Starting phenix.real_space_refine on Fri Jul 3 03:35:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7oh5_12894/07_2026/7oh5_12894.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oh5_12894/07_2026/7oh5_12894.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7oh5_12894/07_2026/7oh5_12894.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oh5_12894/07_2026/7oh5_12894.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7oh5_12894/07_2026/7oh5_12894.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7oh5_12894/07_2026/7oh5_12894.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7oh5_12894/07_2026/7oh5_12894.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oh5_12894/07_2026/7oh5_12894.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.033 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: 8 Type Number sf(0) Gaussians Al 1 5.89 5 P 4 5.49 5 Mg 2 5.21 5 S 48 5.16 5 C 7484 2.51 5 N 1870 2.21 5 O 2190 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11603 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1064, 8504 Classifications: {'peptide': 1064} Link IDs: {'PTRANS': 30, 'TRANS': 1033} Chain: "C" Number of atoms: 2878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2878 Classifications: {'peptide': 355} Link IDs: {'PTRANS': 22, 'TRANS': 332} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 99 Unusual residues: {' MG': 2, '2Y5': 1, 'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 1.88, per 1000 atoms: 0.16 Number of scatterers: 11603 At special positions: 0 Unit cell: (81.4648, 105.182, 169.117, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 48 16.00 P 4 15.00 Al 1 13.00 Mg 2 11.99 F 4 9.00 O 2190 8.00 N 1870 7.00 C 7484 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 80 " - pdb=" SG CYS C 123 " distance=2.06 Simple disulfide: pdb=" SG CYS C 176 " - pdb=" SG CYS C 190 " distance=2.19 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=1, symmetry=0 Links applied BETA1-3 " BMA E 3 " - " BMA E 4 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " NAG-ASN " NAG B 1 " - " ASN C 288 " " NAG C 501 " - " ASN C 237 " " NAG D 1 " - " ASN C 216 " " NAG E 1 " - " ASN C 199 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 420.3 milliseconds 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2684 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 11 sheets defined 47.0% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 189 through 194 removed outlier: 3.643A pdb=" N ASN A 193 " --> pdb=" O ASP A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 222 removed outlier: 4.329A pdb=" N PHE A 219 " --> pdb=" O PRO A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 237 removed outlier: 3.564A pdb=" N LEU A 228 " --> pdb=" O LYS A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 280 removed outlier: 3.635A pdb=" N LYS A 264 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASP A 269 " --> pdb=" O GLU A 265 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU A 278 " --> pdb=" O ASN A 274 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 279 " --> pdb=" O SER A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 302 No H-bonds generated for 'chain 'A' and resid 300 through 302' Processing helix chain 'A' and resid 360 through 366 removed outlier: 3.892A pdb=" N LYS A 364 " --> pdb=" O LYS A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 400 removed outlier: 3.745A pdb=" N MET A 400 " --> pdb=" O PRO A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 424 removed outlier: 3.566A pdb=" N THR A 424 " --> pdb=" O GLY A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 473 removed outlier: 3.870A pdb=" N THR A 471 " --> pdb=" O VAL A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 481 removed outlier: 3.672A pdb=" N LEU A 480 " --> pdb=" O LEU A 477 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR A 481 " --> pdb=" O SER A 478 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 477 through 481' Processing helix chain 'A' and resid 487 through 503 removed outlier: 3.942A pdb=" N PHE A 491 " --> pdb=" O LYS A 487 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N PHE A 492 " --> pdb=" O ALA A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 506 No H-bonds generated for 'chain 'A' and resid 504 through 506' Processing helix chain 'A' and resid 508 through 526 removed outlier: 4.121A pdb=" N VAL A 512 " --> pdb=" O ILE A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 553 removed outlier: 3.715A pdb=" N LEU A 547 " --> pdb=" O THR A 544 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N VAL A 548 " --> pdb=" O SER A 545 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N GLU A 549 " --> pdb=" O SER A 546 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU A 550 " --> pdb=" O LEU A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 614 removed outlier: 3.552A pdb=" N ASP A 614 " --> pdb=" O LYS A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 631 removed outlier: 3.713A pdb=" N ALA A 631 " --> pdb=" O LEU A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 664 removed outlier: 3.514A pdb=" N GLY A 656 " --> pdb=" O SER A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 728 Processing helix chain 'A' and resid 738 through 751 removed outlier: 3.809A pdb=" N ARG A 744 " --> pdb=" O GLU A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 781 removed outlier: 3.545A pdb=" N TYR A 769 " --> pdb=" O SER A 765 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLU A 771 " --> pdb=" O GLY A 767 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N SER A 774 " --> pdb=" O GLU A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 796 Processing helix chain 'A' and resid 816 through 827 Processing helix chain 'A' and resid 838 through 849 removed outlier: 4.170A pdb=" N ALA A 842 " --> pdb=" O ARG A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 882 removed outlier: 3.576A pdb=" N ALA A 879 " --> pdb=" O GLU A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 898 through 905 removed outlier: 3.634A pdb=" N PHE A 904 " --> pdb=" O LYS A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 919 removed outlier: 3.593A pdb=" N VAL A 917 " --> pdb=" O TYR A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 932 through 943 removed outlier: 3.700A pdb=" N VAL A 938 " --> pdb=" O LYS A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 965 removed outlier: 3.614A pdb=" N ILE A 962 " --> pdb=" O ASP A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 982 removed outlier: 3.884A pdb=" N ARG A 981 " --> pdb=" O MET A 977 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER A 982 " --> pdb=" O GLN A 978 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 977 through 982' Processing helix chain 'A' and resid 992 through 997 Processing helix chain 'A' and resid 998 through 1024 removed outlier: 3.559A pdb=" N SER A1002 " --> pdb=" O LEU A 998 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN A1019 " --> pdb=" O SER A1015 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU A1022 " --> pdb=" O LYS A1018 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR A1023 " --> pdb=" O ASN