0.8559 (t) cc_final: 0.8296 (t) REVERT: A 1233 ASN cc_start: 0.7551 (t0) cc_final: 0.7316 (t0) REVERT: A 1321 ILE cc_start: 0.8174 (tt) cc_final: 0.7948 (tp) REVERT: A 1338 GLU cc_start: 0.8073 (tt0) cc_final: 0.7847 (tt0) REVERT: A 1347 GLU cc_start: 0.7847 (tp30) cc_final: 0.7421 (tp30) REVERT: A 1350 MET cc_start: 0.8950 (tpp) cc_final: 0.8721 (mmm) REVERT: B 31 ARG cc_start: 0.7687 (ptt-90) cc_final: 0.7342 (ptt90) REVERT: B 48 ARG cc_start: 0.6594 (mtt90) cc_final: 0.6280 (mtm-85) REVERT: B 63 ASN cc_start: 0.7858 (t0) cc_final: 0.7353 (m110) REVERT: B 68 ARG cc_start: 0.7658 (mtt-85) cc_final: 0.6923 (mmm160) REVERT: B 79 ASP cc_start: 0.7782 (t70) cc_final: 0.7088 (t70) REVERT: B 86 GLU cc_start: 0.8437 (tt0) cc_final: 0.7830 (tt0) REVERT: D 34 ASP cc_start: 0.9038 (t70) cc_final: 0.7991 (t0) REVERT: D 56 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8419 (mm-30) REVERT: D 61 TYR cc_start: 0.9132 (m-80) cc_final: 0.8660 (m-80) REVERT: D 75 ASP cc_start: 0.8599 (p0) cc_final: 0.8074 (p0) REVERT: D 93 LYS cc_start: 0.6620 (mtpp) cc_final: 0.6414 (tptt) REVERT: D 99 ILE cc_start: 0.8492 (OUTLIER) cc_final: 0.8281 (mm) REVERT: D 107 ARG cc_start: 0.8236 (mtm-85) cc_final: 0.7955 (mtm-85) REVERT: D 109 VAL cc_start: 0.9068 (OUTLIER) cc_final: 0.8747 (t) REVERT: D 132 GLN cc_start: 0.6775 (tt0) cc_final: 0.6425 (tm-30) REVERT: D 141 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.7653 (ptp) REVERT: D 150 MET cc_start: 0.8274 (ptm) cc_final: 0.7730 (ppp) REVERT: D 163 GLN cc_start: 0.8358 (mt0) cc_final: 0.7899 (mt0) REVERT: D 165 ASN cc_start: 0.8216 (p0) cc_final: 0.7978 (p0) REVERT: D 168 MET cc_start: 0.7340 (ptp) cc_final: 0.6736 (pmm) REVERT: D 183 MET cc_start: 0.8413 (mmp) cc_final: 0.8109 (mmp) REVERT: D 200 ILE cc_start: 0.9001 (tt) cc_final: 0.8551 (tt) REVERT: D 234 ILE cc_start: 0.8364 (mp) cc_final: 0.8160 (mt) REVERT: D 239 LYS cc_start: 0.7188 (ttmm) cc_final: 0.6849 (mtpt) REVERT: D 245 LEU cc_start: 0.8272 (mt) cc_final: 0.8018 (mt) REVERT: D 273 LYS cc_start: 0.8575 (mmpt) cc_final: 0.7922 (mtpt) REVERT: D 275 ASN cc_start: 0.8007 (m-40) cc_final: 0.7659 (t0) REVERT: D 297 GLU cc_start: 0.8800 (pt0) cc_final: 0.7510 (tt0) REVERT: D 303 ASP cc_start: 0.7410 (t70) cc_final: 0.7204 (t0) REVERT: D 311 GLU cc_start: 0.8006 (tp30) cc_final: 0.7468 (tp30) REVERT: D 316 ASN cc_start: 0.8286 (m110) cc_final: 0.7640 (m110) REVERT: D 326 ASP cc_start: 0.7655 (t70) cc_final: 0.7393 (p0) REVERT: D 337 ASN cc_start: 0.7641 (m-40) cc_final: 0.7203 (t0) REVERT: D 339 ASN cc_start: 0.8077 (t0) cc_final: 0.7830 (t0) REVERT: D 340 GLU cc_start: 0.7304 (mt-10) cc_final: 0.6674 (mm-30) REVERT: D 356 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8738 (pp) REVERT: D 357 SER cc_start: 0.9253 (t) cc_final: 0.8655 (m) REVERT: D 359 ASN cc_start: 0.8536 (p0) cc_final: 0.8330 (p0) REVERT: D 373 THR cc_start: 0.8596 (p) cc_final: 0.8193 (p) REVERT: D 383 ILE cc_start: 0.8566 (tp) cc_final: 0.8182 (tt) REVERT: D 388 TYR cc_start: 0.6233 (m-80) cc_final: 0.5737 (m-80) outliers start: 74 outliers final: 21 residues processed: 549 average time/residue: 0.2742 time to fit residues: 218.7214 Evaluate side-chains 400 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 362 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 728 GLU Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 800 THR Chi-restraints excluded: chain A residue 807 GLU Chi-restraints excluded: chain A residue 824 ASN Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 917 THR Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 1011 LYS Chi-restraints excluded: chain A residue 1036 ILE Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1177 LEU Chi-restraints excluded: chain A residue 1224 ASN Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain B residue 5 HIS Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 141 MET Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 356 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 86 optimal weight: 10.0000 chunk 68 optimal weight: 0.7980 chunk 133 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 99 optimal weight: 0.0970 chunk 154 optimal weight: 0.0270 overall best weight: 0.5840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 419 ASN A 438 ASN A 545 ASN A 576 ASN A 660 HIS A 754 GLN A 931 GLN A 985 HIS A1024 GLN A1145 GLN A1205 ASN ** A1246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1273 GLN A1336 HIS D 205 ASN ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.155394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.132899 restraints weight = 16737.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.137628 restraints weight = 9881.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.139784 restraints weight = 6007.325| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 13990 Z= 0.148 Angle : 0.704 13.111 18943 Z= 0.362 Chirality : 0.049 0.230 2144 Planarity : 0.004 0.048 2412 Dihedral : 7.882 58.910 1910 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.11 % Favored : 93.53 % Rotamer: Outliers : 5.38 % Allowed : 18.28 % Favored : 76.34 % 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: -3.20 (0.18), residues: 1686 helix: -2.20 (0.39), residues: 107 sheet: -2.16 (0.19), residues: 550 loop : -2.13 (0.18), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1001 HIS 0.006 0.001 HIS A 550 PHE 0.018 0.002 PHE A 135 TYR 0.017 0.002 TYR D 358 ARG 0.007 0.001 ARG A1279 Details of bonding type rmsd hydrogen bonds : bond 0.04891 ( 328) hydrogen bonds : angle 8.25291 ( 900) metal coordination : bond 0.01517 ( 8) metal coordination : angle 3.06552 ( 6) covalent geometry : bond 0.00348 (13982) covalent geometry : angle 0.70244 (18937) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 411 time to evaluate : 1.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 THR cc_start: 0.8349 (m) cc_final: 0.8145 (p) REVERT: A 30 LEU cc_start: 0.8291 (mp) cc_final: 0.8044 (mt) REVERT: A 55 LYS cc_start: 0.8288 (tttt) cc_final: 0.7941 (ttpt) REVERT: A 62 ASP cc_start: 0.7676 (t0) cc_final: 0.7357 (t0) REVERT: A 73 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7977 (pt) REVERT: A 92 THR cc_start: 0.8825 (m) cc_final: 0.8464 (p) REVERT: A 129 SER cc_start: 0.7309 (m) cc_final: 0.6659 (p) REVERT: A 334 GLU cc_start: 0.7259 (mm-30) cc_final: 0.6799 (mp0) REVERT: A 336 MET cc_start: 0.7517 (ptt) cc_final: 0.7240 (ptp) REVERT: A 366 MET cc_start: 0.8388 (mtp) cc_final: 0.8006 (mtp) REVERT: A 411 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7470 (pp) REVERT: A 523 ASP cc_start: 0.6718 (OUTLIER) cc_final: 0.6149 (m-30) REVERT: A 527 LYS cc_start: 0.7813 (mmtp) cc_final: 0.7318 (mmtm) REVERT: A 536 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7775 (tt0) REVERT: A 539 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8586 (pt) REVERT: A 542 THR cc_start: 0.9007 (OUTLIER) cc_final: 0.8655 (p) REVERT: A 564 LEU cc_start: 0.8014 (tp) cc_final: 0.7657 (mp) REVERT: A 629 LYS cc_start: 0.7178 (mtpp) cc_final: 0.6959 (mttp) REVERT: A 702 MET cc_start: 0.6632 (mtt) cc_final: 0.6358 (mtt) REVERT: A 731 LEU cc_start: 0.8668 (pp) cc_final: 0.8397 (pp) REVERT: A 786 MET cc_start: 0.7408 (ptp) cc_final: 0.6935 (ptp) REVERT: A 796 GLU cc_start: 0.7596 (mm-30) cc_final: 0.7355 (mm-30) REVERT: A 854 PHE cc_start: 0.8486 (m-80) cc_final: 0.7009 (m-80) REVERT: A 914 TYR cc_start: 0.8347 (m-80) cc_final: 0.7760 (m-80) REVERT: A 969 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.7221 (pp) REVERT: A 1074 LYS cc_start: 0.8307 (mttt) cc_final: 0.7872 (mtpt) REVERT: A 1157 TYR cc_start: 0.8244 (m-80) cc_final: 0.7880 (m-10) REVERT: A 1228 MET cc_start: 0.8263 (tmm) cc_final: 0.7925 (ptm) REVERT: A 1236 PHE cc_start: 0.6372 (t80) cc_final: 0.6097 (t80) REVERT: A 1266 TYR cc_start: 0.8890 (t80) cc_final: 0.8468 (t80) REVERT: A 1269 LEU cc_start: 0.8567 (mt) cc_final: 0.8346 (mt) REVERT: A 1281 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8587 (pp) REVERT: A 1353 LEU cc_start: 0.9007 (mp) cc_final: 0.8570 (mt) REVERT: B 31 ARG cc_start: 0.8130 (ptt-90) cc_final: 0.7561 (ptt-90) REVERT: B 79 ASP cc_start: 0.7352 (t70) cc_final: 0.6683 (t70) REVERT: B 86 GLU cc_start: 0.8244 (tt0) cc_final: 0.7901 (tt0) REVERT: B 91 LYS cc_start: 0.7235 (mttt) cc_final: 0.6843 (mttp) REVERT: D 56 GLU cc_start: 0.8592 (mm-30) cc_final: 0.8375 (mm-30) REVERT: D 58 GLU cc_start: 0.6453 (tm-30) cc_final: 0.5810 (tm-30) REVERT: D 61 TYR cc_start: 0.8722 (m-80) cc_final: 0.8502 (m-80) REVERT: D 71 TYR cc_start: 0.8408 (m-80) cc_final: 0.8118 (m-10) REVERT: D 75 ASP cc_start: 0.7856 (p0) cc_final: 0.7399 (p0) REVERT: D 163 GLN cc_start: 0.8375 (mt0) cc_final: 0.8079 (mt0) REVERT: D 183 MET cc_start: 0.7879 (mmp) cc_final: 0.7423 (mmp) REVERT: D 200 ILE cc_start: 0.9399 (OUTLIER) cc_final: 0.9106 (tt) REVERT: D 234 ILE cc_start: 0.8797 (mp) cc_final: 0.8574 (mt) REVERT: D 283 ASP cc_start: 0.6278 (t70) cc_final: 0.5612 (t70) REVERT: D 297 GLU cc_start: 0.8017 (pt0) cc_final: 0.7799 (tt0) REVERT: D 310 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8455 (pp) REVERT: D 316 ASN cc_start: 0.8192 (m110) cc_final: 0.7911 (m110) REVERT: D 328 SER cc_start: 0.8645 (m) cc_final: 0.8325 (p) outliers start: 83 outliers final: 36 residues processed: 462 average time/residue: 0.2664 time to fit residues: 177.9225 Evaluate side-chains 367 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 322 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASN Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 576 ASN Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 822 TYR Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 1036 ILE Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1062 VAL Chi-restraints excluded: chain A residue 1099 ILE Chi-restraints excluded: chain A residue 1133 SER Chi-restraints excluded: chain A residue 1139 ILE Chi-restraints excluded: chain A residue 1173 SER Chi-restraints excluded: chain A residue 1177 LEU Chi-restraints excluded: chain A residue 1185 PHE Chi-restraints excluded: chain A residue 1213 VAL Chi-restraints excluded: chain A residue 1224 ASN Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain A residue 1281 LEU Chi-restraints excluded: chain A residue 1312 VAL Chi-restraints excluded: chain B residue 5 HIS Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 208 ASN Chi-restraints excluded: chain D residue 211 GLN Chi-restraints excluded: chain D residue 241 ASN Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 344 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 18 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 48 optimal weight: 0.0770 chunk 21 optimal weight: 0.0970 chunk 154 optimal weight: 0.6980 chunk 2 optimal weight: 0.0970 chunk 143 optimal weight: 5.9990 overall best weight: 0.3734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 ASN A1101 GLN A1145 GLN A1273 GLN B 5 HIS B 21 GLN D 275 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.159218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.137831 restraints weight = 16782.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.142491 restraints weight = 9794.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.144360 restraints weight = 5838.035| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 13990 Z= 0.132 Angle : 0.682 11.778 18943 Z= 0.346 Chirality : 0.048 0.174 2144 Planarity : 0.004 0.042 2412 Dihedral : 6.543 49.083 1871 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.00 % Favored : 92.76 % Rotamer: Outliers : 6.61 % Allowed : 20.54 % Favored : 72.85 % 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: -2.95 (0.18), residues: 1686 helix: -1.62 (0.45), residues: 108 sheet: -1.91 (0.20), residues: 544 loop : -2.07 (0.18), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1001 HIS 0.004 0.001 HIS A 550 PHE 0.018 0.002 PHE A 625 TYR 0.018 0.001 TYR A 640 ARG 0.007 0.000 ARG A1279 Details of bonding type rmsd hydrogen bonds : bond 0.04224 ( 328) hydrogen bonds : angle 7.65079 ( 900) metal coordination : bond 0.00973 ( 8) metal coordination : angle 1.76626 ( 6) covalent geometry : bond 0.00309 (13982) covalent geometry : angle 0.68131 (18937) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 341 time to evaluate : 1.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LEU cc_start: 0.8433 (mp) cc_final: 0.8085 (mt) REVERT: A 55 LYS cc_start: 0.8225 (tttt) cc_final: 0.7938 (ttpp) REVERT: A 73 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8036 (pt) REVERT: A 92 THR cc_start: 0.8782 (m) cc_final: 0.8431 (p) REVERT: A 129 SER cc_start: 0.7003 (m) cc_final: 0.6356 (p) REVERT: A 235 LEU cc_start: 0.9235 (mt) cc_final: 0.8956 (mt) REVERT: A 297 ASN cc_start: 0.6826 (OUTLIER) cc_final: 0.6584 (p0) REVERT: A 334 GLU cc_start: 0.7281 (mm-30) cc_final: 0.6779 (mp0) REVERT: A 336 MET cc_start: 0.7555 (ptt) cc_final: 0.7341 (ptp) REVERT: A 520 SER cc_start: 0.8294 (OUTLIER) cc_final: 0.8070 (m) REVERT: A 523 ASP cc_start: 0.6744 (OUTLIER) cc_final: 0.6116 (m-30) REVERT: A 527 LYS cc_start: 0.7769 (mmtp) cc_final: 0.7276 (mmtm) REVERT: A 536 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7627 (tt0) REVERT: A 539 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8724 (pt) REVERT: A 542 THR cc_start: 0.8930 (OUTLIER) cc_final: 0.8667 (p) REVERT: A 564 LEU cc_start: 0.7845 (tp) cc_final: 0.7620 (mp) REVERT: A 605 PHE cc_start: 0.5978 (p90) cc_final: 0.5535 (p90) REVERT: A 621 TYR cc_start: 0.7982 (t80) cc_final: 0.7766 (t80) REVERT: A 629 LYS cc_start: 0.7139 (mtpp) cc_final: 0.6911 (mttp) REVERT: A 656 TYR cc_start: 0.6521 (m-80) cc_final: 0.5942 (m-10) REVERT: A 738 ASP cc_start: 0.7961 (OUTLIER) cc_final: 0.7639 (p0) REVERT: A 753 PHE cc_start: 0.8595 (m-10) cc_final: 0.8339 (m-10) REVERT: A 786 MET cc_start: 0.7462 (ptp) cc_final: 0.7024 (ptp) REVERT: A 1074 LYS cc_start: 0.8295 (mttt) cc_final: 0.7878 (mtpt) REVERT: A 1157 TYR cc_start: 0.8056 (m-80) cc_final: 0.7763 (m-10) REVERT: A 1269 LEU cc_start: 0.8488 (mt) cc_final: 0.8169 (mt) REVERT: B 31 ARG cc_start: 0.8278 (ptt-90) cc_final: 0.7957 (ptt-90) REVERT: B 79 ASP cc_start: 0.7351 (t70) cc_final: 0.6832 (t70) REVERT: B 86 GLU cc_start: 0.8195 (tt0) cc_final: 0.7929 (tt0) REVERT: B 91 LYS cc_start: 0.7213 (mttt) cc_final: 0.6713 (mttp) REVERT: B 92 MET cc_start: 0.5624 (mmm) cc_final: 0.5410 (mmm) REVERT: D 56 GLU cc_start: 0.8720 (mm-30) cc_final: 0.8390 (mm-30) REVERT: D 58 GLU cc_start: 0.6232 (OUTLIER) cc_final: 0.5691 (tm-30) REVERT: D 75 ASP cc_start: 0.7712 (p0) cc_final: 0.7387 (p0) REVERT: D 163 GLN cc_start: 0.8377 (mt0) cc_final: 0.8168 (mt0) REVERT: D 183 MET cc_start: 0.7761 (mmp) cc_final: 0.7244 (mmp) REVERT: D 200 ILE cc_start: 0.9380 (OUTLIER) cc_final: 0.9143 (tt) REVERT: D 241 ASN cc_start: 0.8632 (OUTLIER) cc_final: 0.8308 (p0) REVERT: D 275 ASN cc_start: 0.7875 (OUTLIER) cc_final: 0.7618 (t0) REVERT: D 311 GLU cc_start: 0.7096 (tp30) cc_final: 0.6660 (tp30) REVERT: D 328 SER cc_start: 0.9050 (m) cc_final: 