Starting phenix.real_space_refine on Fri Sep 11 22:31:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6roi_4973/09_2026/6roi_4973.cif Found real_map, /net/cci-nas-00/data/ceres_data/6roi_4973/09_2026/6roi_4973.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6roi_4973/09_2026/6roi_4973.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6roi_4973/09_2026/6roi_4973.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6roi_4973/09_2026/6roi_4973.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6roi_4973/09_2026/6roi_4973.cif" model { file = "/net/cci-nas-00/data/ceres_data/6roi_4973/09_2026/6roi_4973.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6roi_4973/09_2026/6roi_4973.cif" } resolution = 3.7 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= 0.004 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 49 5.16 5 Be 1 3.05 5 C 7599 2.51 5 N 1907 2.21 5 O 2213 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 67 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: 11775 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 8861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1108, 8861 Classifications: {'peptide': 1108} Link IDs: {'PTRANS': 30, 'TRANS': 1077} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Chain: "C" Number of atoms: 2754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2754 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 21, 'TRANS': 317} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 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: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 66 Unusual residues: {' MG': 1, '2Y5': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 3.18, per 1000 atoms: 0.27 Number of scatterers: 11775 At special positions: 0 Unit cell: (74.313, 99.084, 174.474, 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 49 16.00 P 2 15.00 Mg 1 11.99 F 3 9.00 O 2213 8.00 N 1907 7.00 C 7599 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=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-3 " BMA D 3 " - " BMA D 4 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " NAG-ASN " NAG B 1 " - " ASN C 288 " " NAG C 503 " - " ASN C 216 " " NAG D 1 " - " ASN C 199 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.08 Conformation dependent library (CDL) restraints added in 543.3 milliseconds 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2734 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 12 sheets defined 38.7% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 191 through 195 Processing helix chain 'A' and resid 213 through 223 removed outlier: 4.330A pdb=" N PHE A 219 " --> pdb=" O PRO A 215 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN A 220 " --> pdb=" O LYS A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 237 removed outlier: 3.791A pdb=" N LEU A 231 " --> pdb=" O ASN A 227 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N CYS A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 253 Processing helix chain 'A' and resid 253 through 271 removed outlier: 3.901A pdb=" N VAL A 257 " --> pdb=" O THR A 253 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLU A 265 " --> pdb=" O SER A 261 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE A 267 " --> pdb=" O MET A 263 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS A 271 " --> pdb=" O ILE A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 281 removed outlier: 4.696A pdb=" N LEU A 279 " --> pdb=" O SER A 275 " (cutoff:3.500A) 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 440 through 445 Processing helix chain 'A' and resid 448 through 458 removed outlier: 4.228A pdb=" N VAL A 454 " --> pdb=" O ALA A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 473 removed outlier: 3.644A pdb=" N VAL A 467 " --> pdb=" O SER A 463 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR A 471 " --> pdb=" O VAL A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 481 removed outlier: 3.606A pdb=" N LEU A 480 " --> pdb=" O LEU A 477 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR A 481 " --> pdb=" O SER A 478 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 477 through 481' Processing helix chain 'A' and resid 496 through 502 removed outlier: 3.602A pdb=" N PHE A 502 " --> pdb=" O PHE A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 526 removed outlier: 