Starting phenix.real_space_refine on Fri Sep 11 21:15:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6roj_4974/09_2026/6roj_4974.cif Found real_map, /net/cci-nas-00/data/ceres_data/6roj_4974/09_2026/6roj_4974.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/6roj_4974/09_2026/6roj_4974.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6roj_4974/09_2026/6roj_4974.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6roj_4974/09_2026/6roj_4974.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6roj_4974/09_2026/6roj_4974.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6roj_4974/09_2026/6roj_4974.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6roj_4974/09_2026/6roj_4974.cif" } 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= 0.000 sd= 0.002 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 P 2 5.49 5 Mg 1 5.21 5 S 47 5.16 5 Be 1 3.05 5 C 7407 2.51 5 N 1842 2.21 5 O 2162 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11465 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1064, 8508 Classifications: {'peptide': 1064} Link IDs: {'PTRANS': 30, 'TRANS': 1033} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Chain: "C" Number of atoms: 2761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2761 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 21, 'TRANS': 318} Chain: "B" 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: "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: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 68 Unusual residues: {' MG': 1, '2Y5': 1} Classifications: {'undetermined': 2, 'water': 2} Link IDs: {None: 3} Time building chain proxies: 2.73, per 1000 atoms: 0.24 Number of scatterers: 11465 At special positions: 0 Unit cell: (80.775, 105.546, 173.397, 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 47 16.00 P 2 15.00 Mg 1 11.99 F 3 9.00 O 2162 8.00 N 1842 7.00 C 7407 6.00 Be 1 4.00 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=2.03 Simple disulfide: pdb=" SG CYS C 176 " - pdb=" SG CYS C 190 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-3 " BMA B 3 " - " BMA B 4 " " BMA E 3 " - " BMA E 4 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " 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 D 1 " - " ASN C 216 " " NAG E 1 " - " ASN C 199 " Time building additional restraints: 1.04 Conformation dependent library (CDL) restraints added in 601.9 milliseconds 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2658 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 12 sheets defined 45.9% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 192 through 196 Processing helix chain 'A' and resid 212 through 222 removed outlier: 4.063A pdb=" N PHE A 219 " --> pdb=" O PRO A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 235 removed outlier: 3.524A pdb=" N LEU A 228 " --> pdb=" O LYS A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 281 removed outlier: 3.573A pdb=" N SER A 261 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU A 265 " --> pdb=" O SER A 261 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP A 269 " --> pdb=" O GLU A 265 " (cutoff:3.500A) removed outlier: 3.952A 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 362 through 366 removed outlier: 3.774A pdb=" N ASN A 365 " --> pdb=" O THR A 362 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N MET A 366 " --> pdb=" O LEU A 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 362 through 366' Processing helix chain 'A' and resid 396 through 398 No H-bonds generated for 'chain 'A' and resid 396 through 398' Processing helix chain 'A' and resid 420 through 424 removed outlier: 3.975A pdb=" N THR A 424 " --> pdb=" O GLY A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 473 removed outlier: 3.520A pdb=" N ASN A 445 " --> pdb=" O GLU A 441 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG A 446 " --> pdb=" O LYS A 442 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE A 449 " --> pdb=" O ASN A 445 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL A 457 " --> pdb=" O THR A 453 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL A 467 " --> pdb=" O SER A 463 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR A 471 " --> pdb=" O VAL A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 503 removed outlier: 4.348A pdb=" N LEU A 496 " --> pdb=" O PHE A 492 " (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 509 through 514 removed outlier: 3.657A pdb=" N THR A 513 " --> pdb=" O SER A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 526 removed outlier: 3.693A pdb=" N MET A 524 " --> pdb=" O TYR A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 532 Processing helix chain 'A' and resid 544 through 548 removed outlier: 3.611A pdb=" N LEU A 547 " --> pdb=" O THR A 544 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL A 548 " --> pdb=" O SER A 545 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 544 through 548' Processing helix chain 'A' and resid 604 through 614 removed outlier: 3.940A pdb=" N ASP A 614 " --> pdb=" O LYS A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 633 removed outlier: 3.515A pdb=" N ASN A 624 " --> pdb=" O SER A 620 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP A 625 " --> pdb=" O PRO A 621 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 629 " --> pdb=" O ASP A 625 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA A 631 " --> pdb=" O LEU A 627 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS A 633 " --> pdb=" O LEU A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 666 removed outlier: 3.635A pdb=" N LEU A 665 " --> pdb=" O GLY A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 728 removed outlier: 3.577A pdb=" N ILE A 727 " --> pdb=" O ALA A 723 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU A 728 " --> pdb=" O ASP A 724 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 723 through 728' Processing helix chain 'A' and resid 729 through 731 No H-bonds generated for 'chain 'A' and resid 729 through 731' Processing helix chain 'A' and resid 738 through 751 removed outlier: 3.605A pdb=" N THR A 742 " --> pdb=" O TYR A 738 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG A 744 " --> pdb=" O GLU A 740 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR A 749 " --> pdb=" O HIS A 745 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA A 750 " --> pdb=" O