0.8556 (p) outliers start: 102 outliers final: 47 residues processed: 406 average time/residue: 0.2480 time to fit residues: 149.4775 Evaluate side-chains 367 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 309 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASN Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 576 ASN Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 738 ASP Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 792 HIS Chi-restraints excluded: chain A residue 822 TYR Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 955 LEU Chi-restraints excluded: chain A residue 959 SER Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1023 ILE Chi-restraints excluded: chain A residue 1036 ILE Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1062 VAL Chi-restraints excluded: chain A residue 1091 CYS Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1133 SER Chi-restraints excluded: chain A residue 1139 ILE Chi-restraints excluded: chain A residue 1173 SER Chi-restraints excluded: chain A residue 1177 LEU Chi-restraints excluded: chain A residue 1185 PHE Chi-restraints excluded: chain A residue 1213 VAL Chi-restraints excluded: chain A residue 1224 ASN Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain A residue 1273 GLN Chi-restraints excluded: chain A residue 1275 GLN Chi-restraints excluded: chain B residue 5 HIS Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 208 ASN Chi-restraints excluded: chain D residue 211 GLN Chi-restraints excluded: chain D residue 241 ASN Chi-restraints excluded: chain D residue 275 ASN Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 344 THR Chi-restraints excluded: chain D residue 373 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 127 optimal weight: 10.0000 chunk 101 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 31 optimal weight: 0.0870 chunk 166 optimal weight: 8.9990 chunk 82 optimal weight: 8.9990 chunk 131 optimal weight: 0.9990 chunk 150 optimal weight: 8.9990 chunk 154 optimal weight: 1.9990 chunk 165 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 overall best weight: 0.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 ASN A 740 GLN A 828 ASN A1012 ASN A1179 ASN B 63 ASN D 86 HIS ** D 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.161399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.140255 restraints weight = 16622.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.144304 restraints weight = 10107.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.146581 restraints weight = 6371.798| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13990 Z= 0.153 Angle : 0.684 11.976 18943 Z= 0.346 Chirality : 0.048 0.180 2144 Planarity : 0.004 0.041 2412 Dihedral : 6.291 50.038 1864 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.64 % Favored : 93.12 % Rotamer: Outliers : 6.16 % Allowed : 22.10 % Favored : 71.74 % 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: -2.80 (0.19), residues: 1686 helix: -1.38 (0.46), residues: 108 sheet: -1.88 (0.20), residues: 537 loop : -1.94 (0.18), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1001 HIS 0.006 0.001 HIS D 86 PHE 0.019 0.002 PHE A 625 TYR 0.016 0.001 TYR D 61 ARG 0.004 0.000 ARG A 595 Details of bonding type rmsd hydrogen bonds : bond 0.03961 ( 328) hydrogen bonds : angle 7.35989 ( 900) metal coordination : bond 0.00948 ( 8) metal coordination : angle 1.91730 ( 6) covalent geometry : bond 0.00368 (13982) covalent geometry : angle 0.68362 (18937) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 343 time to evaluate : 1.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LEU cc_start: 0.8415 (mp) cc_final: 0.8200 (mt) REVERT: A 73 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7949 (pt) REVERT: A 92 THR cc_start: 0.8745 (m) cc_final: 0.8380 (p) REVERT: A 129 SER cc_start: 0.6909 (m) cc_final: 0.6365 (p) REVERT: A 235 LEU cc_start: 0.9064 (mt) cc_final: 0.8786 (mt) REVERT: A 281 LEU cc_start: 0.9053 (mt) cc_final: 0.8684 (mp) REVERT: A 297 ASN cc_start: 0.6961 (OUTLIER) cc_final: 0.6672 (p0) REVERT: A 334 GLU cc_start: 0.7324 (mm-30) cc_final: 0.6801 (mp0) REVERT: A 336 MET cc_start: 0.7489 (ptt) cc_final: 0.7247 (ptp) REVERT: A 366 MET cc_start: 0.8076 (mtp) cc_final: 0.7875 (mtp) REVERT: A 373 TYR cc_start: 0.8548 (m-80) cc_final: 0.8321 (m-80) REVERT: A 520 SER cc_start: 0.8291 (OUTLIER) cc_final: 0.8069 (m) REVERT: A 536 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7684 (tt0) REVERT: A 605 PHE cc_start: 0.6171 (p90) cc_final: 0.5719 (p90) REVERT: A 629 LYS cc_start: 0.7393 (mtpp) cc_final: 0.7136 (mttp) REVERT: A 713 ASN cc_start: 0.8474 (p0) cc_final: 0.7737 (p0) REVERT: A 754 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.8123 (pt0) REVERT: A 786 MET cc_start: 0.7568 (ptp) cc_final: 0.6780 (ptp) REVERT: A 798 TYR cc_start: 0.8718 (m-80) cc_final: 0.8363 (m-80) REVERT: A 800 THR cc_start: 0.8682 (OUTLIER) cc_final: 0.7706 (p) REVERT: A 1074 LYS cc_start: 0.8295 (mttt) cc_final: 0.7888 (mtpt) REVERT: A 1182 ASP cc_start: 0.7310 (OUTLIER) cc_final: 0.6888 (t0) REVERT: A 1244 PHE cc_start: 0.8812 (m-80) cc_final: 0.8552 (m-80) REVERT: A 1250 GLN cc_start: 0.8557 (mm110) cc_final: 0.7919 (mt0) REVERT: A 1353 LEU cc_start: 0.8902 (mp) cc_final: 0.8509 (mt) REVERT: B 79 ASP cc_start: 0.7159 (t70) cc_final: 0.6825 (t70) REVERT: B 86 GLU cc_start: 0.8161 (tt0) cc_final: 0.7860 (tt0) REVERT: D 58 GLU cc_start: 0.6285 (OUTLIER) cc_final: 0.5453 (tm-30) REVERT: D 60 SER cc_start: 0.8292 (m) cc_final: 0.7443 (p) REVERT: D 75 ASP cc_start: 0.7767 (p0) cc_final: 0.7332 (p0) REVERT: D 163 GLN cc_start: 0.8294 (mt0) cc_final: 0.7910 (mt0) REVERT: D 165 ASN cc_start: 0.8316 (p0) cc_final: 0.7977 (p0) REVERT: D 173 ASP cc_start: 0.5747 (t0) cc_final: 0.5509 (t0) REVERT: D 200 ILE cc_start: 0.9404 (OUTLIER) cc_final: 0.9168 (tt) REVERT: D 241 ASN cc_start: 0.8740 (OUTLIER) cc_final: 0.8418 (p0) REVERT: D 311 GLU cc_start: 0.7092 (tp30) cc_final: 0.6527 (tp30) REVERT: D 328 SER cc_start: 0.8956 (m) cc_final: 0.8419 (p) outliers start: 95 outliers final: 56 residues processed: 396 average time/residue: 0.2545 time to fit residues: 148.9433 Evaluate side-chains 369 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 304 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASN Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 647 ARG Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 724 LYS Chi-restraints excluded: chain A residue 754 GLN Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 792 HIS Chi-restraints excluded: chain A residue 800 THR Chi-restraints excluded: chain A residue 822 TYR Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 879 SER Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 917 THR Chi-restraints excluded: chain A residue 955 LEU Chi-restraints excluded: chain A residue 959 SER Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 994 LEU Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1018 MET Chi-restraints excluded: chain A residue 1037 ILE Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1062 VAL Chi-restraints excluded: chain A residue 1063 VAL Chi-restraints excluded: chain A residue 1091 CYS Chi-restraints excluded: chain A residue 1099 ILE Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1130 ASP Chi-restraints excluded: chain A residue 1133 SER Chi-restraints excluded: chain A residue 1171 THR Chi-restraints excluded: chain A residue 1173 SER Chi-restraints excluded: chain A residue 1177 LEU Chi-restraints excluded: chain A residue 1182 ASP Chi-restraints excluded: chain A residue 1185 PHE Chi-restraints excluded: chain A residue 1213 VAL Chi-restraints excluded: chain A residue 1224 ASN Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 208 ASN Chi-restraints excluded: chain D residue 211 GLN Chi-restraints excluded: chain D residue 241 ASN Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 352 CYS Chi-restraints excluded: chain D residue 373 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 129 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 153 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 chunk 100 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 156 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 ASN ** A 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 63 ASN ** D 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 275 ASN ** D 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.152873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.131158 restraints weight = 17099.