3.773A pdb=" N TYR A 520 " --> pdb=" O LEU A 516 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA A 522 " --> pdb=" O LYS A 518 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY A 526 " --> pdb=" O ALA A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 530 removed outlier: 6.575A pdb=" N ASP A 530 " --> pdb=" O SER A 527 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 527 through 530' Processing helix chain 'A' and resid 548 through 553 removed outlier: 3.574A pdb=" N LEU A 551 " --> pdb=" O VAL A 548 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLY A 552 " --> pdb=" O GLU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 614 removed outlier: 3.785A pdb=" N LEU A 608 " --> pdb=" O LYS A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 628 removed outlier: 3.591A pdb=" N THR A 628 " --> pdb=" O ASN A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 633 removed outlier: 3.923A pdb=" N CYS A 633 " --> pdb=" O LEU A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 663 removed outlier: 3.825A pdb=" N GLN A 660 " --> pdb=" O GLY A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 666 No H-bonds generated for 'chain 'A' and resid 664 through 666' Processing helix chain 'A' and resid 723 through 728 Processing helix chain 'A' and resid 738 through 750 removed outlier: 3.664A pdb=" N HIS A 745 " --> pdb=" O ALA A 741 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA A 750 " --> pdb=" O LEU A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 779 removed outlier: 3.619A pdb=" N TYR A 769 " --> pdb=" O SER A 765 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU A 770 " --> pdb=" O GLU A 766 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TRP A 772 " --> pdb=" O GLU A 768 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N SER A 774 " --> pdb=" O GLU A 770 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ILE A 775 " --> pdb=" O GLU A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 796 removed outlier: 4.981A pdb=" N ASP A 791 " --> pdb=" O ALA A 787 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLU A 792 " --> pdb=" O GLU A 788 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN A 795 " --> pdb=" O ASP A 791 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU A 796 " --> pdb=" O GLU A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 827 removed outlier: 3.836A pdb=" N HIS A 822 " --> pdb=" O PRO A 818 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR A 823 " --> pdb=" O GLU A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 849 removed outlier: 3.657A pdb=" N ALA A 842 " --> pdb=" O ARG A 838 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE A 843 " --> pdb=" O GLN A 839 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ASN A 844 " --> pdb=" O GLU A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 882 removed outlier: 3.619A pdb=" N ASN A 872 " --> pdb=" O ASP A 868 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS A 876 " --> pdb=" O ASN A 872 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU A 880 " --> pdb=" O LYS A 876 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLU A 882 " --> pdb=" O ASN A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 899 through 903 removed outlier: 3.561A pdb=" N GLY A 903 " --> pdb=" O GLY A 899 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 899 through 903' Processing helix chain 'A' and resid 910 through 919 Processing helix chain 'A' and resid 932 through 937 Processing helix chain 'A' and resid 937 through 942 Processing helix chain 'A' and resid 958 through 963 removed outlier: 3.563A pdb=" N GLN A 963 " --> pdb=" O VAL A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 982 removed outlier: 3.798A 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 1007 removed outlier: 3.874A pdb=" N GLY A1001 " --> pdb=" O LEU A 997 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER A1002 " --> pdb=" O LEU A 998 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER A1004 " --> pdb=" O HIS A1000 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLN A1006 " --> pdb=" O SER A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1007 through 1012 removed outlier: 3.913A pdb=" N ALA A1011 " --> pdb=" O ARG A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1022 removed outlier: 3.937A pdb=" N LEU A1022 " --> pdb=" O LYS A1018 " (cutoff:3.500A) Processing helix chain 'A' and resid 1042 through 1048 removed outlier: 3.545A pdb=" N MET A1046 " --> pdb=" O GLU A1042 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER A1047 " --> pdb=" O SER A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1064 removed outlier: 3.794A pdb=" N PHE A1059 " --> pdb=" O VAL A1055 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1076 removed outlier: 3.795A pdb=" N GLU A1074 " --> pdb=" O SER A1070 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1079 No H-bonds generated for 'chain 'A' and resid 1077 through 1079' Processing helix chain 'A' and resid 1080 through 1086 removed outlier: 3.955A pdb=" N LYS A1085 " --> pdb=" O LYS A1081 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY A1086 " --> pdb=" O LEU A1082 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1104 removed outlier: 4.623A pdb=" N GLY A1096 " --> pdb=" O TYR A1092 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TRP A1097 " --> pdb=" O ILE A1093 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN A1100 " --> pdb=" O GLY A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1110 through 1115 removed outlier: 3.569A pdb=" N LEU A1114 " --> pdb=" O ILE A1110 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE A1115 " --> pdb=" O GLY A1111 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1110 through 1115' Processing helix chain 'A' and resid 1131 through 1154 removed outlier: 3.649A pdb=" N VAL A1136 " --> pdb=" O TRP A1132 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N THR A1137 " --> pdb=" O SER A1133 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL A1146 " --> pdb=" O SER A1142 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLY A1148 " --> pdb=" O ILE A1144 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A1152 " --> pdb=" O GLY A1148 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR A1154 " --> pdb=" O ALA A1150 " (cutoff:3.500A) Processing helix chain 'A' and resid 1160 through 1165 removed outlier: 3.734A pdb=" N ALA A1164 " --> pdb=" O PHE A1160 " (cutoff:3.500A) Processing helix chain 'A' and resid 1167 through 1182 removed outlier: 3.663A pdb=" N ILE A1174 " --> pdb=" O LEU A1170 " (cutoff:3.500A) Proline residue: A1177 - end of helix Processing helix chain 'A' and resid 1183 through 1187 Processing helix chain 'A' and resid 1194 through 1201 removed outlier: 3.532A pdb=" N GLY A1201 " --> pdb=" O LYS A1197 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1230 removed outlier: 3.959A pdb=" N TRP A1206 " --> pdb=" O SER A1202 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU A1207 " --> pdb=" O GLY A1203 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE A1210 " --> pdb=" O TRP A1206 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N VAL A1211 " --> pdb=" O LEU A1207 " (cutoff:3.500A) Proline residue: A1213 - end of helix removed outlier: 3.699A pdb=" N ALA A1216 " --> pdb=" O LEU A1212 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ARG A1219 " --> pdb=" O PHE A1215 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ASP A1220 " --> pdb=" O ALA A1216 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR A1225 " --> pdb=" O PHE A1221 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N MET A1229 " --> pdb=" O TYR A1225 " (cutoff:3.500A) Processing helix chain 'A' and resid 1235 through 1245 removed outlier: 3.649A pdb=" N LYS A1243 " --> pdb=" O GLN A1239 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR A1244 " --> pdb=" O GLU A1240 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 61 Processing helix chain 'C' and resid 93 through 95 No H-bonds generated for 'chain 'C' and resid 93 through 95' Processing helix chain 'C' and resid 150 through 155 removed outlier: 4.376A pdb=" N GLN C 155 " --> pdb=" O ARG C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 164 removed outlier: 3.702A pdb=" N LEU C 163 " --> pdb=" O THR C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 196 Processing helix chain 'C' and resid 226 through 231 removed outlier: 3.679A pdb=" N ARG C 230 " --> pdb=" O ILE C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 239 No H-bonds generated for 'chain 'C' and resid 237 through 239' Processing helix chain 'C' and resid 266 through 274 removed outlier: 3.632A pdb=" N GLN C 270 " --> pdb=" O