LEU A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 782 removed outlier: 3.524A pdb=" N GLU A 771 " --> pdb=" O GLY A 767 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER A 774 " --> pdb=" O GLU A 770 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR A 782 " --> pdb=" O GLU A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 795 removed outlier: 4.275A pdb=" N GLU A 792 " --> pdb=" O GLU A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 827 Processing helix chain 'A' and resid 838 through 849 removed outlier: 3.531A pdb=" N ALA A 842 " --> pdb=" O ARG A 838 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER A 848 " --> pdb=" O ASN A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 882 removed outlier: 3.584A pdb=" N THR A 869 " --> pdb=" O THR A 865 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU A 870 " --> pdb=" O ARG A 866 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASN A 881 " --> pdb=" O ILE A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 891 No H-bonds generated for 'chain 'A' and resid 889 through 891' Processing helix chain 'A' and resid 901 through 906 Processing helix chain 'A' and resid 910 through 919 removed outlier: 3.527A pdb=" N LEU A 914 " --> pdb=" O LEU A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 932 through 945 removed outlier: 4.006A pdb=" N VAL A 938 " --> pdb=" O LYS A 934 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS A 944 " --> pdb=" O MET A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 957 No H-bonds generated for 'chain 'A' and resid 955 through 957' Processing helix chain 'A' and resid 958 through 964 Processing helix chain 'A' and resid 977 through 982 removed outlier: 3.510A pdb=" N SER A 982 " --> pdb=" O GLN A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 991 No H-bonds generated for 'chain 'A' and resid 989 through 991' Processing helix chain 'A' and resid 992 through 999 Processing helix chain 'A' and resid 999 through 1024 removed outlier: 3.968A pdb=" N ILE A1008 " --> pdb=" O SER A1004 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN A1019 " --> pdb=" O SER A1015 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU A1022 " --> pdb=" O LYS A1018 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1032 removed outlier: 3.870A pdb=" N PHE A1031 " --> pdb=" O TRP A1028 " (cutoff:3.500A) Processing helix chain 'A' and resid 1042 through 1048 Processing helix chain 'A' and resid 1055 through 1065 removed outlier: 3.545A pdb=" N PHE A1059 " --> pdb=" O VAL A1055 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASP A1065 " --> pdb=" O ILE A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1074 removed outlier: 3.576A pdb=" N GLU A1074 " --> pdb=" O SER A1070 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1079 Processing helix chain 'A' and resid 1080 through 1086 Processing helix chain 'A' and resid 1090 through 1116 removed outlier: 3.841A pdb=" N GLY A1096 " --> pdb=" O TYR A1092 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TRP A1097 " --> pdb=" O ILE A1093 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A1114 " --> pdb=" O ILE A1110 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE A1115 " --> pdb=" O GLY A1111 " (cutoff:3.500A) Processing helix chain 'A' and resid 1130 through 1154 removed outlier: 4.237A pdb=" N THR A1137 " --> pdb=" O SER A1133 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL A1146 " --> pdb=" O SER A1142 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA A1150 " --> pdb=" O VAL A1146 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU A1152 " --> pdb=" O GLY A1148 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1183 removed outlier: 3.896A pdb=" N LEU A1169 " --> pdb=" O ILE A1165 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE A1174 " --> pdb=" O LEU A1170 " (cutoff:3.500A) Proline residue: A1177 - end of helix removed outlier: 4.068A 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: 3.535A pdb=" N TYR A1192 " --> pdb=" O SER A1189 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N TYR A1193 " --> pdb=" O ARG A1190 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1189 through 1193' Processing helix chain 'A' and resid 1194 through 1200 Processing helix chain 'A' and resid 1204 through 1217 removed outlier: 4.187A pdb=" N ILE A1210 " --> pdb=" O TRP A1206 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU A1212 " --> pdb=" O THR A1208 " (cutoff:3.500A) Proline residue: A1213 - end of helix Processing helix chain 'A' and resid 1217 through 1231 removed outlier: 3.611A pdb=" N ARG A1228 " --> pdb=" O LYS A1224 " (cutoff:3.500A) Processing helix chain 'A' and resid 1233 through 1245 removed outlier: 3.999A pdb=" N VAL A1237 " --> pdb=" O GLU A1233 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE A1238 " --> pdb=" O THR A1234 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 69 removed outlier: 3.645A pdb=" N LEU C 46 " --> pdb=" O PRO C 42 " (cutoff:3.500A) Proline residue: C 47 - end of helix Proline residue: C 58 - end of helix removed outlier: 3.530A pdb=" N SER C 66 " --> pdb=" O GLY C 62 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 84 removed outlier: 3.687A pdb=" N LYS C 83 " --> pdb=" O HIS C 79 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA C 84 " --> pdb=" O CYS C 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 79 through 84' Processing helix chain 'C' and resid 150 through 155 removed outlier: 4.566A pdb=" N GLN C 155 " --> pdb=" O ARG C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 164 removed outlier: 3.541A pdb=" N ILE C 162 " --> pdb=" O ASP C 158 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU C 163 " --> pdb=" O THR C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 231 Processing helix chain 'C' and resid 244 through 248 removed outlier: 3.785A pdb=" N MET C 248 " --> pdb=" O PRO C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 274 removed outlier: 3.519A pdb=" N GLN C 270 " --> pdb=" O TRP C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 357 removed outlier: 3.770A pdb=" N LEU C 335 " --> pdb=" O SER C 331 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU C 337 " --> pdb=" O GLY C 333 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL C 339 " --> pdb=" O LEU C 335 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA C 340 " --> pdb=" O TYR C 