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.135888 restraints weight = 9880.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.137964 restraints weight = 5869.660| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 13990 Z= 0.213 Angle : 0.721 12.366 18943 Z= 0.361 Chirality : 0.050 0.225 2144 Planarity : 0.004 0.044 2412 Dihedral : 6.202 51.109 1858 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.41 % Favored : 92.35 % Rotamer: Outliers : 6.48 % Allowed : 23.59 % Favored : 69.93 % 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: -2.66 (0.19), residues: 1686 helix: -1.09 (0.49), residues: 102 sheet: -1.86 (0.20), residues: 544 loop : -1.80 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1001 HIS 0.013 0.001 HIS A 660 PHE 0.030 0.002 PHE B 61 TYR 0.026 0.002 TYR A1157 ARG 0.007 0.001 ARG A1279 Details of bonding type rmsd hydrogen bonds : bond 0.03961 ( 328) hydrogen bonds : angle 7.38300 ( 900) metal coordination : bond 0.00793 ( 8) metal coordination : angle 2.43010 ( 6) covalent geometry : bond 0.00500 (13982) covalent geometry : angle 0.71979 (18937) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 325 time to evaluate : 1.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LEU cc_start: 0.8526 (mp) cc_final: 0.8322 (mt) REVERT: A 47 LYS cc_start: 0.8044 (mtmm) cc_final: 0.7817 (mmtm) REVERT: A 73 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.8002 (pt) REVERT: A 92 THR cc_start: 0.8858 (m) cc_final: 0.8493 (p) REVERT: A 106 GLU cc_start: 0.7615 (tm-30) cc_final: 0.7249 (tt0) REVERT: A 129 SER cc_start: 0.6987 (m) cc_final: 0.6355 (p) REVERT: A 281 LEU cc_start: 0.9101 (mt) cc_final: 0.8791 (mp) REVERT: A 334 GLU cc_start: 0.7439 (mm-30) cc_final: 0.6936 (mp0) REVERT: A 336 MET cc_start: 0.7608 (ptt) cc_final: 0.7224 (ptp) REVERT: A 340 LYS cc_start: 0.8263 (mmtt) cc_final: 0.7938 (mtpt) REVERT: A 366 MET cc_start: 0.8301 (mtp) cc_final: 0.8098 (mtp) REVERT: A 417 ASN cc_start: 0.8034 (t0) cc_final: 0.7592 (t0) REVERT: A 418 LYS cc_start: 0.7001 (mptt) cc_final: 0.6760 (mmtt) REVERT: A 520 SER cc_start: 0.8263 (OUTLIER) cc_final: 0.7943 (m) REVERT: A 536 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7656 (tt0) REVERT: A 542 THR cc_start: 0.9091 (OUTLIER) cc_final: 0.8853 (p) REVERT: A 605 PHE cc_start: 0.6094 (p90) cc_final: 0.5663 (p90) REVERT: A 629 LYS cc_start: 0.7425 (mtpp) cc_final: 0.7147 (mttp) REVERT: A 681 GLU cc_start: 0.8074 (tp30) cc_final: 0.7840 (tp30) REVERT: A 711 LYS cc_start: 0.7729 (tttt) cc_final: 0.7194 (ttpp) REVERT: A 713 ASN cc_start: 0.8751 (p0) cc_final: 0.8028 (p0) REVERT: A 753 PHE cc_start: 0.8714 (m-10) cc_final: 0.8351 (m-10) REVERT: A 761 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8239 (tt) REVERT: A 786 MET cc_start: 0.7678 (ptp) cc_final: 0.6878 (ptp) REVERT: A 798 TYR cc_start: 0.8742 (m-80) cc_final: 0.8320 (m-80) REVERT: A 800 THR cc_start: 0.8799 (OUTLIER) cc_final: 0.7818 (p) REVERT: A 854 PHE cc_start: 0.8579 (m-80) cc_final: 0.7212 (m-80) REVERT: A 1074 LYS cc_start: 0.8317 (mttt) cc_final: 0.7879 (mtpt) REVERT: A 1177 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.7946 (pp) REVERT: A 1250 GLN cc_start: 0.8621 (mm110) cc_final: 0.8015 (mt0) REVERT: A 1252 ASP cc_start: 0.8745 (p0) cc_final: 0.8458 (p0) REVERT: B 79 ASP cc_start: 0.7569 (t70) cc_final: 0.6948 (t70) REVERT: D 56 GLU cc_start: 0.8919 (mm-30) cc_final: 0.8711 (mm-30) REVERT: D 61 TYR cc_start: 0.8804 (m-80) cc_final: 0.8575 (m-10) REVERT: D 163 GLN cc_start: 0.8333 (mt0) cc_final: 0.7910 (mt0) REVERT: D 165 ASN cc_start: 0.8443 (p0) cc_final: 0.8086 (p0) REVERT: D 168 MET cc_start: 0.6018 (tmm) cc_final: 0.5665 (tmm) REVERT: D 173 ASP cc_start: 0.5488 (t0) cc_final: 0.5225 (t0) REVERT: D 186 SER cc_start: 0.9173 (t) cc_final: 0.8960 (t) REVERT: D 200 ILE cc_start: 0.9430 (OUTLIER) cc_final: 0.9171 (tt) REVERT: D 241 ASN cc_start: 0.8716 (OUTLIER) cc_final: 0.8385 (p0) REVERT: D 284 LYS cc_start: 0.7523 (pttm) cc_final: 0.7247 (pttp) REVERT: D 311 GLU cc_start: 0.7366 (tp30) cc_final: 0.6769 (tp30) outliers start: 100 outliers final: 60 residues processed: 393 average time/residue: 0.2491 time to fit residues: 145.9000 Evaluate side-chains 368 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 300 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASN Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 647 ARG Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 662 SER Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 724 LYS Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 792 HIS Chi-restraints excluded: chain A residue 800 THR Chi-restraints excluded: chain A residue 822 TYR Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 879 SER Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 917 THR Chi-restraints excluded: chain A residue 955 LEU Chi-restraints excluded: chain A residue 959 SER Chi-restraints excluded: chain A residue 994 LEU Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1018 MET Chi-restraints excluded: chain A residue 1036 ILE Chi-restraints excluded: chain A residue 1037 ILE Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1062 VAL Chi-restraints excluded: chain A residue 1063 VAL Chi-restraints excluded: chain A residue 1091 CYS Chi-restraints excluded: chain A residue 1099 ILE Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1130 ASP Chi-restraints excluded: chain A residue 1133 SER Chi-restraints excluded: chain A residue 1171 THR Chi-restraints excluded: chain A residue 1173 SER Chi-restraints excluded: chain A residue 1177 LEU Chi-restraints excluded: chain A residue 1213 VAL Chi-restraints excluded: chain A residue 1224 ASN Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 208 ASN Chi-restraints excluded: chain D residue 211 GLN Chi-restraints excluded: chain D residue 241 ASN Chi-restraints excluded: chain D residue 275 ASN Chi-restraints excluded: chain D residue 286 CYS Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 352 CYS Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain D residue 373 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 39 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 127 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 137 optimal weight: 0.5980 chunk 53 optimal weight: 20.0000 chunk 37 optimal weight: 0.8980 chunk 86 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 925 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.155309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.133494 restraints weight = 16931.