TRP C 266 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TRP C 272 " --> pdb=" O GLU C 268 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG C 274 " --> pdb=" O GLN C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 346 removed outlier: 3.670A pdb=" N LEU C 337 " --> pdb=" O GLY C 333 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL C 339 " --> pdb=" O LEU C 335 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA C 340 " --> pdb=" O TYR C 336 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA C 344 " --> pdb=" O ALA C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 354 Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 186 Processing sheet with id=AA2, first strand: chain 'A' and resid 293 through 298 removed outlier: 3.710A pdb=" N ASP A 293 " --> pdb=" O SER A 288 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER A 288 " --> pdb=" O ASP A 293 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLU A 285 " --> pdb=" O ARG A 309 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ILE A 307 " --> pdb=" O PHE A 287 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N PHE A 414 " --> pdb=" O LEU A 323 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 314 through 315 removed outlier: 3.780A pdb=" N GLU A 314 " --> pdb=" O LEU A 407 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR A 406 " --> pdb=" O GLU A 335 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR A 333 " --> pdb=" O ARG A 408 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 532 through 533 Processing sheet with id=AA5, first strand: chain 'A' and resid 541 through 542 removed outlier: 3.579A pdb=" N ILE A 985 " --> pdb=" O GLY A 968 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ALA A 951 " --> pdb=" O VAL A 969 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N ILE A 971 " --> pdb=" O ALA A 951 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLY A 953 " --> pdb=" O ILE A 971 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N TYR A 556 " --> pdb=" O LEU A 950 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ILE A 952 " --> pdb=" O TYR A 556 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N PHE A 558 " --> pdb=" O ILE A 952 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N ILE A 557 " --> pdb=" O TRP A 832 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LEU A 834 " --> pdb=" O ILE A 557 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL A 924 " --> pdb=" O ILE A 831 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N LEU A 893 " --> pdb=" O ALA A 923 " (cutoff:3.500A) removed outlier: 8.990A pdb=" N ILE A 925 " --> pdb=" O LEU A 893 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU A 895 " --> pdb=" O ILE A 925 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N CYS A 927 " --> pdb=" O LEU A 895 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ILE A 897 " --> pdb=" O CYS A 927 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP A 898 " --> pdb=" O ILE A 861 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 580 through 583 removed outlier: 7.016A pdb=" N LYS A 812 " --> pdb=" O ARG A 567 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ILE A 569 " --> pdb=" O GLU A 810 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N GLU A 810 " --> pdb=" O ILE A 569 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N GLU A 571 " --> pdb=" O ALA A 808 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N ALA A 808 " --> pdb=" O GLU A 571 " (cutoff:3.500A) removed outlier: 9.743A pdb=" N LYS A 573 " --> pdb=" O ALA A 806 " (cutoff:3.500A) removed outlier: 12.363A pdb=" N ALA A 806 " --> pdb=" O LYS A 573 " (cutoff:3.500A) removed outlier: 10.689A pdb=" N CYS A 575 " --> pdb=" O ILE A 804 " (cutoff:3.500A) removed outlier: 11.942A pdb=" N ILE A 804 " --> pdb=" O CYS A 575 " (cutoff:3.500A) removed outlier: 12.060A pdb=" N ILE A 577 " --> pdb=" O ILE A 802 " (cutoff:3.500A) removed outlier: 14.708A pdb=" N ILE A 802 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU A 759 " --> pdb=" O ILE A 804 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ALA A 806 " --> pdb=" O LEU A 757 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU A 757 " --> pdb=" O ALA A 806 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ALA A 808 " --> pdb=" O ARG A 755 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ARG