336 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE C 348 " --> pdb=" O ALA C 344 " (cutoff:3.500A) removed outlier: 4.014A 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: 3.531A pdb=" N LYS A 369 " --> pdb=" O THR A 387 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 293 through 298 removed outlier: 3.756A pdb=" N ASP A 293 " --> pdb=" O SER A 288 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLU A 285 " --> pdb=" O ARG A 309 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ILE A 307 " --> pdb=" O PHE A 287 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL A 310 " --> pdb=" O ILE A 413 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N PHE A 414 " --> pdb=" O LEU A 323 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ASP A 319 " --> pdb=" O ILE A 418 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 345 through 349 removed outlier: 3.755A pdb=" N TYR A 333 " --> pdb=" O ARG A 408 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 541 through 542 removed outlier: 6.385A pdb=" N GLY A 968 " --> pdb=" O ILE A 985 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N VAL A 987 " --> pdb=" O GLY A 968 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N GLY A 970 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU A 949 " --> pdb=" O VAL A 967 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N VAL A 969 " --> pdb=" O LEU A 949 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ALA A 951 " --> pdb=" O VAL A 969 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N ILE A 971 " --> pdb=" O ALA A 951 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N GLY A 953 " --> pdb=" O ILE A 971 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ILE A 557 " --> pdb=" O TRP A 832 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N LEU A 834 " --> pdb=" O ILE A 557 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N SER A 559 " --> pdb=" O LEU A 834 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE A 831 " --> pdb=" O VAL A 924 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N CYS A 926 " --> pdb=" O ILE A 831 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL A 833 " --> pdb=" O CYS A 926 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA A 923 " --> pdb=" O LEU A 893 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 566 through 577 removed outlier: 7.144A pdb=" N LYS A 812 " --> pdb=" O ARG A 567 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ILE A 569 " --> pdb=" O GLU A 810 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N GLU A 810 " --> pdb=" O ILE A 569 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N GLU A 571 " --> pdb=" O ALA A 808 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ALA A 808 " --> pdb=" O GLU A 571 " (cutoff:3.500A) removed outlier: 9.165A pdb=" N LYS A 573 " --> pdb=" O ALA A 806 " (cutoff:3.500A) removed outlier: 11.706A pdb=" N ALA A 806 " --> pdb=" O LYS A 573 " (cutoff:3.500A) removed outlier: 10.150A pdb=" N CYS A 575 " --> pdb=" O ILE A 804 " (cutoff:3.500A) removed outlier: 11.833A pdb=" N ILE A 804 " --> pdb=" O CYS A 575 " (cutoff:3.500A) removed outlier: 11.706A pdb=" N ILE A 577 " --> pdb=" O ILE A 802 " (cutoff:3.500A) removed outlier: 14.697A pdb=" N ILE A 802 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU A 759 " --> pdb=" O ILE A 804 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ALA A 806 " --> pdb=" O LEU A 757 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU A 757 " --> pdb=" O ALA A 806 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ALA A 808 " --> pdb=" O ARG A 755 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ARG A 755 " --> pdb=" O ALA A 808 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE A 716 " --> pdb=" O ILE A 764 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N SER A 706 " --> pdb=" O ILE A 695 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ILE A 695 " --> pdb=" O SER A 706 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N ILE A 708 " --> pdb=" O LEU A 693 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A 693 " --> pdb=" O ILE A 708 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 637 through 639 Processing sheet with id=AA7, first strand: chain 'A' and resid 667 through 673 removed outlier: 4.402A pdb=" N THR A 678 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N ARG A 672 " --> pdb=" O SER A 676 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N SER A 676 " --> pdb=" O ARG A 672 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 97 through 100 removed outlier: 6.408A pdb=" N TYR C 141 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N LEU C 284 " --> pdb=" O TYR C 141 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE C 143 " --> pdb=" O TYR C 282 " (cutoff:3.500A) removed outlier: 5.657A 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 Processing sheet with id=AB1, first strand: chain 'C' and resid 113 through 115 removed outlier: 3.572A pdb=" N GLU C 303 " --> pdb=" O THR C 201 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR C 201 " --> pdb=" O GLU C 303 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 128 through 129 removed outlier: 4.436A pdb=" N LYS C 297 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N ASN C 301 " --> pdb=" O VAL C 205 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N VAL C 205 " --> pdb=" O ASN C 301 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 181 through 182 removed outlier: 6.031A pdb=" N ILE C 186 " --> pdb=" O VAL C 242 " (cutoff:3.500A) 432 hydrogen bonds defined for protein. 