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.137681 restraints weight = 10156.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.139609 restraints weight = 6362.406| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.4005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13990 Z= 0.174 Angle : 0.701 14.214 18943 Z= 0.348 Chirality : 0.048 0.184 2144 Planarity : 0.005 0.069 2412 Dihedral : 6.203 56.937 1858 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 18.22 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.64 % Favored : 93.18 % Rotamer: Outliers : 5.38 % Allowed : 25.15 % Favored : 69.48 % 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: -2.68 (0.19), residues: 1686 helix: -1.21 (0.47), residues: 110 sheet: -1.92 (0.20), residues: 539 loop : -1.79 (0.19), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1001 HIS 0.006 0.001 HIS B 5 PHE 0.034 0.002 PHE A1176 TYR 0.021 0.002 TYR A 621 ARG 0.006 0.000 ARG D 292 Details of bonding type rmsd hydrogen bonds : bond 0.03737 ( 328) hydrogen bonds : angle 7.25481 ( 900) metal coordination : bond 0.00695 ( 8) metal coordination : angle 1.71349 ( 6) covalent geometry : bond 0.00412 (13982) covalent geometry : angle 0.70000 (18937) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 316 time to evaluate : 1.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LEU cc_start: 0.8614 (mp) cc_final: 0.8383 (mt) REVERT: A 47 LYS cc_start: 0.8174 (mtmm) cc_final: 0.7833 (mmtm) REVERT: A 73 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7915 (mp) REVERT: A 92 THR cc_start: 0.8870 (m) cc_final: 0.8475 (p) REVERT: A 106 GLU cc_start: 0.7629 (tm-30) cc_final: 0.7254 (tt0) REVERT: A 129 SER cc_start: 0.7161 (m) cc_final: 0.6589 (p) REVERT: A 281 LEU cc_start: 0.9048 (mt) cc_final: 0.8699 (mp) REVERT: A 336 MET cc_start: 0.7545 (ptt) cc_final: 0.7122 (ptp) REVERT: A 340 LYS cc_start: 0.8237 (mmtt) cc_final: 0.7915 (mtpt) REVERT: A 417 ASN cc_start: 0.8178 (t0) cc_final: 0.7776 (t0) REVERT: A 418 LYS cc_start: 0.6872 (mptt) cc_final: 0.6614 (mmtt) REVERT: A 520 SER cc_start: 0.8407 (OUTLIER) cc_final: 0.8103 (m) REVERT: A 536 GLU cc_start: 0.8137 (tm-30) cc_final: 0.7655 (tt0) REVERT: A 542 THR cc_start: 0.9065 (OUTLIER) cc_final: 0.8828 (p) REVERT: A 605 PHE cc_start: 0.6085 (p90) cc_final: 0.5689 (p90) REVERT: A 629 LYS cc_start: 0.7627 (mtpp) cc_final: 0.7214 (mttp) REVERT: A 681 GLU cc_start: 0.8051 (tp30) cc_final: 0.7781 (tp30) REVERT: A 711 LYS cc_start: 0.7684 (tttt) cc_final: 0.7185 (ttpp) REVERT: A 713 ASN cc_start: 0.8751 (p0) cc_final: 0.8536 (p0) REVERT: A 761 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8211 (tt) REVERT: A 786 MET cc_start: 0.7646 (ptp) cc_final: 0.7367 (ptp) REVERT: A 798 TYR cc_start: 0.8555 (m-80) cc_final: 0.8081 (m-80) REVERT: A 854 PHE cc_start: 0.8573 (m-80) cc_final: 0.7235 (m-80) REVERT: A 1022 MET cc_start: 0.6329 (ptt) cc_final: 0.6111 (ptp) REVERT: A 1074 LYS cc_start: 0.8286 (mttt) cc_final: 0.7880 (mtpt) REVERT: A 1134 PHE cc_start: 0.8976 (t80) cc_final: 0.8717 (t80) REVERT: A 1269 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8062 (mt) REVERT: B 79 ASP cc_start: 0.7529 (t70) cc_final: 0.6961 (t70) REVERT: D 163 GLN cc_start: 0.8412 (mt0) cc_final: 0.8026 (mt0) REVERT: D 165 ASN cc_start: 0.8480 (p0) cc_final: 0.8049 (p0) REVERT: D 173 ASP cc_start: 0.5856 (t0) cc_final: 0.5645 (t0) REVERT: D 186 SER cc_start: 0.9197 (t) cc_final: 0.8975 (t) REVERT: D 200 ILE cc_start: 0.9427 (OUTLIER) cc_final: 0.9171 (tt) REVERT: D 241 ASN cc_start: 0.8679 (OUTLIER) cc_final: 0.8336 (p0) REVERT: D 263 THR cc_start: 0.7157 (OUTLIER) cc_final: 0.6890 (t) REVERT: D 311 GLU cc_start: 0.7437 (tp30) cc_final: 0.6868 (tp30) REVERT: D 370 LYS cc_start: 0.7474 (ptpt) cc_final: 0.6882 (mtpp) outliers start: 83 outliers final: 63 residues processed: 369 average time/residue: 0.2512 time to fit residues: 138.8572 Evaluate side-chains 366 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 295 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASN Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 647 ARG Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 724 LYS Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 792 HIS Chi-restraints excluded: chain A residue 822 TYR Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 837 ASP Chi-restraints excluded: chain A residue 879 SER Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 917 THR Chi-restraints excluded: chain A residue 955 LEU Chi-restraints excluded: chain A residue 959 SER Chi-restraints excluded: chain A residue 994 LEU Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1037 ILE Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1062 VAL Chi-restraints excluded: chain A residue 1063 VAL Chi-restraints excluded: chain A residue 1091 CYS Chi-restraints excluded: chain A residue 1099 ILE Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1130 ASP Chi-restraints excluded: chain A residue 1133 SER Chi-restraints excluded: chain A residue 1171 THR Chi-restraints excluded: chain A residue 1173 SER Chi-restraints excluded: chain A residue 1177 LEU Chi-restraints excluded: chain A residue 1213 VAL Chi-restraints excluded: chain A residue 1224 ASN Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain A residue 1269 LEU Chi-restraints excluded: chain B residue 38 ASN Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 208 ASN Chi-restraints excluded: chain D residue 211 GLN Chi-restraints excluded: chain D residue 241 ASN Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 373 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 58 optimal weight: 8.9990 chunk 69 optimal weight: 0.6980 chunk 168 optimal weight: 10.0000 chunk 92 optimal weight: 7.9990 chunk 164 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 57 HIS ** A 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 545 ASN A 716 ASN A 740 GLN ** A 925 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1148 GLN ** A1193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1282 GLN ** D 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 275 ASN ** D 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.143905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.121064 restraints weight = 17218.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.125182 restraints weight = 10502.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.127333 restraints weight = 6577.017| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.095 13990 Z= 0.336 Angle : 0.813 15.267 18943 Z= 0.408 Chirality : 0.053 0.228 2144 Planarity : 0.005 0.056 2412 Dihedral : 6.574 59.594 1858 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 20.85 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.01 % Favored : 91.81 % Rotamer: Outliers : 6.29 % Allowed : 24.69 % Favored : 69.02 % 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: -2.85 (0.19), residues: 1686 helix: -1.41 (0.47), residues: 112 sheet: -2.04 (0.20), residues: 538 loop : -1.88 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 237 HIS 0.006 0.002 HIS D 134 PHE 0.040 0.003 PHE A1176 TYR 0.023 0.003 TYR A1157 ARG 0.007 0.001 ARG D 292 Details of bonding type rmsd hydrogen bonds : bond 0.04306 ( 328) hydrogen bonds : angle 7.55711 ( 900) metal coordination : bond 0.00728 ( 8) metal coordination : angle 3.23921 ( 6) covalent geometry : bond 0.00787 (13982) covalent geometry : angle 0.81148 (18937) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 321 time to evaluate : 1.