A 755 " --> pdb=" O ALA A 808 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ARG A 710 " --> pdb=" O LEU A 692 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N LEU A 692 " --> pdb=" O ARG A 710 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 637 through 640 Processing sheet with id=AA8, first strand: chain 'C' and resid 97 through 100 Processing sheet with id=AA9, first strand: chain 'C' and resid 90 through 91 removed outlier: 3.620A pdb=" N GLU C 90 " --> pdb=" O TRP C 111 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TRP C 111 " --> pdb=" O GLU C 90 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N ASN C 301 " --> pdb=" O VAL C 205 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N VAL C 205 " --> pdb=" O ASN C 301 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 137 through 140 Processing sheet with id=AB2, first strand: chain 'C' and resid 143 through 144 Processing sheet with id=AB3, first strand: chain 'C' and resid 186 through 187 removed outlier: 6.268A pdb=" N ILE C 186 " --> pdb=" O VAL C 242 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 318 hydrogen bonds defined for protein. 888 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: 2.54 Time building geometry restraints manager: 1.41 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: 1908 1.31 - 1.44: 3273 1.44 - 1.57: 6774 1.57 - 1.70: 3 1.70 - 1.82: 79 Bond restraints: 12037 Sorted by residual: bond pdb=" OD1 BFD A 560 " pdb="BE BFD A 560 " ideal model delta sigma weight residual 1.737 1.515 0.222 2.00e-02 2.50e+03 1.24e+02 bond pdb=" C10 2Y5 A1502 " pdb=" O16 2Y5 A1502 " ideal model delta sigma weight residual 1.333 1.404 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" C11 2Y5 A1502 " pdb=" O18 2Y5 A1502 " ideal model delta sigma weight residual 1.335 1.403 -0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" O4 2Y5 A1502 " pdb=" P4 2Y5 A1502 " ideal model delta sigma weight residual 1.703 1.646 0.057 2.00e-02 2.50e+03 8.21e+00 bond pdb=" C1 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.60e+00 ... (remaining 12032 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.95: 15955 2.95 - 5.91: 302 5.91 - 8.86: 38 8.86 - 11.82: 8 11.82 - 14.77: 3 Bond angle restraints: 16306 Sorted by residual: angle pdb=" N GLY A1283 " pdb=" CA GLY A1283 " pdb=" C GLY A1283 " ideal model delta sigma weight residual 115.80 105.83 9.97 1.74e+00 3.30e-01 3.29e+01 angle pdb=" CA TYR A1192 " pdb=" CB TYR A1192 " pdb=" CG TYR A1192 " ideal model delta sigma weight residual 113.90 123.25 -9.35 1.80e+00 3.09e-01 2.70e+01 angle pdb=" O1 2Y5 A1502 " pdb=" P1 2Y5 A1502 " pdb=" O13 2Y5 A1502 " ideal model delta sigma weight residual 97.01 111.78 -14.77 3.00e+00 1.11e-01 2.42e+01 angle pdb=" CA ASN A1033 " pdb=" CB ASN A1033 " pdb=" CG ASN A1033 " ideal model delta sigma weight residual 112.60 117.12 -4.52 1.00e+00 1.00e+00 2.04e+01 angle pdb=" N ILE A 671 " pdb=" CA ILE A 671 " pdb=" C ILE A 671 " ideal model delta sigma weight residual 109.34 118.42 -9.08 2.08e+00 2.31e-01 1.91e+01 ... (remaining 16301 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.33: 6615 24.33 - 48.65: 468 48.65 - 72.97: 57 72.97 - 97.30: 20 97.30 - 121.62: 9 Dihedral angle restraints: 7169 sinusoidal: 2928 harmonic: 4241 Sorted by residual: 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 -153.44 -26.56 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA GLU A1191 " pdb=" C GLU A1191 " pdb=" N TYR A1192 " pdb=" CA TYR A1192 " ideal model delta harmonic sigma weight residual -180.00 -154.60 -25.40 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA PHE A1031 " pdb=" C PHE A1031 " pdb=" N ALA A1032 " pdb=" CA ALA A1032 " ideal model delta harmonic sigma weight residual 180.00 155.46 24.54 0 5.00e+00 4.00e-02 2.41e+01 ... (remaining 7166 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.998: 1856 0.998 - 1.996: 0 1.996 - 2.994: 0 2.994 - 3.992: 0 3.992 - 4.990: 1 Chirality restraints: 1857 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 2.46 -4.99 2.00e-01 2.50e+01 6.22e+02 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN C 199 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.72 -0.68 2.00e-01 2.50e+01 1.17e+01 chirality pdb=" C5 BMA D 4 " pdb=" C4 BMA D 4 " pdb=" C6 BMA D 4 " pdb=" O5 BMA D 4 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.30 