A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1029 Processing helix chain 'A' and resid 1042 through 1048 removed outlier: 3.681A pdb=" N SER A1047 " --> pdb=" O SER A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1064 Processing helix chain 'A' and resid 1069 through 1076 removed outlier: 3.617A pdb=" N GLU A1074 " --> pdb=" O SER A1070 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG A1075 " --> pdb=" O ARG A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1086 removed outlier: 4.361A pdb=" N GLY A1083 " --> pdb=" O LEU A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1116 removed outlier: 3.566A pdb=" N GLY A1096 " --> pdb=" O TYR A1092 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A1114 " --> pdb=" O ILE A1110 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE A1115 " --> pdb=" O GLY A1111 " (cutoff:3.500A) Processing helix chain 'A' and resid 1130 through 1154 removed outlier: 4.251A pdb=" N THR A1137 " --> pdb=" O SER A1133 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU A1152 " --> pdb=" O GLY A1148 " (cutoff:3.500A) Processing helix chain 'A' and resid 1158 through 1165 removed outlier: 3.557A pdb=" N LEU A1162 " --> pdb=" O THR A1158 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE A1163 " --> pdb=" O LYS A1159 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1183 removed outlier: 3.768A pdb=" N LEU A1169 " --> pdb=" O ILE A1165 " (cutoff:3.500A) Proline residue: A1177 - end of helix removed outlier: 3.573A pdb=" N SER A1181 " --> pdb=" O PRO A1177 " (cutoff:3.500A) Processing helix chain 'A' and resid 1184 through 1187 Processing helix chain 'A' and resid 1189 through 1193 removed outlier: 3.970A pdb=" N TYR A1193 " --> pdb=" O ARG A1190 " (cutoff:3.500A) Processing helix chain 'A' and resid 1194 through 1201 removed outlier: 3.948A pdb=" N HIS A1198 " --> pdb=" O GLY A1194 " (cutoff:3.500A) Processing helix chain 'A' and resid 1204 through 1230 removed outlier: 3.640A pdb=" N LEU A1209 " --> pdb=" O PHE A1205 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ILE A1210 " --> pdb=" O TRP A1206 " (cutoff:3.500A) Proline residue: A1213 - end of helix removed outlier: 5.013A pdb=" N ARG A1219 " --> pdb=" O PHE A1215 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N ASP A1220 " --> pdb=" O ALA A1216 " (cutoff:3.500A) Processing helix chain 'A' and resid 1233 through 1245 removed outlier: 3.755A pdb=" N VAL A1237 " --> pdb=" O GLU A1233 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE A1238 " --> pdb=" O THR A1234 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU A1240 " --> pdb=" O HIS A1236 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 44 Processing helix chain 'C' and resid 45 through 69 Proline residue: C 58 - end of helix Processing helix chain 'C' and resid 79 through 84 removed outlier: 3.626A pdb=" N ALA C 84 " --> pdb=" O CYS C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 155 removed outlier: 4.027A pdb=" N GLN C 155 " --> pdb=" O ARG C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 164 removed outlier: 3.757A pdb=" N LEU C 163 " --> pdb=" O THR C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 177 removed outlier: 3.670A pdb=" N CYS C 176 " --> pdb=" O ASP C 173 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER C 177 " --> pdb=" O THR C 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 173 through 177' Processing helix chain 'C' and resid 181 through 185 removed outlier: 4.100A pdb=" N ASP C 184 " --> pdb=" O SER C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 196 removed outlier: 3.754A pdb=" N ASN C 195 " --> pdb=" O GLY C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 231 Processing helix chain 'C' and resid 244 through 248 Processing helix chain 'C' and resid 266 through 274 removed outlier: 3.527A pdb=" N GLN C 270 " --> pdb=" O TRP C 266 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG C 274 " --> pdb=" O GLN C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 357 removed outlier: 3.604A pdb=" N TYR C 336 " --> pdb=" O LEU C 332 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU C 337 " --> pdb=" O GLY C 333 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU C 351 " --> pdb=" O GLY C 347 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 183 through 186 removed outlier: 3.611A pdb=" N LYS A 369 " --> pdb=" O THR A 387 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET A 386 " --> pdb=" O ILE A 393 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 283 through 288 removed outlier: 3.700A pdb=" N ASP A 293 " --> pdb=" O SER A 288 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 307 through 311 removed outlier: 6.921A pdb=" N TRP A 412 " --> pdb=" O SER A 325 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N SER A 325 " --> pdb=" O TRP A 412 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N PHE A 414 " --> pdb=" O LEU A 323 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ASP A 319 " --> pdb=" O ILE A 418 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 532 through 533 removed outlier: 3.805A pdb=" N TYR A 533 " --> pdb=" O THR A 538 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N THR A 538 " --> pdb=" O TYR A 533 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 541 through 542 removed outlier: 6.825A pdb=" N LEU A 949 " --> pdb=" O VAL A 967 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N VAL A 969 " --> pdb=" O LEU A 949 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ALA A 951 " --> pdb=" O VAL A 969 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ILE A 971 " --> pdb=" O ALA A 951 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLY A 953 " --> pdb=" O ILE A 971 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ILE A 557 " --> pdb=" O TRP A 832 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LEU A 834 " --> pdb=" O ILE A 557 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N SER A 559 " --> pdb=" O LEU A 834 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE A 831 " --> pdb=" O VAL A 924 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N CYS A 926 " --> pdb=" O ILE A 831 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N VAL A 833 " --> pdb=" O CYS A 926 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU A 893 " --> pdb=" O ALA A 923 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N ILE A 925 " --> pdb=" O LEU A 893 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU A 895 " --> pdb=" O ILE A 925 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 580 through 582 removed outlier: 7.161A pdb=" N ALA A 808 " --> pdb=" O LYS A 573 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N CYS A 575 " --> pdb=" O ALA A 806 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ALA A 806 " --> pdb=" O CYS A 575 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ILE A 577 " --> pdb=" O ILE A 804 " (cutoff:3.500A) removed outlier: 8.738A pdb=" N ILE A 804 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N LEU A 803 " --> pdb=" O MET A 761 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N MET A 761 " --> pdb=" O LEU A 803 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY A 