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LYS cc_start: 0.8472 (mtmm) cc_final: 0.8238 (mmtp) REVERT: A 73 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.7985 (mp) REVERT: A 106 GLU cc_start: 0.7848 (tm-30) cc_final: 0.7497 (tt0) REVERT: A 129 SER cc_start: 0.7621 (m) cc_final: 0.7047 (p) REVERT: A 281 LEU cc_start: 0.9263 (mt) cc_final: 0.8981 (mp) REVERT: A 336 MET cc_start: 0.7760 (ptt) cc_final: 0.7241 (ptp) REVERT: A 340 LYS cc_start: 0.8269 (mmtt) cc_final: 0.7964 (mtpt) REVERT: A 520 SER cc_start: 0.8390 (OUTLIER) cc_final: 0.8113 (m) REVERT: A 536 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7646 (tt0) REVERT: A 542 THR cc_start: 0.9243 (OUTLIER) cc_final: 0.8969 (p) REVERT: A 711 LYS cc_start: 0.7862 (tttt) cc_final: 0.7356 (ttpp) REVERT: A 713 ASN cc_start: 0.8953 (p0) cc_final: 0.8520 (p0) REVERT: A 786 MET cc_start: 0.7904 (ptp) cc_final: 0.7538 (ptp) REVERT: A 820 ARG cc_start: 0.8125 (ttm-80) cc_final: 0.7112 (mtp-110) REVERT: A 854 PHE cc_start: 0.8664 (m-80) cc_final: 0.7258 (m-80) REVERT: A 1022 MET cc_start: 0.6629 (ptt) cc_final: 0.6410 (ptp) REVERT: A 1056 ILE cc_start: 0.8094 (mt) cc_final: 0.7876 (mt) REVERT: A 1074 LYS cc_start: 0.8292 (mttt) cc_final: 0.7901 (mtpt) REVERT: A 1177 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8003 (pp) REVERT: A 1250 GLN cc_start: 0.8666 (mm110) cc_final: 0.8044 (mt0) REVERT: A 1269 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8263 (mt) REVERT: B 79 ASP cc_start: 0.7876 (t70) cc_final: 0.7072 (t70) REVERT: B 86 GLU cc_start: 0.8276 (tt0) cc_final: 0.7939 (tt0) REVERT: D 163 GLN cc_start: 0.8456 (mt0) cc_final: 0.8021 (mt0) REVERT: D 200 ILE cc_start: 0.9446 (OUTLIER) cc_final: 0.9179 (tt) REVERT: D 263 THR cc_start: 0.7280 (OUTLIER) cc_final: 0.7078 (t) REVERT: D 278 MET cc_start: 0.8119 (tmm) cc_final: 0.7709 (ttp) REVERT: D 283 ASP cc_start: 0.7893 (t0) cc_final: 0.7073 (t70) REVERT: D 370 LYS cc_start: 0.7639 (ptpt) cc_final: 0.7189 (mtpp) REVERT: D 388 TYR cc_start: 0.7499 (m-80) cc_final: 0.7240 (m-80) outliers start: 97 outliers final: 74 residues processed: 390 average time/residue: 0.2496 time to fit residues: 145.9310 Evaluate side-chains 373 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 292 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 647 ARG Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 724 LYS Chi-restraints excluded: chain A residue 746 LYS Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 792 HIS Chi-restraints excluded: chain A residue 822 TYR Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 837 ASP Chi-restraints excluded: chain A residue 879 SER Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 917 THR Chi-restraints excluded: chain A residue 929 LEU Chi-restraints excluded: chain A residue 959 SER Chi-restraints excluded: chain A residue 994 LEU Chi-restraints excluded: chain A residue 1018 MET Chi-restraints excluded: chain A residue 1037 ILE Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1062 VAL Chi-restraints excluded: chain A residue 1063 VAL Chi-restraints excluded: chain A residue 1091 CYS Chi-restraints excluded: chain A residue 1099 ILE Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1130 ASP Chi-restraints excluded: chain A residue 1133 SER Chi-restraints excluded: chain A residue 1173 SER Chi-restraints excluded: chain A residue 1177 LEU Chi-restraints excluded: chain A residue 1213 VAL Chi-restraints excluded: chain A residue 1224 ASN Chi-restraints excluded: chain A residue 1229 LEU Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain A residue 1269 LEU Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 208 ASN Chi-restraints excluded: chain D residue 211 GLN Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 241 ASN Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 275 ASN Chi-restraints excluded: chain D residue 286 CYS Chi-restraints excluded: chain D residue 352 CYS Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain D residue 373 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 34 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 117 optimal weight: 0.0060 chunk 158 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 138 optimal weight: 2.9990 chunk 161 optimal weight: 0.8980 chunk 131 optimal weight: 0.5980 chunk 151 optimal weight: 9.9990 chunk 94 optimal weight: 0.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 ASN A 740 GLN ** A 925 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 275 ASN ** D 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 HIS ** 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 = 0.3631 r_free = 0.3631 target = 0.154228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.130592 restraints weight = 16910.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.134498 restraints weight = 9579.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.137084 restraints weight = 6559.176| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.4416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13990 Z= 0.148 Angle : 0.719 11.560 18943 Z= 0.358 Chirality : 0.049 0.228 2144 Planarity : 0.004 0.060 2412 Dihedral : 6.326 57.404 1858 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 19.24 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.70 % Favored : 93.12 % Rotamer: Outliers : 5.06 % Allowed : 26.96 % Favored : 67.98 % 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: -2.68 (0.19), residues: 1686 helix: -1.15 (0.48), residues: 109 sheet: -1.92 (0.21), residues: 524 loop : -1.81 (0.19), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 237 HIS 0.005 0.001 HIS D 134 PHE 0.034 0.002 PHE A1176 TYR 0.029 0.002 TYR A 798 ARG 0.011 0.001 ARG D 292 Details of bonding type rmsd hydrogen bonds : bond 0.03642 ( 328) hydrogen bonds : angle 7.22610 ( 900) metal coordination : bond 0.00846 ( 8) metal coordination : angle 1.78611 ( 6) covalent geometry : bond 0.00350 (13982) covalent geometry : angle 0.71816 (18937) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 318 time to evaluate : 1.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LEU cc_start: 0.8566 (mp) cc_final: 0.8318 (mt) REVERT: A 47 LYS cc_start: 0.8249 (mtmm) cc_final: 0.8004 (mmtp) REVERT: A 73 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8158 (mp) REVERT: A 106 GLU cc_start: 0.7660 (tm-30) cc_final: 0.7328 (tt0) REVERT: A 129 SER cc_start: 0.7304 (m) cc_final: 0.6665 (p) REVERT: A 536 GLU cc_start: 0.8143 (tm-30) cc_final: 0.7693 (tt0) REVERT: A 542 THR cc_start: 0.9078 (OUTLIER) cc_final: 0.8803 (p) REVERT: A 605 PHE cc_start: 0.6161 (p90) cc_final: 0.5753 (p90) REVERT: A 711 LYS cc_start: 0.7711 (tttt) cc_final: 0.7003 (ttpp) REVERT: A 786 MET cc_start: 0.7846 (ptp) cc_final: 0.7522 (ptp) REVERT: A 854 PHE cc_start: 0.8553 (m-80) cc_final: 0.7433 (m-80) REVERT: A 1022 MET cc_start: 0.6445 (ptt) cc_final: 0.6227 (ptp) REVERT: A 1056 ILE cc_start: 0.7996 (mt) cc_final: 0.7741 (mt) REVERT: A 1074 LYS cc_start: 0.8198 (mttt) cc_final: 0.7826 (mtpt) REVERT: A 1175 GLU cc_start: 0.7250 (tp30) cc_final: 0.6413 (tp30) REVERT: A 1250 GLN cc_start: 0.8506 (mm110) cc_final: 0.7802 (mt0) REVERT: A 1269 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.7963 (mt) REVERT: D 163 GLN cc_start: 0.8459 (mt0) cc_final: 0.8132 (mt0) REVERT: D 200 ILE cc_start: 0.9406 (OUTLIER) cc_final: 0.9150 (tt) REVERT: D 263 THR cc_start: 0.7216 (OUTLIER) cc_final: 0.6881 (t) REVERT: D 278 MET cc_start: 0.7896 (tmm) cc_final: 0.7610 (ttp) REVERT: D 308 MET cc_start: 0.6987 (ttm) cc_final: 0.6702 (ttm) REVERT: D 311 GLU cc_start: 0.7535 (tp30) cc_final: 0.6786 (tp30) REVERT: D 333 ASP cc_start: 0.7804 (OUTLIER) cc_final: 0.7538 (m-30) REVERT: D 370 LYS cc_start: 0.7537 (ptpt) cc_final: 0.7088 (mmmt) REVERT: D 388 TYR cc_start: 0.7487 (m-80) cc_final: 0.7257 (m-80) outliers start: 78 outliers final: 60 residues processed: 372 average time/residue: 0.2368 time to fit residues: 132.6262 Evaluate side-chains 365 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 299 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASN Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 792 HIS Chi-restraints excluded: chain A residue 822 TYR Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 917 THR Chi-restraints excluded: chain A residue 959 SER Chi-restraints excluded: chain A residue 994 LEU Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1018 MET Chi-restraints excluded: chain A residue 1037 ILE Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1091 CYS Chi-restraints excluded: chain A residue 1099 ILE Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1130 ASP Chi-restraints excluded: chain A residue 1133 SER Chi-restraints excluded: chain A residue 1173 SER Chi-restraints excluded: chain A residue 1177 LEU Chi-restraints excluded: chain A residue 1213 VAL Chi-restraints excluded: chain A residue 1224 ASN Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain A residue 1269 LEU Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 182 ASP Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 208 ASN Chi-restraints excluded: chain D residue 211 GLN Chi-restraints excluded: chain D residue 241 ASN Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 286 CYS Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 333 ASP Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 373 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 63 optimal weight: 0.1980 chunk 94 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 134 optimal weight: 0.8980 chunk 144 optimal weight: 10.0000 chunk 55 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 164 optimal weight: 10.0000 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 ASN ** A 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 740 GLN ** A 925 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1012 ASN ** D 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 HIS ** 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 = 0.3641 r_free = 0.3641 target = 0.154945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.133341 restraints weight = 16896.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.137442 restraints weight = 10201.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.139291 restraints weight = 6377.023| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.4609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13990 Z= 0.151 Angle : 0.712 10.965 18943 Z= 0.355 Chirality : 0.048 0.230 2144 Planarity : 0.005 0.057 2412 Dihedral : 6.234 59.848 1857 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 19.42 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.53 % Favored : 92.29 % Rotamer: Outliers : 5.18 % Allowed : 26.64 % Favored : 68.18 % 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: -2.60 (0.19), residues: 1686 helix: -1.00 (0.49), residues: 109 sheet: -1.87 (0.21), residues: 533 loop : -1.74 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 237 HIS 0.006 0.001 HIS D 48 PHE 0.024 0.002 PHE A 497 TYR 0.038 0.002 TYR A1157 ARG 0.005 0.000 ARG A 630 Details of bonding type rmsd hydrogen bonds : bond 0.03573 ( 328) hydrogen bonds : angle 7.08264 ( 900) metal coordination : bond 0.00552 ( 8) metal coordination : angle 1.93568 ( 6) covalent geometry : bond 0.00360 (13982) covalent geometry : angle 0.71144 (18937) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 315 time to evaluate : 1.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LEU cc_start: 0.8586 (mp) cc_final: 0.8337 (mt) REVERT: A 47 LYS cc_start: 0.8222 (mtmm) cc_final: 0.7805 (mmtp) REVERT: A 73 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8119 (mp) REVERT: A 106 GLU cc_start: 0.7573 (tm-30) cc_final: 0.7273 (tt0) REVERT: A 129 SER cc_start: 0.7379 (m) cc_final: 0.6838 (p) REVERT: A 205 GLU cc_start: 0.6738 (tp30) cc_final: 0.6426 (tp30) REVERT: A 536 GLU cc_start: 0.8063 (tm-30) cc_final: 0.7679 (tt0) REVERT: A 605 PHE cc_start: 0.6134 (p90) cc_final: 0.5716 (p90) REVERT: A 624 MET cc_start: 0.7954 (mtt) cc_final: 0.7572 (mtt) REVERT: A 664 MET cc_start: 0.6878 (mtt) cc_final: 0.6524 (mmm) REVERT: A 786 MET cc_start: 0.7837 (ptp) cc_final: 0.7551 (ptp) REVERT: A 854 PHE cc_start: 0.8529 (m-80) cc_final: 0.7484 (m-80) REVERT: A 1056 ILE cc_start: 0.7955 (mt) cc_final: 0.7749 (mt) REVERT: A 1074 LYS cc_start: 0.8214 (mttt) cc_final: 0.7867 (mtpt) REVERT: A 1250 GLN cc_start: 0.8513 (mm110) cc_final: 0.7885 (mt0) REVERT: A 1269 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8004 (mt) REVERT: D 163 GLN cc_start: 0.8431 (mt0) cc_final: 0.8060 (mt0) REVERT: D 200 ILE cc_start: 0.9412 (OUTLIER) cc_final: 0.9166 (tt) REVERT: D 263 THR cc_start: 0.6945 (OUTLIER) cc_final: 0.6641 (t) REVERT: D 278 MET cc_start: 0.7851 (tmm) cc_final: 0.7594 (ttp) REVERT: D 311 GLU cc_start: 0.7696 (tp30) cc_final: 0.6895 (tp30) REVERT: D 370 LYS cc_start: 0.7535 (ptpt) cc_final: 0.7130 (mmmt) REVERT: D 388 TYR cc_start: 0.7532 (m-80) cc_final: 0.7256 (m-80) outliers start: 80 outliers final: 69 residues processed: 366 average time/residue: 0.2399 time to fit residues: 132.8364 Evaluate side-chains 372 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 299 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASN Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 543 SER Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 792 HIS Chi-restraints excluded: chain A residue 822 TYR Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 917 THR Chi-restraints excluded: chain A residue 955 LEU Chi-restraints excluded: chain A residue 959 SER Chi-restraints excluded: chain A residue 994 LEU Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1018 MET Chi-restraints excluded: chain A residue 1037 ILE Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1062 VAL Chi-restraints excluded: chain A residue 1063 VAL Chi-restraints excluded: chain A residue 1091 CYS Chi-restraints excluded: chain A residue 1099 ILE Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1130 ASP Chi-restraints excluded: chain A residue 1133 SER Chi-restraints excluded: chain A residue 1171 THR Chi-restraints excluded: chain A residue 1173 SER Chi-restraints excluded: chain A residue 1177 LEU Chi-restraints excluded: chain A residue 1213 VAL Chi-restraints excluded: chain A residue 1224 ASN Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain A residue 1269 LEU Chi-restraints excluded: chain B residue 38 ASN Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 182 ASP Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 208 ASN Chi-restraints excluded: chain D residue 211 GLN Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 241 ASN Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 286 CYS Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 373 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 34 optimal weight: 3.9990 chunk 156 optimal weight: 0.5980 chunk 49 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 116 optimal weight: 2.9990 chunk 135 optimal weight: 0.8980 chunk 80 optimal weight: 0.0050 chunk 105 optimal weight: 7.9990 chunk 65 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 overall best weight: 0.8596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 ASN ** A 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1012 ASN ** D 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 GLN D 145 HIS ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.156556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.134675 restraints weight = 17064.