2.00e-01 2.50e+01 2.24e+00 ... (remaining 1854 not shown) Planarity restraints: 2042 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU A 342 " 0.024 2.00e-02 2.50e+03 4.78e-02 2.28e+01 pdb=" CD GLU A 342 " -0.083 2.00e-02 2.50e+03 pdb=" OE1 GLU A 342 " 0.029 2.00e-02 2.50e+03 pdb=" OE2 GLU A 342 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A1057 " 0.064 5.00e-02 4.00e+02 9.51e-02 1.45e+01 pdb=" N PRO A1058 " -0.164 5.00e-02 4.00e+02 pdb=" CA PRO A1058 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO A1058 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A1212 " -0.047 5.00e-02 4.00e+02 7.03e-02 7.90e+00 pdb=" N PRO A1213 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO A1213 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A1213 " -0.040 5.00e-02 4.00e+02 ... (remaining 2039 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 23 2.35 - 2.99: 5788 2.99 - 3.62: 16946 3.62 - 4.26: 26595 4.26 - 4.90: 43776 Nonbonded interactions: 93128 Sorted by model distance: nonbonded pdb=" F2 BFD A 560 " pdb="MG MG A1501 " model vdw 1.709 2.120 nonbonded pdb="MG MG A1501 " pdb=" O HOH A1601 " model vdw 1.740 2.170 nonbonded pdb="MG MG A1501 " pdb=" O HOH A1602 " model vdw 1.805 2.170 nonbonded pdb=" O THR A 562 " pdb="MG MG A1501 " model vdw 1.999 2.170 nonbonded pdb=" OD2 BFD A 560 " pdb="MG MG A1501 " model vdw 2.076 2.170 ... (remaining 93123 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.440 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: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 13.380 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.222 12047 Z= 0.377 Angle : 1.056 14.769 16331 Z= 0.561 Chirality : 0.131 4.990 1857 Planarity : 0.007 0.095 2039 Dihedral : 17.309 121.624 4429 Min Nonbonded Distance : 1.709 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.23 % Allowed : 9.47 % Favored : 90.30 % 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: -5.18 (0.16), residues: 1438 helix: -4.68 (0.08), residues: 537 sheet: -2.28 (0.33), residues: 201 loop : -2.65 (0.18), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1219 TYR 0.046 0.002 TYR A1192 PHE 0.042 0.003 PHE A 605 TRP 0.047 0.003 TRP C 111 HIS 0.007 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00849 / 0.38 (12037) covalent geometry : angle 1.04692 / 0.56 (16306) SS BOND : bond 0.01350 / 0.96 ( 2) SS BOND : angle 1.86357 / 1.11 ( 4) hydrogen bonds : bond 0.29893 / 19.40 ( 318) hydrogen bonds : angle 10.78002 / 7.43 ( 888) Misc. bond : bond 0.00488 / 0.33 ( 1) link_BETA1-3 : bond 0.00182 / 0.12 ( 1) link_BETA1-3 : angle 3.61286 / 2.19 ( 3) link_BETA1-4 : bond 0.00756 / 0.46 ( 3) link_BETA1-4 : angle 1.17816 / 0.81 ( 9) link_NAG-ASN : bond 0.00775 / 0.52 ( 3) link_NAG-ASN : angle 5.38194 / 3.59 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 231 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 263 MET cc_start: 0.5012 (tpt) cc_final: 0.4486 (ptt) REVERT: A 272 ARG cc_start: 0.7824 (ttm110) cc_final: 0.7155 (ttp-110) REVERT: A 321 ILE cc_start: 0.7668 (mm) cc_final: 0.7235 (pt) REVERT: A 349 GLN cc_start: 0.7769 (tt0) cc_final: 0.7435 (tm-30) REVERT: A 366 MET cc_start: 0.7363 (mmp) cc_final: 0.7149 (mmt) REVERT: A 382 TYR cc_start: 0.8671 (t80) cc_final: 0.8170 (t80) REVERT: A 660 GLN cc_start: 0.8512 (tp40) cc_final: 0.8299 (tp40) REVERT: A 721 LYS cc_start: 0.7800 (pttt) cc_final: 0.7386 (pttp) REVERT: A 729 GLU cc_start: 0.8373 (mp0) cc_final: 0.8153 (mp0) REVERT: A 744 ARG cc_start: 0.7889 (tpt-90) cc_final: 0.6888 (tpm170) REVERT: A 748 ASP cc_start: 0.8501 (t0) cc_final: 0.8046 (t0) REVERT: A 792 GLU cc_start: 0.8779 (tp30) cc_final: 0.8571 (tp30) REVERT: A 810 GLU cc_start: 0.8831 (pp20) cc_final: 0.7970 (pp20) REVERT: A 819 GLU cc_start: 0.7991 (mp0) cc_final: 0.7558 (tp30) REVERT: A 844 ASN cc_start: 0.8448 (t0) cc_final: 0.8198 (t0) REVERT: A 900 LYS cc_start: 0.8110 (ttmt) cc_final: 0.7408 (pttp) REVERT: A 928 ARG cc_start: 0.7837 (ttm170) cc_final: 0.7318 (ttm-80) REVERT: A 944 LYS cc_start: 0.7928 (tppp) cc_final: 0.7254 (tptt) REVERT: A 1024 MET cc_start: 0.8066 (mmp) cc_final: 0.7808 (tpt) REVERT: A 1087 GLN cc_start: 0.7727 (mt0) cc_final: 0.7256 (tt0) REVERT: A 1159 LYS cc_start: 0.8678 (pttt) cc_final: 0.8212 (tptt) REVERT: A 1188 ILE cc_start: 0.7654 (tp) cc_final: 0.7318 (tp) REVERT: C 168 LYS cc_start: 