1218 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: 2.39 Time building geometry restraints manager: 1.26 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: 1846 1.31 - 1.43: 3185 1.43 - 1.56: 6610 1.56 - 1.69: 8 1.69 - 1.81: 75 Bond restraints: 11724 Sorted by residual: bond pdb=" OD1 BFD A 560 " pdb="BE BFD A 560 " ideal model delta sigma weight residual 1.737 1.530 0.207 2.00e-02 2.50e+03 1.07e+02 bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.516 -0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" C1 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.406 1.511 -0.105 2.00e-02 2.50e+03 2.76e+01 bond pdb=" C11 2Y5 A1502 " pdb=" O18 2Y5 A1502 " ideal model delta sigma weight residual 1.335 1.400 -0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" C10 2Y5 A1502 " pdb=" O16 2Y5 A1502 " ideal model delta sigma weight residual 1.333 1.395 -0.062 2.00e-02 2.50e+03 9.63e+00 ... (remaining 11719 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 15457 2.53 - 5.05: 367 5.05 - 7.58: 55 7.58 - 10.11: 12 10.11 - 12.63: 5 Bond angle restraints: 15896 Sorted by residual: angle pdb=" C VAL A 929 " pdb=" N SER A 930 " pdb=" CA SER A 930 " ideal model delta sigma weight residual 120.86 128.04 -7.18 1.60e+00 3.91e-01 2.01e+01 angle pdb=" N SER A 312 " pdb=" CA SER A 312 " pdb=" C SER A 312 " ideal model delta sigma weight residual 110.97 115.61 -4.64 1.09e+00 8.42e-01 1.81e+01 angle pdb=" O1 2Y5 A1502 " pdb=" P1 2Y5 A1502 " pdb=" O13 2Y5 A1502 " ideal model delta sigma weight residual 97.01 109.34 -12.33 3.00e+00 1.11e-01 1.69e+01 angle pdb=" C ILE A 670 " pdb=" N ILE A 671 " pdb=" CA ILE A 671 " ideal model delta sigma weight residual 121.97 129.16 -7.19 1.80e+00 3.09e-01 1.60e+01 angle pdb=" N ILE A 508 " pdb=" CA ILE A 508 " pdb=" C ILE A 508 " ideal model delta sigma weight residual 113.39 107.61 5.78 1.47e+00 4.63e-01 1.55e+01 ... (remaining 15891 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.00: 6564 25.00 - 50.01: 332 50.01 - 75.01: 37 75.01 - 100.01: 11 100.01 - 125.02: 8 Dihedral angle restraints: 6952 sinusoidal: 2831 harmonic: 4121 Sorted by residual: dihedral pdb=" CB CYS C 176 " pdb=" SG CYS C 176 " pdb=" SG CYS C 190 " pdb=" CB CYS C 190 " ideal model delta sinusoidal sigma weight residual 93.00 154.31 -61.31 1 1.00e+01 1.00e-02 4.99e+01 dihedral pdb=" CA TYR C 236 " pdb=" C TYR C 236 " pdb=" N ASN C 237 " pdb=" CA ASN C 237 " ideal model delta harmonic sigma weight residual 180.00 153.02 26.98 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA ILE A 670 " pdb=" C ILE A 670 " pdb=" N ILE A 671 " pdb=" CA ILE A 671 " ideal model delta harmonic sigma weight residual 180.00 -153.08 -26.92 0 5.00e+00 4.00e-02 2.90e+01 ... (remaining 6949 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.988: 1828 0.988 - 1.975: 0 1.975 - 2.963: 0 2.963 - 3.951: 0 3.951 - 4.939: 1 Chirality restraints: 1829 Sorted by residual: chirality pdb=" C1 2Y5 A1502 " pdb=" C2 2Y5 A1502 " pdb=" C6 2Y5 A1502 " pdb=" O1 2Y5 A1502 " both_signs ideal model delta sigma weight residual False -2.53 2.40 -4.94 2.00e-01 2.50e+01 6.10e+02 chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.44 0.04 2.00e-02 2.50e+03 4.74e+00 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN C 288 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.84e+00 ... (remaining 1826 not shown) Planarity restraints: 1981 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 111 " 0.032 2.00e-02 2.50e+03 2.79e-02 1.94e+01 pdb=" CG TRP C 111 " -0.073 2.00e-02 2.50e+03 pdb=" CD1 TRP C 111 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 TRP C 111 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP C 111 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP C 111 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 111 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 111 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 111 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP C 111 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A1057 " 0.052 5.00e-02 4.00e+02 7.72e-02 9.54e+00 pdb=" N PRO A1058 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO A1058 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A1058 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 673 " -0.047 5.00e-02 4.00e+02 6.99e-02 7.83e+00 pdb=" N PRO A 674 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO A 674 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 674 " -0.039 5.00e-02 4.00e+02 ... (remaining 1978 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.34: 13 2.34 - 2.98: 5373 2.98 - 3.62: 16147 3.62 - 4.26: 27059 4.26 - 4.90: 44799 Nonbonded interactions: 93391 Sorted by model distance: nonbonded pdb=" F2 BFD A 560 " pdb="MG MG A1501 " model vdw 1.705 2.120 nonbonded pdb="MG MG A1501 " pdb=" O HOH A1602 " model vdw 1.884 2.170 nonbonded pdb="MG MG A1501 " pdb=" O HOH A1601 " model vdw 1.916 2.170 nonbonded pdb=" O THR A 562 " pdb="MG MG A1501 " model vdw 2.056 2.170 nonbonded pdb=" OD2 BFD A 560 " pdb="MG MG A1501 " model vdw 2.111 2.170 ... (remaining 93386 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 'E' } 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: 1.680 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.090 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:7.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.207 11736 Z= 0.300 Angle : 0.986 12.632 15930 Z= 0.531 Chirality : 0.128 4.939 1829 Planarity : 0.007 0.077 1978 Dihedral : 15.681 125.018 4288 Min Nonbonded Distance : 1.705 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.16 % Allowed : 5.87 % Favored : 93.97 % 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: -4.91 (0.17), residues: 1397 helix: -4.55 (0.08), residues: 596 sheet: -1.72 (0.32), residues: 212 loop : -2.15 (0.22), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1219 TYR 0.031 0.002 TYR C 236 PHE 0.029 0.002 PHE A 711 TRP 0.073 0.002 TRP C 111 HIS 0.007 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00655 / 0.30 (11724) covalent geometry : angle 0.97824 / 0.53 (15896) SS BOND : bond 0.00577 / 0.41 ( 2) SS BOND : angle 2.25037 / 1.75 ( 4) hydrogen bonds : bond 0.30859 / 19.76 ( 432) hydrogen bonds : angle 11.25437 / 7.86 ( 1218) link_BETA1-3 : bond 0.01351 / 0.91 ( 2) link_BETA1-3 : angle 2.89076 / 1.62 ( 6) link_BETA1-4 : bond 0.00749 / 0.49 ( 5) link_BETA1-4 : angle 2.51569 / 1.48 ( 15) link_NAG-ASN : bond 0.00831 / 0.50 ( 3) link_NAG-ASN : angle 3.26723 / 1.44 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 106 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 705 MET cc_start: 0.7693 (tpt) cc_final: 0.7315 (tmt) REVERT: A 726 VAL cc_start: 0.8467 (p) cc_final: 0.8267 (p) REVERT: A 891 ASN cc_start: 0.8313 (m110) cc_final: 0.7629 (t0) REVERT: A 1241 MET cc_start: 0.8562 (mtt) cc_final: 0.8352 (mtt) outliers start: 2 outliers final: 0 residues processed: 108 average time/residue: 0.6410 time to fit residues: 74.7910 Evaluate side-chains 66 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 280 ASN A 399 GLN A 649 GLN A 675 ASN A 891 ASN A1187 ASN C 30 GLN ** C 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.116761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.079378 