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.138305 restraints weight = 9803.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.140703 restraints weight = 6805.817| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.4763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13990 Z= 0.152 Angle : 0.711 11.022 18943 Z= 0.354 Chirality : 0.048 0.221 2144 Planarity : 0.004 0.057 2412 Dihedral : 6.202 55.525 1857 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 17.96 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.30 % Favored : 92.53 % Rotamer: Outliers : 5.12 % Allowed : 26.70 % Favored : 68.18 % 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: -2.56 (0.19), residues: 1686 helix: -0.93 (0.49), residues: 109 sheet: -1.88 (0.20), residues: 555 loop : -1.68 (0.19), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 237 HIS 0.005 0.001 HIS D 48 PHE 0.029 0.002 PHE A1176 TYR 0.045 0.002 TYR A1157 ARG 0.006 0.000 ARG A 630 Details of bonding type rmsd hydrogen bonds : bond 0.03544 ( 328) hydrogen bonds : angle 7.05496 ( 900) metal coordination : bond 0.00632 ( 8) metal coordination : angle 1.73142 ( 6) covalent geometry : bond 0.00365 (13982) covalent geometry : angle 0.71014 (18937) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 314 time to evaluate : 1.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7303 (tt0) cc_final: 0.6942 (tt0) REVERT: A 30 LEU cc_start: 0.8563 (mp) cc_final: 0.8308 (mt) REVERT: A 47 LYS cc_start: 0.8168 (mtmm) cc_final: 0.7763 (mmtp) REVERT: A 73 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8096 (mp) REVERT: A 106 GLU cc_start: 0.7570 (tm-30) cc_final: 0.7306 (tt0) REVERT: A 129 SER cc_start: 0.7463 (m) cc_final: 0.6972 (p) REVERT: A 205 GLU cc_start: 0.6762 (tp30) cc_final: 0.6451 (tp30) REVERT: A 536 GLU cc_start: 0.8013 (tm-30) cc_final: 0.7576 (tt0) REVERT: A 605 PHE cc_start: 0.6093 (p90) cc_final: 0.5663 (p90) REVERT: A 624 MET cc_start: 0.7881 (mtt) cc_final: 0.7531 (mtt) REVERT: A 786 MET cc_start: 0.7833 (ptp) cc_final: 0.7580 (ptp) REVERT: A 854 PHE cc_start: 0.8519 (m-80) cc_final: 0.7458 (m-80) REVERT: A 914 TYR cc_start: 0.8477 (m-80) cc_final: 0.7740 (m-80) REVERT: A 1056 ILE cc_start: 0.7958 (mt) cc_final: 0.7723 (mt) REVERT: A 1074 LYS cc_start: 0.8209 (mttt) cc_final: 0.7871 (mtpt) REVERT: A 1175 GLU cc_start: 0.7383 (tp30) cc_final: 0.6546 (tp30) REVERT: A 1269 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.7985 (mt) REVERT: A 1290 MET cc_start: 0.8408 (tpt) cc_final: 0.7901 (tpt) REVERT: D 163 GLN cc_start: 0.8417 (mt0) cc_final: 0.8065 (mt0) REVERT: D 200 ILE cc_start: 0.9409 (OUTLIER) cc_final: 0.9192 (tt) REVERT: D 263 THR cc_start: 0.6914 (OUTLIER) cc_final: 0.6581 (t) REVERT: D 311 GLU cc_start: 0.7623 (tp30) cc_final: 0.6764 (tp30) REVERT: D 370 LYS cc_start: 0.7532 (ptpt) cc_final: 0.7127 (mmmt) REVERT: D 383 ILE cc_start: 0.8672 (tp) cc_final: 0.8416 (tt) REVERT: D 388 TYR cc_start: 0.7493 (m-80) cc_final: 0.7210 (m-80) outliers start: 79 outliers final: 69 residues processed: 361 average time/residue: 0.2351 time to fit residues: 129.2801 Evaluate side-chains 365 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 292 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASN Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 543 SER Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 792 HIS Chi-restraints excluded: chain A residue 822 TYR Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 879 SER Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 917 THR Chi-restraints excluded: chain A residue 955 LEU Chi-restraints excluded: chain A residue 959 SER Chi-restraints excluded: chain A residue 1012 ASN Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1018 MET Chi-restraints excluded: chain A residue 1037 ILE Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1062 VAL Chi-restraints excluded: chain A residue 1063 VAL Chi-restraints excluded: chain A residue 1091 CYS Chi-restraints excluded: chain A residue 1099 ILE Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1130 ASP Chi-restraints excluded: chain A residue 1133 SER Chi-restraints excluded: chain A residue 1173 SER Chi-restraints excluded: chain A residue 1177 LEU Chi-restraints excluded: chain A residue 1213 VAL Chi-restraints excluded: chain A residue 1224 ASN Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain A residue 1269 LEU Chi-restraints excluded: chain A residue 1312 VAL Chi-restraints excluded: chain B residue 38 ASN Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 182 ASP Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 208 ASN Chi-restraints excluded: chain D residue 211 GLN Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 241 ASN Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 286 CYS Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 373 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 74 optimal weight: 2.9990 chunk 112 optimal weight: 0.4980 chunk 65 optimal weight: 0.2980 chunk 68 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 58 optimal weight: 0.0470 chunk 62 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 114 optimal weight: 0.6980 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 729 GLN ** A 828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1012 ASN A1311 ASN ** D 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 GLN ** D 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.162231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.141951 restraints weight = 17008.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.146098 restraints weight = 10084.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.148249 restraints weight = 6188.897| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.4913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13990 Z= 0.139 Angle : 0.711 11.307 18943 Z= 0.354 Chirality : 0.048 0.213 2144 Planarity : 0.004 0.057 2412 Dihedral : 6.196 56.244 1857 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 18.07 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.00 % Favored : 92.82 % Rotamer: Outliers : 4.47 % Allowed : 27.35 % Favored : 68.18 % 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: -2.44 (0.19), residues: 1686 helix: -0.82 (0.49), residues: 109 sheet: -1.72 (0.21), residues: 533 loop : -1.68 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 237 HIS 0.006 0.001 HIS D 86 PHE 0.028 0.002 PHE A1176 TYR 0.028 0.002 TYR A 621 ARG 0.005 0.000 ARG A 630 Details of bonding type rmsd hydrogen bonds : bond 0.03504 ( 328) hydrogen bonds : angle 6.96323 ( 900) metal coordination : bond 0.00533 ( 8) metal coordination : angle 1.53720 ( 6) covalent geometry : bond 0.00329 (13982) covalent geometry : angle 0.71102 (18937) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4739.27 seconds wall clock time: 83 minutes 9.54 seconds (4989.54 seconds total)