805 " --> pdb=" O LEU A 759 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A 757 " --> pdb=" O THR A 807 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ILE A 716 " --> pdb=" O ILE A 764 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER A 706 " --> pdb=" O CYS A 696 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ARG A 710 " --> pdb=" O LEU A 692 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N LEU A 692 " --> pdb=" O ARG A 710 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N SER A 676 " --> pdb=" O ARG A 672 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ARG A 672 " --> pdb=" O SER A 676 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N THR A 678 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A 670 " --> pdb=" O THR A 678 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 637 through 640 removed outlier: 3.815A pdb=" N ILE A 637 " --> pdb=" O GLN A 649 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 97 through 100 removed outlier: 6.504A pdb=" N TYR C 141 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N LEU C 284 " --> pdb=" O TYR C 141 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE C 143 " --> pdb=" O TYR C 282 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N TYR C 282 " --> pdb=" O ILE C 143 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 90 through 91 removed outlier: 3.735A pdb=" N THR C 201 " --> pdb=" O GLU C 303 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 186 through 187 removed outlier: 6.415A pdb=" N ILE C 186 " --> pdb=" O VAL C 242 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 205 through 206 474 hydrogen bonds defined for protein. 1338 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: 1.67 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1870 1.31 - 1.44: 3233 1.44 - 1.56: 6673 1.56 - 1.69: 8 1.69 - 1.82: 81 Bond restraints: 11865 Sorted by residual: bond pdb=" C3' ADP A1504 " pdb=" C4' ADP A1504 " ideal model delta sigma weight residual 1.524 1.277 0.247 2.00e-02 2.50e+03 1.53e+02 bond pdb=" C1' ADP A1504 " pdb=" C2' ADP A1504 " ideal model delta sigma weight residual 1.524 1.285 0.239 2.00e-02 2.50e+03 1.43e+02 bond pdb=" C6 ADP A1504 " pdb=" N6 ADP A1504 " ideal model delta sigma weight residual 1.355 1.492 -0.137 2.00e-02 2.50e+03 4.70e+01 bond pdb=" C4' ADP A1504 " pdb=" O4' ADP A1504 " ideal model delta sigma weight residual 1.426 1.562 -0.136 2.00e-02 2.50e+03 4.60e+01 bond pdb=" C2' ADP A1504 " pdb=" C3' ADP A1504 " ideal model delta sigma weight residual 1.524 1.654 -0.130 2.00e-02 2.50e+03 4.21e+01 ... (remaining 11860 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.03: 16085 14.03 - 28.06: 4 28.06 - 42.08: 0 42.08 - 56.11: 0 56.11 - 70.14: 2 Bond angle restraints: 16091 Sorted by residual: angle pdb=" F1 ALF A1502 " pdb="AL ALF A1502 " pdb=" F2 ALF A1502 " ideal model delta sigma weight residual 108.68 178.82 -70.14 3.00e+00 1.11e-01 5.47e+02 angle pdb=" F3 ALF A1502 " pdb="AL ALF A1502 " pdb=" F4 ALF A1502 " ideal model delta sigma weight residual 109.63 179.54 -69.91 3.00e+00 1.11e-01 5.43e+02 angle pdb=" F2 ALF A1502 " pdb="AL ALF A1502 " pdb=" F4 ALF A1502 " ideal model delta sigma weight residual 110.21 89.84 20.37 3.00e+00 1.11e-01 4.61e+01 angle pdb=" F1 ALF A1502 " pdb="AL ALF A1502 " pdb=" F4 ALF A1502 " ideal model delta sigma weight residual 109.02 89.56 19.46 3.00e+00 1.11e-01 4.21e+01 angle pdb=" F2 ALF A1502 " pdb="AL ALF A1502 " pdb=" F3 ALF A1502 " ideal model delta sigma weight residual 109.59 90.14 19.45 3.00e+00 1.11e-01 4.20e+01 ... (remaining 16086 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.16: 6870 26.16 - 52.32: 128 52.32 - 78.48: 23 78.48 - 104.63: 12 104.63 - 130.79: 2 Dihedral angle restraints: 7035 sinusoidal: 2872 harmonic: 4163 Sorted by residual: dihedral pdb=" C16 2Y5 A1505 " pdb=" C17 2Y5 A1505 " pdb=" C18 2Y5 A1505 " pdb=" C19 2Y5 A1505 " ideal model delta sinusoidal sigma weight residual 249.33 118.54 130.79 1 3.00e+01 1.11e-03 1.76e+01 dihedral pdb=" C2' ADP A1504 " pdb=" C1' ADP A1504 " pdb=" N9 ADP A1504 " pdb=" C4 ADP A1504 " ideal model delta sinusoidal sigma weight residual 91.55 164.92 -73.38 1 2.00e+01 2.50e-03 1.71e+01 dihedral pdb=" C10 2Y5 A1505 " pdb=" C12 2Y5 A1505 " pdb=" C13 2Y5 A1505 " pdb=" C14 2Y5 A1505 " ideal model delta sinusoidal sigma weight residual 182.96 76.75 106.21 1 3.00e+01 1.11e-03 1.36e+01 ... (remaining 7032 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.996: 1843 0.996 - 1.992: 0 1.992 - 2.988: 0 2.988 - 3.984: 0 3.984 - 4.980: 1 Chirality restraints: 1844 Sorted by residual: chirality pdb=" C1 2Y5 A1505 " pdb=" C2 2Y5 A1505 " pdb=" C6 2Y5 A1505 " pdb=" O1 2Y5 A1505 " both_signs ideal model delta sigma weight residual False -2.53 2.45 -4.98 2.00e-01 2.50e+01 6.20e+02 chirality pdb=" C5 BMA E 4 " pdb=" C4 BMA E 4 " pdb=" C6 BMA E 4 " pdb=" O5 BMA E 4 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.81e+00 ... (remaining 1841 not shown) Planarity restraints: 2007 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP A1056 " 0.029 5.00e-02 4.00e+02 4.28e-02 2.93e+00 pdb=" N PRO A1057 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A1057 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A1057 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A1183 " -0.024 5.00e-02 4.00e+02 3.68e-02 2.17e+00 pdb=" N PRO A1184 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A1184 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A1184 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A1057 " -0.023 5.00e-02 4.00e+02 3.50e-02 1.96e+00 pdb=" N PRO A1058 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO A1058 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A1058 " -0.020 5.00e-02 4.00e+02 ... (remaining 2004 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.30: 17 2.30 - 2.95: 5101 2.95 - 3.60: 15948 3.60 - 4.25: 26716 4.25 - 4.90: 44687 Nonbonded interactions: 92469 Sorted by model distance: nonbonded pdb=" OD1 ASP A 560 " pdb=" F1 ALF A1502 " model vdw 1.656 2.990 nonbonded pdb=" OD1 ASP A 560 " pdb="AL ALF A1502 " model vdw 1.714 2.760 nonbonded pdb=" F4 ALF A1502 " pdb="MG MG A1503 " model vdw 1.726 2.120 nonbonded pdb=" O THR A 562 " pdb="MG MG A1503 " model vdw 2.030 2.170 nonbonded pdb="MG MG A1503 " pdb=" O HOH A1601 " model vdw 2.031 2.170 ... (remaining 92464 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.920 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.670 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:5.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 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 : 0.008 0.605 11877 Z= 0.626 Angle : 1.058 70.140 16122 Z= 0.411 Chirality : 0.123 4.980 1844 Planarity : 0.003 0.043 2003 Dihedral : 11.601 130.792 4345 Min Nonbonded Distance : 1.656 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.19 % Allowed : 4.53 % Favored : 94.