restraints weight = 18227.290| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 2.53 r_work: 0.3017 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11736 Z= 0.167 Angle : 0.646 9.229 15930 Z= 0.334 Chirality : 0.046 0.405 1829 Planarity : 0.005 0.049 1978 Dihedral : 10.581 93.934 1596 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.37 % Allowed : 10.69 % Favored : 87.94 % 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: -3.30 (0.19), residues: 1397 helix: -2.69 (0.16), residues: 602 sheet: -1.42 (0.33), residues: 216 loop : -1.69 (0.24), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 838 TYR 0.020 0.002 TYR C 236 PHE 0.016 0.001 PHE A1094 TRP 0.031 0.001 TRP C 111 HIS 0.005 0.001 HIS A1198 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 (11724) covalent geometry : angle 0.64076 / 0.33 (15896) SS BOND : bond 0.00225 / 0.16 ( 2) SS BOND : angle 1.47746 / 1.17 ( 4) hydrogen bonds : bond 0.05252 / 3.38 ( 432) hydrogen bonds : angle 5.81104 / 4.06 ( 1218) link_BETA1-3 : bond 0.01506 / 1.02 ( 2) link_BETA1-3 : angle 2.21884 / 1.22 ( 6) link_BETA1-4 : bond 0.00884 / 0.56 ( 5) link_BETA1-4 : angle 1.99721 / 1.20 ( 15) link_NAG-ASN : bond 0.00941 / 0.47 ( 3) link_NAG-ASN : angle 1.80088 / 0.82 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.439 Fit side-chains revert: symmetry clash REVERT: A 342 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7741 (mm-30) REVERT: A 400 MET cc_start: 0.8856 (OUTLIER) cc_final: 0.8437 (tpt) REVERT: A 675 ASN cc_start: 0.8002 (m110) cc_final: 0.7244 (p0) REVERT: A 1241 MET cc_start: 0.8559 (mtt) cc_final: 0.8255 (mtt) REVERT: C 184 ASP cc_start: 0.8059 (t70) cc_final: 0.7744 (p0) outliers start: 17 outliers final: 6 residues processed: 83 average time/residue: 0.5851 time to fit residues: 53.1854 Evaluate side-chains 68 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 400 MET Chi-restraints excluded: chain A residue 703 LYS Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 321 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 31 optimal weight: 0.6980 chunk 114 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 3 optimal weight: 0.6980 chunk 68 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 60 optimal weight: 9.9990 chunk 54 optimal weight: 8.9990 chunk 74 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 227 ASN A 338 ASN A 399 GLN A 649 GLN ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.118410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.083616 restraints weight = 18159.413| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.73 r_work: 0.3038 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11736 Z= 0.149 Angle : 0.595 8.801 15930 Z= 0.302 Chirality : 0.044 0.411 1829 Planarity : 0.004 0.044 1978 Dihedral : 9.269 91.209 1596 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.53 % Allowed : 12.38 % Favored : 86.09 % 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: -2.27 (0.21), residues: 1397 helix: -1.60 (0.19), residues: 597 sheet: -1.21 (0.34), residues: 210 loop : -1.30 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 838 TYR 0.020 0.001 TYR C 236 PHE 0.015 0.001 PHE A1205 TRP 0.024 0.001 TRP C 111 HIS 0.005 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (11724) covalent geometry : angle 0.58949 / 0.30 (15896) SS BOND : bond 0.00227 / 0.16 ( 2) SS BOND : angle 1.40585 / 1.11 ( 4) hydrogen bonds : bond 0.04400 / 2.84 ( 432) hydrogen bonds : angle 5.17138 / 3.60 ( 1218) link_BETA1-3 : bond 0.01347 / 0.91 ( 2) link_BETA1-3 : angle 2.18813 / 1.19 ( 6) link_BETA1-4 : bond 0.00671 / 0.44 ( 5) link_BETA1-4 : angle 1.72719 / 1.02 ( 15) link_NAG-ASN : bond 0.00805 / 0.42 ( 3) link_NAG-ASN : angle 1.93968 / 0.89 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 0.398 Fit side-chains revert: symmetry clash REVERT: A 342 GLU cc_start: 0.8312 (mt-10) cc_final: 0.7976 (mm-30) REVERT: A 399 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.7553 (pm20) REVERT: A 675 ASN cc_start: 0.7977 (m110) cc_final: 0.7288 (p0) REVERT: A 1241 MET cc_start: 0.8778 (mtt) cc_final: 0.8533 (mtt) REVERT: C 184 ASP cc_start: 0.8042 (t70) cc_final: 0.7749 (p0) outliers start: 19 outliers final: 9 residues processed: 78 average time/residue: 0.5303 time to fit residues: 45.6037 Evaluate side-chains 72 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 399 GLN Chi-restraints excluded: chain A residue 703 LYS Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 321 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 105 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 41 optimal weight: 0.0000 chunk 136 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 55 optimal weight: 0.3980 chunk 132 optimal weight: 0.7980 chunk 43 optimal weight: 0.1980 chunk 119 optimal weight: 0.5980 overall best weight: 0.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.120435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.086203 restraints weight = 18014.679| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.56 r_work: 0.3075 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11736 Z= 0.101 Angle : 0.545 8.395 15930 Z= 0.275 Chirality : 0.043 0.389 1829 Planarity : 0.004 0.043 1978 Dihedral : 8.750 89.563 1596 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.53 % Allowed : 13.67 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.64 (0.22), residues: 1397 helix: -0.94 (0.21), residues: 589 sheet: -1.06 (0.34), residues: 209 loop : -1.05 (0.25), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 351 TYR 0.018 0.001 TYR A 738 PHE 0.011 0.001 PHE A1205 TRP 0.013 0.001 TRP C 111 HIS 0.004 0.000 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (11724) covalent geometry : angle 0.53958 / 0.27 (15896) SS BOND : bond 0.00205 / 0.15 ( 2) SS BOND : angle 1.19365 / 0.87 ( 4) hydrogen bonds : bond 0.03623 / 2.34 ( 432) hydrogen bonds : angle 4.85302 / 3.38 ( 1218) link_BETA1-3 : bond 0.01055 / 0.71 ( 2) link_BETA1-3 : angle 1.98678 / 1.09 ( 6) link_BETA1-4 : bond 0.00582 / 0.36 ( 5) link_BETA1-4 : angle 1.57512 / 0.88 ( 15) link_NAG-ASN : bond 0.00720 / 0.36 ( 3) link_NAG-ASN : angle 1.84304 / 0.79 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 69 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 342 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7884 (mm-30) REVERT: A 386 MET cc_start: 0.8039 (ttm) cc_final: 0.7781 (tmm) REVERT: A 738 TYR cc_start: 0.7796 (m-10) cc_final: 0.7493 (m-80) REVERT: A 838 ARG cc_start: 0.7804 (mtp85) cc_final: 0.7470 (mmm160) REVERT: A 974 MET cc_start: 0.6805 (OUTLIER) cc_final: 0.6130 (ppp) REVERT: A 1231 GLU cc_start: 0.8387 (tt0) cc_final: 0.8090 (tt0) REVERT: A 1241 MET cc_start: 0.8705 (mtt) cc_final: 0.8496 (mtt) REVERT: C 184 ASP cc_start: 0.8036 (t70) cc_final: 0.7803 (p0) REVERT: C 303 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.8105 (mp0) outliers start: 19 outliers final: 10 residues processed: 83 average time/residue: 0.5298 time to fit residues: 48.3563 Evaluate side-chains 74 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 703 LYS Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 974 MET Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain C residue 321 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 36 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 73 optimal weight: 6.9990 chunk 125 optimal weight: 7.9990 chunk 113 optimal weight: 4.9990 chunk 52 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 399 GLN ** C 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.115230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.077406 restraints weight = 18287.556| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.53 r_work: 0.2977 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 11736 Z= 0.229 Angle : 0.633 8.820 15930 Z= 0.319 Chirality : 0.047 0.441 1829 Planarity : 0.004 0.047 1978 Dihedral : 8.710 84.552 1596 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.77 % Allowed : 14.23 % Favored : 84.00 % 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: -1.56 (0.22), residues: 1397 helix: -0.97 (0.21), residues: 601 sheet: -0.91 (0.34), residues: 211 loop : -0.94 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 391 TYR 0.023 0.002 TYR C 236 PHE 0.018 0.002 PHE A1205 TRP 0.012 0.001 TRP C 111 HIS 0.007 0.001 HIS A1198 Details of bonding type rmsd/Z covalent geometry : bond 0.00536 / 0.23 (11724) covalent geometry : angle 0.62785 / 0.32 (15896) SS BOND : bond 0.00343 / 0.24 ( 2) SS BOND : angle 1.38360 / 1.19 ( 4) hydrogen bonds : bond 0.04318 / 2.76 ( 432) hydrogen bonds : angle 4.87386 / 3.40 ( 1218) link_BETA1-3 : bond 0.01112 / 0.75 ( 2) link_BETA1-3 : angle 2.04518 / 1.12 ( 6) link_BETA1-4 : bond 0.00660 / 0.42 ( 5) link_BETA1-4 : angle 1.75163 / 1.10 ( 15) link_NAG-ASN : bond 0.00764 / 0.43 ( 3) link_NAG-ASN : angle 2.27901 / 1.10 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 60 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7730 (mm-30) REVERT: A 738 TYR cc_start: 0.7782 (m-10) cc_final: 0.7388 (m-80) REVERT: A 838 ARG cc_start: 0.7631 (mtp85) cc_final: 0.7284 (mmm160) REVERT: A 974 MET cc_start: 0.6559 (OUTLIER) cc_final: 0.5888 (ppp) REVERT: A 1241 MET cc_start: 0.8483 (mtt) cc_final: 0.8186 (mtt) REVERT: A 1242 GLN cc_start: 0.8387 (tt0) cc_final: 0.8181 (tt0) REVERT: C 184 ASP cc_start: 0.8086 (t70) cc_final: 0.7754 (p0) REVERT: C 303 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7993 (mp0) outliers start: 22 outliers final: 12 residues processed: 80 average time/residue: 0.5404 time to fit residues: 47.6516 Evaluate side-chains 74 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 399 GLN Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 703 LYS Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 974 MET Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain C residue 321 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 6 optimal weight: 8.9990 chunk 115 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 105 optimal weight: 0.4980 chunk 89 optimal weight: 0.7980 chunk 134 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1084 GLN ** C 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.117554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.079864 restraints weight = 18200.030| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.53 r_work: 0.3026 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11736 Z= 0.118 Angle : 0.561 8.359 15930 Z= 0.283 Chirality : 0.044 0.401 1829 Planarity : 0.004 0.044 1978 Dihedral : 8.243 84.142 1596 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.69 % Allowed : 14.87 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.27 (0.22), residues: 1397 helix: -0.62 (0.21), residues: 589 sheet: -0.89 (0.34), residues: 214 loop : -0.86 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 838 TYR 0.018 0.001 TYR C 236 PHE 0.012 0.001 PHE A1205 TRP 0.009 0.001 TRP C 111 HIS 0.004 0.000 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (11724) covalent geometry : angle 0.55646 / 0.28 (15896) SS BOND : bond 0.00214 / 0.15 ( 2) SS BOND : angle 1.25099 / 0.95 ( 4) hydrogen bonds : bond 0.03669 / 2.36 ( 432) hydrogen bonds : angle 4.68861 / 3.27 ( 1218) link_BETA1-3 : bond 0.01147 / 0.77 ( 2) link_BETA1-3 : angle 1.91481 / 1.04 ( 6) link_BETA1-4 : bond 0.00563 / 0.36 ( 5) link_BETA1-4 : angle 1.51000 / 0.85 ( 15) link_NAG-ASN : bond 0.00669 / 0.35 ( 3) link_NAG-ASN : angle 2.05062 / 0.90 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 63 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7668 (mm-30) REVERT: A 349 GLN cc_start: 0.8037 (pt0) cc_final: 0.7729 (tm-30) REVERT: A 460 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7810 (tp) REVERT: A 705 MET cc_start: 0.8115 (tpt) cc_final: 0.7458 (tpp) REVERT: A 838 ARG cc_start: 0.7523 (mtp85) cc_final: 0.7193 (mmm160) REVERT: A 891 ASN cc_start: 0.8203 (m-40) cc_final: 0.7125 (t0) REVERT: A 974 MET cc_start: 0.6475 (OUTLIER) cc_final: 0.5828 (ppp) REVERT: A 1231 GLU cc_start: 0.8220 (tt0) cc_final: 0.7850 (tt0) REVERT: A 1241 MET cc_start: 0.8446 (mtt) cc_final: 0.8157 (mtt) REVERT: C 184 ASP cc_start: 0.8073 (t70) cc_final: 0.7746 (p0) REVERT: C 303 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.8072 (pm20) outliers start: 21 outliers final: 9 residues processed: 80 average time/residue: 0.5866 time to fit residues: 51.4441 Evaluate side-chains 73 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 703 LYS Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 974 MET Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain C residue 321 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 86 optimal weight: 0.4980 chunk 22 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 101 optimal