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.15 (0.18), residues: 1415 helix: -3.56 (0.13), residues: 564 sheet: -2.10 (0.31), residues: 219 loop : -2.01 (0.22), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 182 TYR 0.012 0.001 TYR C 141 PHE 0.009 0.001 PHE A1205 TRP 0.007 0.001 TRP C 36 HIS 0.003 0.000 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00560 / 0.28 (11865) covalent geometry : angle 1.05738 / 0.41 (16091) SS BOND : bond 0.11583 / 8.26 ( 2) SS BOND : angle 1.20078 / 0.67 ( 4) hydrogen bonds : bond 0.28235 / 17.91 ( 474) hydrogen bonds : angle 8.97800 / 6.21 ( 1338) Misc. bond : bond 0.60503 / 40.34 ( 1) link_BETA1-3 : bond 0.00379 / 0.25 ( 1) link_BETA1-3 : angle 1.28487 / 0.78 ( 3) link_BETA1-4 : bond 0.00301 / 0.20 ( 4) link_BETA1-4 : angle 1.23387 / 0.80 ( 12) link_NAG-ASN : bond 0.00283 / 0.18 ( 4) link_NAG-ASN : angle 1.29957 / 0.83 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 225 time to evaluate : 0.383 Fit side-chains revert: symmetry clash REVERT: A 277 LYS cc_start: 0.7389 (OUTLIER) cc_final: 0.6941 (tptp) REVERT: A 322 ILE cc_start: 0.7118 (mp) cc_final: 0.6525 (tt) REVERT: A 535 LYS cc_start: 0.8066 (tttt) cc_final: 0.7574 (ttmm) REVERT: A 678 THR cc_start: 0.6641 (p) cc_final: 0.6327 (p) REVERT: A 761 MET cc_start: 0.7321 (ptm) cc_final: 0.6881 (ptt) REVERT: A 790 LEU cc_start: 0.6816 (pp) cc_final: 0.6448 (mt) REVERT: A 898 ASP cc_start: 0.7811 (p0) cc_final: 0.7565 (p0) REVERT: A 1042 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.6806 (tm-30) outliers start: 15 outliers final: 3 residues processed: 236 average time/residue: 0.5099 time to fit residues: 129.9905 Evaluate side-chains 118 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 113 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 560 ASP Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 1042 GLU Chi-restraints excluded: chain C residue 260 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.2980 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 193 ASN A 201 ASN A 504 ASN ** A 888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1084 GLN C 107 ASN C 116 ASN C 155 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.144423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.108747 restraints weight = 15097.999| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.57 r_work: 0.3453 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.125 11877 Z= 0.180 Angle : 0.850 31.560 16122 Z= 0.383 Chirality : 0.046 0.268 1844 Planarity : 0.005 0.050 2003 Dihedral : 9.802 126.438 1635 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.88 % Favored : 95.05 % Rotamer: Outliers : 3.66 % Allowed : 11.69 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.55 (0.20), residues: 1415 helix: -1.53 (0.19), residues: 579 sheet: -1.70 (0.32), residues: 225 loop : -1.68 (0.24), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 32 TYR 0.019 0.002 TYR A 769 PHE 0.022 0.002 PHE C 89 TRP 0.012 0.001 TRP A1056 HIS 0.015 0.001 HIS A 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.18 (11865) covalent geometry : angle 0.84764 / 0.38 (16091) SS BOND : bond 0.01157 / 0.83 ( 2) SS BOND : angle 1.45076 / 0.83 ( 4) hydrogen bonds : bond 0.06106 / 3.91 ( 474) hydrogen bonds : angle 5.31607 / 3.69 ( 1338) Misc. bond : bond 0.00209 / 0.14 ( 1) link_BETA1-3 : bond 0.00641 / 0.43 ( 1) link_BETA1-3 : angle 1.07557 / 0.64 ( 3) link_BETA1-4 : bond 0.00416 / 0.24 ( 4) link_BETA1-4 : angle 1.60822 / 1.02 ( 12) link_NAG-ASN : bond 0.00456 / 0.30 ( 4) link_NAG-ASN : angle 1.83022 / 1.31 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 117 time to evaluate : 0.340 Fit side-chains REVERT: A 269 ASP cc_start: 0.5581 (OUTLIER) cc_final: 0.5318 (t0) REVERT: A 277 LYS cc_start: 0.7038 (OUTLIER) cc_final: 0.6560 (tptp) REVERT: A 400 MET cc_start: 0.7101 (tpt) cc_final: 0.6587 (tpt) REVERT: A 418 ILE cc_start: 0.5593 (OUTLIER) cc_final: 0.5138 (mp) REVERT: A 535 LYS cc_start: 0.7931 (tttt) cc_final: 0.7284 (ttmm) REVERT: A 555 GLU cc_start: 0.7030 (mt-10) cc_final: 0.6262 (pm20) REVERT: A 687 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7548 (mm-30) REVERT: A 726 VAL cc_start: 0.8028 (OUTLIER) cc_final: 0.7811 (p) REVERT: A 744 ARG cc_start: 0.5744 (tmt-80) cc_final: 0.5540 (tpt-90) REVERT: A 761 MET cc_start: 0.7367 (ptm) cc_final: 0.6630 (ptt) REVERT: A 864 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.6983 (tp30) REVERT: A 871 ARG cc_start: 0.6784 (mtm110) cc_final: 0.6355 (ttm110) REVERT: A 890 MET cc_start: 0.6022 (mmt) cc_final: 0.5517 (ptt) REVERT: A 1042 GLU cc_start: 0.6609 (OUTLIER) cc_final: 0.6381 (tm-30) REVERT: C 115 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7038 (tm-30) REVERT: C 213 GLU cc_start: 0.7917 (mp0) cc_final: 0.7699 (mp0) REVERT: C 258 GLU cc_start: 0.8170 (mp0) cc_final: 0.7961 (mp0) outliers start: 46 outliers final: 17 residues processed: 156 average time/residue: 0.4263 time to fit residues: 73.2851 Evaluate side-chains 114 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 89 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 864 GLU Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1042 GLU Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1165 ILE Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 330 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 2 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 chunk 42 optimal weight: 0.9980 chunk 70 optimal weight: 0.0470 chunk 82 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 58 optimal weight: 4.9990 chunk 50 optimal weight: 9.9990 chunk 84 optimal weight: 3.9990 overall best weight: 0.9480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 ASN C 155 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.145146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.109557 restraints weight = 15161.700| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 2.58 r_work: 0.3473 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 11877 Z= 0.129 Angle : 0.789 30.305 16122 Z= 0.344 Chirality : 0.044 0.267 1844 Planarity : 0.004 0.038 2003 Dihedral : 9.298 123.749 1631 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.52 % Favored : 95.41 % Rotamer: Outliers : 3.50 % Allowed : 12.49 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.21), residues: 1415 helix: -0.54 (0.21), residues: 579 sheet: -1.26 (0.34), residues: 224 loop : -1.51 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 603 TYR 0.019 0.001 TYR A 382 PHE 0.013 0.001 PHE A1205 TRP 0.008 0.001 TRP A1134 HIS 0.014 0.001 HIS A 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (11865) covalent geometry : angle 0.78765 / 0.34 (16091) SS BOND : bond 0.00398 / 0.28 ( 2) SS BOND : angle 0.97834 / 0.83 ( 4) hydrogen bonds : bond 0.04580 / 2.94 ( 474) hydrogen bonds : angle 4.70521 / 3.30 ( 1338) Misc. bond : bond 0.00132 / 0.09 ( 1) link_BETA1-3 : bond 0.00665 / 0.44 ( 1) link_BETA1-3 : angle 1.27314 / 0.78 ( 3) link_BETA1-4 : bond 0.00322 / 0.21 ( 4) link_BETA1-4 : angle 1.39340 / 0.85 ( 12) link_NAG-ASN : bond 0.00339 / 0.22 ( 4) link_NAG-ASN : angle 1.55568 / 1.12 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 103 time to evaluate : 0.460 Fit side-chains REVERT: A 269 ASP cc_start: 0.5611 (OUTLIER) cc_final: 0.5368 (t0) REVERT: A 277 LYS cc_start: 0.7002 (OUTLIER) cc_final: 0.6501 (tptp) REVERT: A 418 ILE cc_start: 0.5579 (OUTLIER) cc_final: 0.5173 (mp) REVERT: A 437 ARG cc_start: 0.7606 (mtm180) cc_final: 0.7271 (mtp-110) REVERT: A 504 ASN cc_start: 0.7858 (t0) cc_final: 0.7599 (t0) REVERT: A 535 LYS cc_start: 0.7877 (tttt) cc_final: 0.7220 (ttmm) REVERT: A 555 GLU cc_start: 0.6963 (mt-10) cc_final: 0.6333 (pm20) REVERT: A 687 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7619 (mm-30) REVERT: A 761 MET cc_start: 0.7360 (ptm) cc_final: 0.6660 (ptt) REVERT: A 862 ASN cc_start: 0.7413 (OUTLIER) cc_final: 0.7085 (m110) REVERT: A 864 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.6691 (mp0) REVERT: A 871 ARG cc_start: 0.6754 (mtm110) cc_final: 0.6449 (ttm110) REVERT: A 890 MET cc_start: 0.5696 (mmt) cc_final: 0.5414 (ptt) REVERT: A 987 VAL cc_start: 0.8291 (t) cc_final: 0.7986 (p) REVERT: A 1190 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.6747 (mtp85) REVERT: C 115 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7083 (tm-30) REVERT: C 184 ASP cc_start: 0.8051 (m-30) cc_final: 0.7254 (t0) REVERT: C 213 GLU cc_start: 0.7751 (mp0) cc_final: 0.7452 (mp0) REVERT: C 258 GLU cc_start: 0.8161 (mp0) cc_final: 0.7952 (mp0) outliers start: 44 outliers final: 18 residues processed: 142 average time/residue: 0.4254 time to fit residues: 66.4471 Evaluate side-chains 115 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 89 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 862 ASN Chi-restraints excluded: chain A residue 864 GLU Chi-restraints excluded: chain A residue 978 GLN Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1107 ILE Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1190 ARG Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 352 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 64 optimal weight: 4.9990 chunk 99 optimal weight: 0.7980 chunk 109 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 chunk 58 optimal weight: 8.9990 chunk 53 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 825 GLN ** A1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 ASN C 155 GLN C 161 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.145754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.115592 restraints weight = 15319.841| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 2.02 r_work: 0.3539 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3411 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.124 11877 Z= 0.194 Angle : 0.857 30.769 16122 Z= 0.377 Chirality : 0.047 0.277 1844 Planarity : 0.004 0.045 2003 Dihedral : 9.037 118.406 1628 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.30 % Favored : 94.63 % Rotamer: Outliers : 4.38 % Allowed : 13.37 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.22), residues: 1415 helix: -0.54 (0.21), residues: 585 sheet: -1.21 (0.35), residues: 226 loop : -1.56 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 744 TYR 0.019 0.002 TYR A 382 PHE 0.019 0.002 PHE C 269 TRP 0.011 0.001 TRP C 36 HIS 0.013 0.001 HIS A 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.19 (11865) covalent geometry : angle 0.85418 / 0.38 (16091) SS BOND : bond 0.01360 / 0.97 ( 2) SS BOND : angle 1.29734 / 1.09 ( 4) hydrogen bonds : bond 0.04918 / 3.13 ( 474) hydrogen bonds : angle 4.69848 / 3.31 ( 1338) Misc. bond : bond 0.00141 / 0.09 ( 1) link_BETA1-3 : bond 0.00568 / 0.38 ( 1) link_BETA1-3 : angle 1.13318 / 0.61 ( 3) link_BETA1-4 : bond 0.00562 / 0.30 ( 4) link_BETA1-4 : angle 1.65779 / 1.10 ( 12) link_NAG-ASN : bond 0.00513 / 0.35 ( 4) link_NAG-ASN : angle 2.25638 / 1.64 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 100 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 TYR cc_start: 0.6032 (m-10) cc_final: 0.5396 (m-10) REVERT: A 265 GLU cc_start: 0.7468 (mm-30) cc_final: 0.7154 (mm-30) REVERT: A 269 ASP cc_start: 0.6420 (OUTLIER) cc_final: 0.6158 (t0) REVERT: A 277 LYS cc_start: 0.7404 (OUTLIER) cc_final: 0.6933 (tptp) REVERT: A 386 MET cc_start: 0.6415 (ttp) cc_final: 0.6179 (ttm) REVERT: A 400 MET cc_start: 0.7677 (tpt) cc_final: 0.6920 (tpt) REVERT: A 418 ILE cc_start: 0.5938 (OUTLIER) cc_final: 0.5328 (mp) REVERT: A 437 ARG cc_start: 0.7603 (mtm180) cc_final: 0.7352 (mtp-110) REVERT: A 535 LYS cc_start: 0.8206 (tttt) cc_final: 0.7661 (ttmm) REVERT: A 555 GLU cc_start: 0.7263 (mt-10) cc_final: 0.6130 (tt0) REVERT: A 687 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7775 (mm-30) REVERT: A 726 VAL cc_start: 0.8651 (p) cc_final: 0.8445 (p) REVERT: A 864 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.6929 (mp0) REVERT: A 871 ARG cc_start: 0.7169 (mtm110) cc_final: 0.6920 (ttm110) REVERT: A 978 GLN cc_start: 0.7894 (OUTLIER) cc_final: 0.7562 (mt0) REVERT: A 1190 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7015 (mtp85) REVERT: C 168 LYS cc_start: 0.8462 (mptp) cc_final: 0.8021 (mppt) REVERT: C 184 ASP cc_start: 0.7968 (m-30) cc_final: 0.7480 (t0) REVERT: C 213 GLU cc_start: 0.7999 (mp0) cc_final: 0.7746 (mp0) REVERT: C 361 MET cc_start: 0.5728 (ppp) cc_final: 0.5408 (mtm) outliers start: 55 outliers final: 23 residues processed: 148 average time/residue: 0.4555 time to fit residues: 74.5505 Evaluate side-chains 121 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 91 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 220 GLN Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 864 GLU Chi-restraints excluded: chain A residue 978 GLN Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1107 ILE Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1190 ARG Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain C residue 352 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 60 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 chunk 134 optimal weight: 0.0050 chunk 118 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 504 ASN C 116 ASN C 155 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.145136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.110160 restraints weight = 15092.422| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.49 r_work: 0.3474 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 11877 Z= 0.112 Angle : 0.779 29.808 16122 Z= 0.335 Chirality : 0.043 0.271 1844 Planarity : 0.004 0.041 2003 Dihedral : 8.634 115.694 1628 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.60 % Favored : 96.33 % Rotamer: Outliers : 3.18 % Allowed : 15.35 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.22), residues: 1415 helix: -0.01 (0.22), residues: 583 sheet: -0.95 (0.36), residues: 216 loop : -1.46 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 603 TYR 0.016 0.001 TYR A1192 PHE 0.012 0.001 PHE A1205 TRP 0.013 0.001 TRP A 299 HIS 0.010 0.001 HIS A 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (11865) covalent geometry : angle 0.77757 / 0.33 (16091) SS BOND : bond 0.01037 / 0.74 ( 2) SS BOND : angle 0.97549 / 0.84 ( 4) hydrogen bonds : bond 0.03941 / 2.53 ( 474) hydrogen bonds : angle 4.42287 / 3.12 ( 1338) Misc. bond : bond 0.00124 / 0.08 ( 1) link_BETA1-3 : bond 0.00633 / 0.42 ( 1) link_BETA1-3 : angle 1.19449 / 0.74 ( 3) link_BETA1-4 : bond 0.00296 / 0.20 ( 4) link_BETA1-4 : angle 1.27845 / 0.79 ( 12) link_NAG-ASN : bond 0.00299 / 0.20 ( 4) link_NAG-ASN : angle 1.62299 / 1.15 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 96 time to evaluate : 