weight: 0.0970 chunk 133 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 399 GLN ** C 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.115067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.077624 restraints weight = 18446.725| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.48 r_work: 0.2990 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 11736 Z= 0.234 Angle : 0.630 8.750 15930 Z= 0.317 Chirality : 0.047 0.436 1829 Planarity : 0.004 0.048 1978 Dihedral : 8.281 80.939 1596 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.61 % Allowed : 15.59 % Favored : 82.80 % 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: -1.36 (0.22), residues: 1397 helix: -0.70 (0.21), residues: 595 sheet: -0.84 (0.35), residues: 204 loop : -0.95 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1228 TYR 0.021 0.002 TYR C 236 PHE 0.019 0.002 PHE A1205 TRP 0.009 0.001 TRP C 111 HIS 0.006 0.001 HIS A1198 Details of bonding type rmsd/Z covalent geometry : bond 0.00551 / 0.23 (11724) covalent geometry : angle 0.62486 / 0.32 (15896) SS BOND : bond 0.00356 / 0.25 ( 2) SS BOND : angle 1.41320 / 1.23 ( 4) hydrogen bonds : bond 0.04211 / 2.68 ( 432) hydrogen bonds : angle 4.77475 / 3.33 ( 1218) link_BETA1-3 : bond 0.01084 / 0.73 ( 2) link_BETA1-3 : angle 1.97333 / 1.09 ( 6) link_BETA1-4 : bond 0.00583 / 0.36 ( 5) link_BETA1-4 : angle 1.70167 / 1.07 ( 15) link_NAG-ASN : bond 0.00711 / 0.41 ( 3) link_NAG-ASN : angle 2.37036 / 1.14 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 64 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 342 GLU cc_start: 0.8328 (mt-10) cc_final: 0.7882 (mm-30) REVERT: A 349 GLN cc_start: 0.8193 (pt0) cc_final: 0.7757 (tm-30) REVERT: A 460 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7946 (tp) REVERT: A 571 GLU cc_start: 0.7696 (tm-30) cc_final: 0.7369 (tm-30) REVERT: A 738 TYR cc_start: 0.7683 (m-10) cc_final: 0.7268 (m-80) REVERT: A 891 ASN cc_start: 0.8186 (m-40) cc_final: 0.7122 (t0) REVERT: A 974 MET cc_start: 0.6596 (OUTLIER) cc_final: 0.5886 (ppp) REVERT: A 1040 ILE cc_start: 0.8483 (OUTLIER) cc_final: 0.8233 (pt) REVERT: A 1241 MET cc_start: 0.8496 (mtt) cc_final: 0.8197 (mtt) REVERT: C 184 ASP cc_start: 0.8098 (t70) cc_final: 0.7784 (p0) REVERT: C 303 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7948 (mp0) outliers start: 20 outliers final: 11 residues processed: 81 average time/residue: 0.5541 time to fit residues: 49.4106 Evaluate side-chains 76 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 399 GLN Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 703 LYS Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 974 MET Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain C residue 321 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 128 optimal weight: 0.9990 chunk 114 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 99 optimal weight: 0.5980 chunk 12 optimal weight: 5.9990 chunk 131 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 21 optimal weight: 0.0000 chunk 125 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 399 GLN ** C 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.118083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.084462 restraints weight = 17970.009| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.47 r_work: 0.3041 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11736 Z= 0.116 Angle : 0.565 10.479 15930 Z= 0.285 Chirality : 0.044 0.398 1829 Planarity : 0.004 0.044 1978 Dihedral : 7.994 82.622 1596 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.29 % Allowed : 16.24 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.04 (0.22), residues: 1397 helix: -0.43 (0.22), residues: 589 sheet: -0.79 (0.36), residues: 188 loop : -0.75 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 710 TYR 0.018 0.001 TYR C 236 PHE 0.012 0.001 PHE A1205 TRP 0.009 0.001 TRP A1132 HIS 0.004 0.000 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (11724) covalent geometry : angle 0.56041 / 0.28 (15896) SS BOND : bond 0.00192 / 0.14 ( 2) SS BOND : angle 1.32113 / 0.99 ( 4) hydrogen bonds : bond 0.03615 / 2.32 ( 432) hydrogen bonds : angle 4.60645 / 3.22 ( 1218) link_BETA1-3 : bond 0.01136 / 0.77 ( 2) link_BETA1-3 : angle 1.83396 / 1.00 ( 6) link_BETA1-4 : bond 0.00540 / 0.35 ( 5) link_BETA1-4 : angle 1.46453 / 0.82 ( 15) link_NAG-ASN : bond 0.00618 / 0.32 ( 3) link_NAG-ASN : angle 2.12488 / 0.93 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 342 GLU cc_start: 0.8274 (mt-10) cc_final: 0.7909 (mm-30) REVERT: A 349 GLN cc_start: 0.8181 (pt0) cc_final: 0.7883 (tm-30) REVERT: A 460 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8056 (tp) REVERT: A 705 MET cc_start: 0.8279 (tpt) cc_final: 0.7674 (tpp) REVERT: A 738 TYR cc_start: 0.7721 (m-10) cc_final: 0.7290 (m-80) REVERT: A 743 MET cc_start: 0.9075 (mmm) cc_final: 0.8195 (mpp) REVERT: A 891 ASN cc_start: 0.8283 (m-40) cc_final: 0.7203 (t0) REVERT: A 1231 GLU cc_start: 0.8368 (tt0) cc_final: 0.8098 (tt0) REVERT: A 1241 MET cc_start: 0.8700 (mtt) cc_final: 0.8428 (mtt) REVERT: C 184 ASP cc_start: 0.8045 (t70) cc_final: 0.7772 (p0) outliers start: 16 outliers final: 8 residues processed: 78 average time/residue: 0.5258 time to fit residues: 45.1234 Evaluate side-chains 71 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 321 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 21 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 116 optimal weight: 4.9990 chunk 96 optimal weight: 0.6980 chunk 9 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 41 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 131 optimal weight: 0.9980 chunk 114 optimal weight: 0.0770 overall best weight: 1.0940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 399 GLN ** C 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.117619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.083557 restraints weight = 17800.923| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.55 r_work: 0.3037 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11736 Z= 0.150 Angle : 0.577 9.759 15930 Z= 0.290 Chirality : 0.044 0.413 1829 Planarity : 0.004 0.046 1978 Dihedral : 7.899 82.602 1596 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.53 % Allowed : 16.00 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.96 (0.22), residues: 1397 helix: -0.34 (0.22), residues: 589 sheet: -0.75 (0.36), residues: 188 