0.447 Fit side-chains revert: symmetry clash REVERT: A 208 TYR cc_start: 0.5481 (m-10) cc_final: 0.4819 (m-10) REVERT: A 265 GLU cc_start: 0.7191 (mm-30) cc_final: 0.6832 (mm-30) REVERT: A 277 LYS cc_start: 0.6956 (OUTLIER) cc_final: 0.6470 (tptp) REVERT: A 400 MET cc_start: 0.7065 (tpt) cc_final: 0.6422 (tpt) REVERT: A 535 LYS cc_start: 0.7908 (tttt) cc_final: 0.7234 (ttmm) REVERT: A 555 GLU cc_start: 0.7068 (mt-10) cc_final: 0.5796 (tt0) REVERT: A 761 MET cc_start: 0.7421 (ptm) cc_final: 0.6713 (ptt) REVERT: A 864 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.6817 (mp0) REVERT: A 987 VAL cc_start: 0.8303 (t) cc_final: 0.8006 (p) REVERT: C 114 THR cc_start: 0.7391 (m) cc_final: 0.7054 (p) REVERT: C 115 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7474 (tm-30) REVERT: C 132 ASP cc_start: 0.7887 (OUTLIER) cc_final: 0.7362 (m-30) REVERT: C 184 ASP cc_start: 0.8052 (m-30) cc_final: 0.7290 (t0) REVERT: C 213 GLU cc_start: 0.7730 (mp0) cc_final: 0.7373 (mp0) REVERT: C 259 ASN cc_start: 0.6297 (OUTLIER) cc_final: 0.5636 (p0) REVERT: C 308 ILE cc_start: 0.7244 (OUTLIER) cc_final: 0.6712 (mt) outliers start: 40 outliers final: 15 residues processed: 130 average time/residue: 0.4421 time to fit residues: 63.2031 Evaluate side-chains 113 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 220 GLN Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 864 GLU Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1237 VAL Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 259 ASN Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 352 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 129 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 19 optimal weight: 8.9990 chunk 68 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 chunk 136 optimal weight: 5.9990 chunk 138 optimal weight: 3.9990 chunk 99 optimal weight: 0.5980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 116 ASN C 155 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.144887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.111732 restraints weight = 15035.525| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 2.28 r_work: 0.3485 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 11877 Z= 0.141 Angle : 0.809 30.340 16122 Z= 0.348 Chirality : 0.045 0.269 1844 Planarity : 0.004 0.046 2003 Dihedral : 8.511 109.844 1628 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.52 % Favored : 95.41 % Rotamer: Outliers : 3.18 % Allowed : 15.83 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.22), residues: 1415 helix: 0.05 (0.22), residues: 583 sheet: -0.90 (0.35), residues: 215 loop : -1.43 (0.24), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 359 TYR 0.022 0.001 TYR A1023 PHE 0.015 0.001 PHE A1205 TRP 0.012 0.001 TRP A 299 HIS 0.010 0.001 HIS A 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.14 (11865) covalent geometry : angle 0.80684 / 0.35 (16091) SS BOND : bond 0.01140 / 0.81 ( 2) SS BOND : angle 1.36065 / 0.77 ( 4) hydrogen bonds : bond 0.04102 / 2.62 ( 474) hydrogen bonds : angle 4.39746 / 3.11 ( 1338) Misc. bond : bond 0.00113 / 0.08 ( 1) link_BETA1-3 : bond 0.00586 / 0.39 ( 1) link_BETA1-3 : angle 1.06426 / 0.62 ( 3) link_BETA1-4 : bond 0.00376 / 0.23 ( 4) link_BETA1-4 : angle 1.42162 / 0.92 ( 12) link_NAG-ASN : bond 0.00382 / 0.26 ( 4) link_NAG-ASN : angle 1.87542 / 1.37 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 101 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: A 208 TYR cc_start: 0.5731 (m-10) cc_final: 0.4937 (m-10) REVERT: A 265 GLU cc_start: 0.7308 (mm-30) cc_final: 0.6994 (mm-30) REVERT: A 277 LYS cc_start: 0.7143 (OUTLIER) cc_final: 0.6674 (tptp) REVERT: A 400 MET cc_start: 0.7263 (tpt) cc_final: 0.6728 (tpt) REVERT: A 418 ILE cc_start: 0.5762 (OUTLIER) cc_final: 0.5202 (mp) REVERT: A 420 THR cc_start: 0.6288 (p) cc_final: 0.5585 (t) REVERT: A 437 ARG cc_start: 0.7622 (mtp-110) cc_final: 0.7378 (mtp-110) REVERT: A 535 LYS cc_start: 0.8035 (tttt) cc_final: 0.7365 (ttmm) REVERT: A 555 GLU cc_start: 0.7273 (mt-10) cc_final: 0.5991 (tt0) REVERT: A 687 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7973 (mm-30) REVERT: A 726 VAL cc_start: 0.8318 (OUTLIER) cc_final: 0.8110 (p) REVERT: A 761 MET cc_start: 0.7685 (ptm) cc_final: 0.7087 (ptt) REVERT: A 987 VAL cc_start: 0.8600 (t) cc_final: 0.8349 (p) REVERT: C 32 ARG cc_start: 0.7962 (ttp-110) cc_final: 0.7743 (ttp-110) REVERT: C 132 ASP cc_start: 0.8065 (OUTLIER) cc_final: 0.7563 (m-30) REVERT: C 184 ASP cc_start: 0.8085 (m-30) cc_final: 0.7409 (t0) REVERT: C 213 GLU cc_start: 0.7842 (mp0) cc_final: 0.7487 (mp0) REVERT: C 259 ASN cc_start: 0.6252 (OUTLIER) cc_final: 0.5852 (p0) outliers start: 40 outliers final: 18 residues processed: 133 average time/residue: 0.4079 time to fit residues: 60.0206 Evaluate side-chains 118 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 94 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1237 VAL Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 259 ASN Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 352 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 41 optimal weight: 20.0000 chunk 129 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 15 optimal weight: 8.9990 chunk 128 optimal weight: 0.0270 chunk 136 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 overall best weight: 1.0040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 116 ASN C 155 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.147535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.113628 restraints weight = 15096.764| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 2.26 r_work: 0.3556 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 11877 Z= 0.127 Angle : 0.798 30.189 16122 Z= 0.341 Chirality : 0.044 0.272 1844 Planarity : 0.004 0.040 2003 Dihedral : 8.226 104.207 1628 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.89 % Favored : 96.04 % Rotamer: Outliers : 3.18 % Allowed : 16.07 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.22), residues: 1415 helix: 0.18 (0.23), residues: 577 sheet: -0.83 (0.35), residues: 216 loop : -1.37 (0.24), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 603 TYR 0.020 0.001 TYR A1023 PHE 0.013 0.001 PHE A1205 TRP 0.021 0.001 TRP A 299 HIS 0.008 0.001 HIS A 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (11865) covalent geometry : angle 0.79567 / 0.34 (16091) SS BOND : bond 0.01230 / 0.88 ( 2) SS BOND : angle 1.19679 / 0.89 ( 4) hydrogen bonds : bond 0.03915 / 2.51 ( 474) hydrogen bonds : angle 4.32673 / 3.06 ( 1338) Misc. bond : bond 0.00104 / 0.07 ( 1) link_BETA1-3 : bond 0.00596 / 0.40 ( 1) link_BETA1-3 : angle 1.11553 / 0.66 ( 3) link_BETA1-4 : bond 0.00321 / 0.20 ( 4) link_BETA1-4 : angle 1.33545 / 0.85 ( 12) link_NAG-ASN : bond 0.00337 / 0.23 ( 4) link_NAG-ASN : angle 1.76634 / 1.28 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 100 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: A 265 GLU cc_start: 0.7446 (mm-30) cc_final: 0.7205 (mm-30) REVERT: A 277 LYS cc_start: 0.7344 (OUTLIER) cc_final: 0.6894 (tptp) REVERT: A 366 MET cc_start: 0.6778 (tpt) cc_final: 0.6499 (tpt) REVERT: A 394 PRO cc_start: 0.8466 (Cg_exo) cc_final: 