loop : -0.72 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 928 TYR 0.019 0.001 TYR C 236 PHE 0.014 0.001 PHE A1205 TRP 0.008 0.001 TRP A1132 HIS 0.005 0.001 HIS A1198 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (11724) covalent geometry : angle 0.57161 / 0.29 (15896) SS BOND : bond 0.00196 / 0.14 ( 2) SS BOND : angle 1.31918 / 1.06 ( 4) hydrogen bonds : bond 0.03728 / 2.39 ( 432) hydrogen bonds : angle 4.56840 / 3.19 ( 1218) link_BETA1-3 : bond 0.00951 / 0.64 ( 2) link_BETA1-3 : angle 1.80474 / 0.99 ( 6) link_BETA1-4 : bond 0.00559 / 0.36 ( 5) link_BETA1-4 : angle 1.54992 / 0.92 ( 15) link_NAG-ASN : bond 0.00626 / 0.34 ( 3) link_NAG-ASN : angle 2.23272 / 1.01 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 61 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 342 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7902 (mm-30) REVERT: A 349 GLN cc_start: 0.8184 (pt0) cc_final: 0.7910 (tm-30) REVERT: A 460 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8129 (tp) REVERT: A 705 MET cc_start: 0.8243 (tpt) cc_final: 0.7661 (tpp) REVERT: A 738 TYR cc_start: 0.7697 (m-10) cc_final: 0.7237 (m-80) REVERT: A 743 MET cc_start: 0.9082 (mmm) cc_final: 0.8186 (mpp) REVERT: A 891 ASN cc_start: 0.8288 (m-40) cc_final: 0.7217 (t0) REVERT: A 1040 ILE cc_start: 0.8552 (OUTLIER) cc_final: 0.8293 (pt) REVERT: A 1241 MET cc_start: 0.8697 (mtt) cc_final: 0.8436 (mtt) REVERT: C 184 ASP cc_start: 0.8023 (t70) cc_final: 0.7778 (p0) outliers start: 19 outliers final: 12 residues processed: 78 average time/residue: 0.4964 time to fit residues: 43.3045 Evaluate side-chains 76 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 703 LYS Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain C residue 321 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 137 optimal weight: 0.5980 chunk 130 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 102 optimal weight: 0.7980 chunk 133 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 11 optimal weight: 7.9990 chunk 5 optimal weight: 0.0040 chunk 33 optimal weight: 0.7980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 399 GLN ** C 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.119054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.085131 restraints weight = 18090.842| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.42 r_work: 0.3068 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11736 Z= 0.110 Angle : 0.541 9.586 15930 Z= 0.273 Chirality : 0.043 0.392 1829 Planarity : 0.004 0.045 1978 Dihedral : 7.672 85.028 1596 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.21 % Allowed : 16.40 % Favored : 82.40 % 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: -0.75 (0.23), residues: 1397 helix: -0.13 (0.22), residues: 590 sheet: -0.69 (0.36), residues: 198 loop : -0.63 (0.26), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 710 TYR 0.018 0.001 TYR C 236 PHE 0.011 0.001 PHE A1205 TRP 0.010 0.001 TRP A1132 HIS 0.003 0.000 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (11724) covalent geometry : angle 0.53641 / 0.27 (15896) SS BOND : bond 0.00210 / 0.15 ( 2) SS BOND : angle 1.44591 / 0.98 ( 4) hydrogen bonds : bond 0.03378 / 2.17 ( 432) hydrogen bonds : angle 4.44247 / 3.11 ( 1218) link_BETA1-3 : bond 0.01073 / 0.73 ( 2) link_BETA1-3 : angle 1.72042 / 0.94 ( 6) link_BETA1-4 : bond 0.00521 / 0.34 ( 5) link_BETA1-4 : angle 1.41694 / 0.78 ( 15) link_NAG-ASN : bond 0.00570 / 0.30 ( 3) link_NAG-ASN : angle 2.12017 / 0.91 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 342 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7914 (mm-30) REVERT: A 349 GLN cc_start: 0.8178 (pt0) cc_final: 0.7862 (tm-30) REVERT: A 705 MET cc_start: 0.8240 (tpt) cc_final: 0.7701 (tpp) REVERT: A 738 TYR cc_start: 0.7748 (m-10) cc_final: 0.7278 (m-80) REVERT: A 743 MET cc_start: 0.9124 (mmm) cc_final: 0.8246 (mpp) REVERT: A 891 ASN cc_start: 0.8301 (m-40) cc_final: 0.7253 (t0) REVERT: A 974 MET cc_start: 0.6777 (OUTLIER) cc_final: 0.6171 (ppp) REVERT: A 1231 GLU cc_start: 0.8372 (tt0) cc_final: 0.8108 (tt0) REVERT: A 1241 MET cc_start: 0.8691 (mtt) cc_final: 0.8438 (mtt) REVERT: C 184 ASP cc_start: 0.7984 (t70) cc_final: 0.7762 (p0) outliers start: 15 outliers final: 10 residues processed: 85 average time/residue: 0.5313 time to fit residues: 49.9885 Evaluate side-chains 73 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 703 LYS Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 974 MET Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain C residue 321 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 1.9990 chunk 134 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 58 optimal weight: 0.0270 chunk 88 optimal weight: 0.9990 chunk 133 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 100 optimal weight: 0.0670 chunk 109 optimal weight: 0.7980 overall best weight: 0.5576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 399 GLN ** C 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.118497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.081021 restraints weight = 18065.119| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.51 r_work: 0.3043 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 11736 Z= 0.106 Angle : 0.537 9.162 15930 Z= 0.272 Chirality : 0.043 0.391 1829 Planarity : 0.003 0.046 1978 Dihedral : 7.596 86.335 1596 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.13 % Allowed : 16.72 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.60 (0.23), residues: 1397 helix: 0.02 (0.22), residues: 590 sheet: -0.62 (0.36), residues: 198 loop : -0.58 (0.26), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 603 TYR 0.017 0.001 TYR C 236 PHE 0.018 0.001 PHE A1103 TRP 0.011 0.001 TRP C 111 HIS 0.003 0.000 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (11724) covalent geometry : angle 0.53206 / 0.27 (15896) SS BOND : bond 0.00191 / 0.14 ( 2) SS BOND : angle 1.33976 / 0.97 ( 4) hydrogen bonds : bond 0.03312 / 2.13 ( 432) hydrogen bonds : angle 4.38740 / 3.07 ( 1218) link_BETA1-3 : bond 0.01041 / 0.70 ( 2) link_BETA1-3 : angle 1.69077 / 0.93 ( 6) link_BETA1-4 : bond 0.00528 / 0.34 ( 5) link_BETA1-4 : angle 1.41669 / 0.80 ( 15) link_NAG-ASN : bond 0.00580 / 0.30 ( 3) link_NAG-ASN : angle 2.11871 / 0.92 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4118.03 seconds wall clock time: 71 minutes 3.63 seconds (4263.63 seconds total)