0.8263 (Cg_endo) REVERT: A 420 THR cc_start: 0.6563 (p) cc_final: 0.5929 (t) REVERT: A 437 ARG cc_start: 0.7669 (mtp-110) cc_final: 0.7468 (mtp-110) REVERT: A 535 LYS cc_start: 0.8314 (tttt) cc_final: 0.7770 (ttmm) REVERT: A 555 GLU cc_start: 0.7175 (mt-10) cc_final: 0.6031 (tt0) REVERT: A 761 MET cc_start: 0.7958 (ptm) cc_final: 0.7541 (ptt) REVERT: A 943 ARG cc_start: 0.7687 (OUTLIER) cc_final: 0.7234 (ttm170) REVERT: A 1190 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.6972 (mtp85) REVERT: C 114 THR cc_start: 0.8007 (m) cc_final: 0.7718 (p) REVERT: C 115 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7852 (tm-30) REVERT: C 132 ASP cc_start: 0.8261 (OUTLIER) cc_final: 0.7760 (m-30) REVERT: C 184 ASP cc_start: 0.8022 (m-30) cc_final: 0.7522 (t0) REVERT: C 213 GLU cc_start: 0.8003 (mp0) cc_final: 0.7708 (mp0) REVERT: C 259 ASN cc_start: 0.6416 (OUTLIER) cc_final: 0.6207 (p0) REVERT: C 308 ILE cc_start: 0.7473 (OUTLIER) cc_final: 0.7123 (mt) outliers start: 40 outliers final: 21 residues processed: 134 average time/residue: 0.4592 time to fit residues: 67.7348 Evaluate side-chains 116 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 88 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 890 MET Chi-restraints excluded: chain A residue 943 ARG Chi-restraints excluded: chain A residue 961 MET Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1113 ILE Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1190 ARG Chi-restraints excluded: chain A residue 1237 VAL Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 259 ASN Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 352 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 35 optimal weight: 0.0050 chunk 78 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 chunk 123 optimal weight: 0.7980 chunk 30 optimal weight: 0.0060 chunk 22 optimal weight: 0.9980 chunk 118 optimal weight: 0.9990 chunk 11 optimal weight: 9.9990 chunk 114 optimal weight: 3.9990 overall best weight: 0.5210 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 116 ASN C 155 GLN C 259 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.146725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.111293 restraints weight = 15165.473| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.58 r_work: 0.3496 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 11877 Z= 0.108 Angle : 0.787 29.728 16122 Z= 0.336 Chirality : 0.043 0.265 1844 Planarity : 0.004 0.043 2003 Dihedral : 7.816 100.805 1628 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.39 % Favored : 96.54 % Rotamer: Outliers : 2.55 % Allowed : 17.18 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.22), residues: 1415 helix: 0.41 (0.23), residues: 577 sheet: -0.67 (0.36), residues: 213 loop : -1.31 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 32 TYR 0.021 0.001 TYR A1023 PHE 0.011 0.001 PHE A1205 TRP 0.027 0.001 TRP A 299 HIS 0.008 0.001 HIS A 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (11865) covalent geometry : angle 0.78552 / 0.34 (16091) SS BOND : bond 0.00833 / 0.59 ( 2) SS BOND : angle 0.77147 / 0.61 ( 4) hydrogen bonds : bond 0.03514 / 2.28 ( 474) hydrogen bonds : angle 4.20225 / 2.98 ( 1338) Misc. bond : bond 0.00095 / 0.06 ( 1) link_BETA1-3 : bond 0.00620 / 0.41 ( 1) link_BETA1-3 : angle 1.16231 / 0.74 ( 3) link_BETA1-4 : bond 0.00334 / 0.21 ( 4) link_BETA1-4 : angle 1.20304 / 0.75 ( 12) link_NAG-ASN : bond 0.00314 / 0.21 ( 4) link_NAG-ASN : angle 1.46212 / 1.03 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 102 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: A 208 TYR cc_start: 0.5635 (m-10) cc_final: 0.4864 (m-10) REVERT: A 265 GLU cc_start: 0.7183 (mm-30) cc_final: 0.6845 (mm-30) REVERT: A 277 LYS cc_start: 0.6924 (OUTLIER) cc_final: 0.6499 (tptp) REVERT: A 366 MET cc_start: 0.6384 (tpt) cc_final: 0.6162 (tpt) REVERT: A 400 MET cc_start: 0.6435 (OUTLIER) cc_final: 0.5005 (tmt) REVERT: A 420 THR cc_start: 0.6135 (p) cc_final: 0.5456 (t) REVERT: A 437 ARG cc_start: 0.7713 (mtp-110) cc_final: 0.7438 (mtp-110) REVERT: A 535 LYS cc_start: 0.7917 (tttt) cc_final: 0.7221 (ttmm) REVERT: A 555 GLU cc_start: 0.7054 (mt-10) cc_final: 0.5751 (tt0) REVERT: A 585 LYS cc_start: 0.8067 (tptt) cc_final: 0.7853 (mmtt) REVERT: A 761 MET cc_start: 0.7462 (ptm) cc_final: 0.6814 (ptt) REVERT: A 943 ARG cc_start: 0.7659 (OUTLIER) cc_final: 0.7333 (ttm170) REVERT: A 1190 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.6774 (mtp85) REVERT: C 114 THR cc_start: 0.7400 (m) cc_final: 0.7054 (p) REVERT: C 115 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7484 (tm-30) REVERT: C 132 ASP cc_start: 0.7934 (OUTLIER) cc_final: 0.7417 (m-30) REVERT: C 184 ASP cc_start: 0.8034 (m-30) cc_final: 0.7310 (t0) REVERT: C 213 GLU cc_start: 0.7738 (mp0) cc_final: 0.7352 (mp0) REVERT: C 308 ILE cc_start: 0.7081 (OUTLIER) cc_final: 0.6687 (mt) outliers start: 32 outliers final: 16 residues processed: 129 average time/residue: 0.4455 time to fit residues: 63.5156 Evaluate side-chains 114 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 400 MET Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 943 ARG Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1113 ILE Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1190 ARG Chi-restraints excluded: chain A residue 1237 VAL Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain C residue 352 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 12 optimal weight: 9.9990 chunk 140 optimal weight: 0.3980 chunk 23 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 123 optimal weight: 0.2980 chunk 72 optimal weight: 0.0770 chunk 34 optimal weight: 5.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.8980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1026 GLN C 116 ASN C 155 GLN ** C 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.147349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.112136 restraints weight = 14964.228| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 2.55 r_work: 0.3507 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 11877 Z= 0.104 Angle : 0.782 29.663 16122 Z= 0.333 Chirality : 0.043 0.266 1844 Planarity : 0.004 0.054 2003 Dihedral : 7.609 98.045 1628 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.46 % Favored : 96.47 % Rotamer: Outliers : 2.63 % Allowed : 17.26 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.23), residues: 1415 helix: 0.47 (0.23), residues: 587 sheet: -0.61 (0.36), residues: 203 loop : -1.27 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 32 TYR 0.021 0.001 TYR A1023 PHE 0.011 0.001 PHE A1205 TRP 0.031 0.001 TRP A 299 HIS 0.008 0.001 HIS A 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 (11865) covalent geometry : angle 0.78056 / 0.33 (16091) SS BOND : bond 0.00836 / 0.60 ( 2) SS BOND : angle 1.60529 / 0.94 ( 4) hydrogen bonds : bond 0.03372 / 2.19 ( 474) hydrogen bonds : angle 4.13973 / 2.94 ( 1338) Misc. bond : bond 0.00084 / 0.06 ( 1) link_BETA1-3 : bond 0.00523 / 0.35 ( 1) link_BETA1-3 : angle 1.12995 / 0.71 ( 3) link_BETA1-4 : bond 0.00306 / 0.20 ( 4) link_BETA1-4 : angle 1.17824 / 0.75 ( 12) link_NAG-ASN : bond 0.00316 / 0.21 ( 4) link_NAG-ASN : angle 1.39372 / 0.98 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 98 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: A 208 TYR cc_start: 0.5668 (m-10) cc_final: 0.4896 (m-10) REVERT: A 265 GLU cc_start: 0.7194 (mm-30) cc_final: 0.6859 (mm-30) REVERT: A 388 LEU cc_start: 0.4866 (OUTLIER) cc_final: 0.4431 (tp) REVERT: A 420 THR cc_start: 0.6072 (p) cc_final: 0.5399 (t) REVERT: A 437 ARG cc_start: 0.7703 (mtp-110) cc_final: 0.7422 (mtp-110) REVERT: A 535 LYS cc_start: 0.7901 (tttt) cc_final: 0.7208 (ttmm) REVERT: A 555 GLU cc_start: 0.7134 (mt-10) cc_final: 0.5938 (tt0) REVERT: A 761 MET cc_start: 0.7405 (ptm) cc_final: 0.6759 (ptt) REVERT: A 943 ARG cc_start: 0.7638 (OUTLIER) cc_final: 0.7326 (ttm170) REVERT: A 1190 ARG cc_start: 0.7725 (OUTLIER) cc_final: 0.6809 (mtp85) REVERT: C 114 THR cc_start: 0.7407 (m) cc_final: 0.7063 (p) REVERT: C 115 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7470 (tm-30) REVERT: C 132 ASP cc_start: 0.7990 (OUTLIER) cc_final: 0.7484 (m-30) REVERT: C 184 ASP cc_start: 0.8036 (m-30) cc_final: 0.7309 (t0) REVERT: C 213 GLU cc_start: 0.7648 (mp0) cc_final: 0.7258 (mp0) REVERT: C 308 ILE cc_start: 0.7084 (OUTLIER) cc_final: 0.6733 (mt) outliers start: 33 outliers final: 18 residues processed: 124 average time/residue: 0.4083 time to fit residues: 55.7048 Evaluate side-chains 114 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 847 MET Chi-restraints excluded: chain A residue 890 MET Chi-restraints excluded: chain A residue 943 ARG Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1113 ILE Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1190 ARG Chi-restraints excluded: chain A residue 1237 VAL Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain C residue 352 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 0 optimal weight: 10.0000 chunk 90 optimal weight: 5.9990 chunk 112 optimal weight: 0.6980 chunk 126 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 133 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 35 optimal weight: 0.0870 chunk 13 optimal weight: 0.6980 overall best weight: 0.8962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 116 ASN C 161 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.147457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.114021 restraints weight = 15025.591| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.42 r_work: 0.3487 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 11877 Z= 0.123 Angle : 0.805 30.056 16122 Z= 0.346 Chirality : 0.044 0.266 1844 Planarity : 0.004 0.053 2003 Dihedral : 7.582 94.657 1624 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.03 % Favored : 95.90 % Rotamer: Outliers : 2.07 % Allowed : 18.06 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.22), residues: 1415 helix: 0.37 (0.22), residues: 593 sheet: -0.75 (0.35), residues: 213 loop : -1.23 (0.24), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 32 TYR 0.023 0.001 TYR A1023 PHE 0.013 0.001 PHE A1205 TRP 0.037 0.001 TRP A 299 HIS 0.008 0.001 HIS A 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.12 (11865) covalent geometry : angle 0.80345 / 0.35 (16091) SS BOND : bond 0.01418 / 1.01 ( 2) SS BOND : angle 1.78036 / 0.98 ( 4) hydrogen bonds : bond 0.03606 / 2.33 ( 474) hydrogen bonds : angle 4.19050 / 2.98 ( 1338) Misc. bond : bond 0.00084 / 0.06 ( 1) link_BETA1-3 : bond 0.00636 / 0.42 ( 1) link_BETA1-3 : angle 1.16397 / 0.69 ( 3) link_BETA1-4 : bond 0.00338 / 0.21 ( 4) link_BETA1-4 : angle 1.32143 / 0.85 ( 12) link_NAG-ASN : bond 0.00347 / 0.23 ( 4) link_NAG-ASN : angle 1.64159 / 1.21 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 97 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: A 208 TYR cc_start: 0.5559 (m-10) cc_final: 0.4750 (m-10) REVERT: A 265 GLU cc_start: 0.7207 (mm-30) cc_final: 0.6871 (mm-30) REVERT: A 366 MET cc_start: 0.6387 (tpt) cc_final: 0.6166 (tpt) REVERT: A 388 LEU cc_start: 0.4759 (OUTLIER) cc_final: 0.4551 (tp) REVERT: A 400 MET cc_start: 0.6602 (OUTLIER) cc_final: 0.4862 (tmt) REVERT: A 420 THR cc_start: 0.6182 (p) cc_final: 0.5486 (t) REVERT: A 437 ARG cc_start: 0.7677 (mtp-110) cc_final: 0.7401 (mtp-110) REVERT: A 535 LYS cc_start: 0.7978 (tttt) cc_final: 0.7310 (ttmm) REVERT: A 555 GLU cc_start: 0.7101 (mt-10) cc_final: 0.5800 (tt0) REVERT: A 761 MET cc_start: 0.7467 (ptm) cc_final: 0.6830 (ptt) REVERT: A 1190 ARG cc_start: 0.7753 (OUTLIER) cc_final: 0.6801 (mtp85) REVERT: C 114 THR cc_start: 0.7479 (m) cc_final: 0.6971 (p) REVERT: C 115 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7488 (tm-30) REVERT: C 132 ASP cc_start: 0.8065 (OUTLIER) cc_final: 0.7555 (m-30) REVERT: C 184 ASP cc_start: 0.8058 (m-30) cc_final: 0.7328 (t0) REVERT: C 213 GLU cc_start: 0.7701 (mp0) cc_final: 0.7306 (mp0) REVERT: C 308 ILE cc_start: 0.7108 (OUTLIER) cc_final: 0.6736 (mt) outliers start: 26 outliers final: 19 residues processed: 118 average time/residue: 0.4230 time to fit residues: 55.0875 Evaluate side-chains 118 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 400 MET Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 890 MET Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1113 ILE Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1190 ARG Chi-restraints excluded: chain A residue 1237 VAL Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain C residue 352 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 35 optimal weight: 0.0010 chunk 120 optimal weight: 0.5980 chunk 22 optimal weight: 7.9990 chunk 106 optimal weight: 0.6980 chunk 128 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 chunk 108 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 116 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.146751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.111344 restraints weight = 15146.711| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 2.58 r_work: 0.3497 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11877 Z= 0.111 Angle : 0.788 29.822 16122 Z= 0.337 Chirality : 0.043 0.268 1844 Planarity : 0.004 0.050 2003 Dihedral : 7.452 93.485 1624 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.46 % Favored : 96.47 % Rotamer: Outliers : 2.55 % Allowed : 17.74 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.23), residues: 1415 helix: 0.47 (0.23), residues: 593 sheet: -0.56 (0.37), residues: 203 loop : -1.26 (0.24), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 32 TYR 0.021 0.001 TYR A1023 PHE 0.012 0.001 PHE A1205 TRP 0.033 0.001 TRP A 299 HIS 0.007 0.001 HIS A 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (11865) covalent geometry : angle 0.78630 / 0.34 (16091) SS BOND : bond 0.01098 / 0.78 ( 2) SS BOND : angle 1.62331 / 0.86 ( 4) hydrogen bonds : bond 0.03443 / 2.23 ( 474) hydrogen bonds : angle 4.13253 / 2.93 ( 1338) Misc. bond : bond 0.00080 / 0.05 ( 1) link_BETA1-3 : bond 0.00592 / 0.39 ( 1) link_BETA1-3 : angle 1.16656 / 0.72 ( 3) link_BETA1-4 : bond 0.00310 / 0.20 ( 4) link_BETA1-4 : angle 1.21962 / 0.77 ( 12) link_NAG-ASN : bond 0.00303 / 0.20 ( 4) link_NAG-ASN : angle 1.47863 / 1.06 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3764.49 seconds wall clock time: 64 minutes 50.10 seconds (3890.10 seconds total)