0.8068 (mmmt) cc_final: 0.7667 (pttp) REVERT: C 220 LYS cc_start: 0.9123 (mtmt) cc_final: 0.8782 (mttm) outliers start: 3 outliers final: 2 residues processed: 233 average time/residue: 0.1228 time to fit residues: 40.2480 Evaluate side-chains 166 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 164 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 898 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.0570 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 103 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 54.5692 > 50:) chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 374 GLN A 409 ASN A 580 HIS A 613 ASN A 694 ASN A 844 ASN A1019 ASN A1050 ASN A1245 ASN ** A1279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 GLN C 116 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.157544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.127050 restraints weight = 15209.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.126559 restraints weight = 16129.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.128092 restraints weight = 14854.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.128426 restraints weight = 10211.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.128684 restraints weight = 10096.247| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12047 Z= 0.135 Angle : 0.645 9.422 16331 Z= 0.330 Chirality : 0.046 0.313 1857 Planarity : 0.005 0.065 2039 Dihedral : 10.187 100.874 1648 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.80 % Allowed : 15.96 % Favored : 82.24 % 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: -4.02 (0.18), residues: 1438 helix: -3.44 (0.15), residues: 554 sheet: -1.91 (0.34), residues: 207 loop : -2.08 (0.21), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1117 TYR 0.030 0.001 TYR A1192 PHE 0.017 0.001 PHE C 51 TRP 0.018 0.001 TRP C 111 HIS 0.007 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (12037) covalent geometry : angle 0.63766 / 0.33 (16306) SS BOND : bond 0.00700 / 0.50 ( 2) SS BOND : angle 1.31327 / 0.77 ( 4) hydrogen bonds : bond 0.04578 / 3.09 ( 318) hydrogen bonds : angle 6.19949 / 4.32 ( 888) Misc. bond : bond 0.00332 / 0.22 ( 1) link_BETA1-3 : bond 0.00774 / 0.52 ( 1) link_BETA1-3 : angle 2.45568 / 1.53 ( 3) link_BETA1-4 : bond 0.00496 / 0.27 ( 3) link_BETA1-4 : angle 1.19144 / 0.66 ( 9) link_NAG-ASN : bond 0.00420 / 0.27 ( 3) link_NAG-ASN : angle 3.70963 / 2.49 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 187 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 263 MET cc_start: 0.5772 (tpt) cc_final: 0.5479 (ptt) REVERT: A 321 ILE cc_start: 0.8014 (mm) cc_final: 0.7532 (pt) REVERT: A 407 LEU cc_start: 0.8932 (tp) cc_final: 0.8632 (tp) REVERT: A 441 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7313 (tt0) REVERT: A 705 MET cc_start: 0.7482 (ppp) cc_final: 0.7152 (ptt) REVERT: A 721 LYS cc_start: 0.8344 (pttt) cc_final: 0.7918 (ptpp) REVERT: A 744 ARG cc_start: 0.7989 (tpt-90) cc_final: 0.7562 (tpm170) REVERT: A 791 ASP cc_start: 0.6903 (p0) cc_final: 0.6515 (m-30) REVERT: A 792 GLU cc_start: 0.7553 (tp30) cc_final: 0.7287 (tp30) REVERT: A 810 GLU cc_start: 0.8595 (pp20) cc_final: 0.8192 (pp20) REVERT: A 898 ASP cc_start: 0.8570 (OUTLIER) cc_final: 0.8321 (p0) REVERT: A 944 LYS cc_start: 0.8015 (tppp) cc_final: 0.7605 (tptt) REVERT: A 1188 ILE cc_start: 0.7498 (tp) cc_final: 0.7222 (tp) REVERT: C 77 TYR cc_start: 0.9184 (p90) cc_final: 0.8912 (p90) outliers start: 23 outliers final: 17 residues processed: 201 average time/residue: 0.1052 time to fit residues: 31.2361 Evaluate side-chains 181 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 162 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 795 ASN Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 898 ASP Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1195 VAL Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 256 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 105 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 60 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 chunk 125 optimal weight: 0.7980 chunk 138 optimal weight: 0.7980 chunk 25 optimal weight: 6.9990 chunk 139 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1100 ASN ** A1236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1245 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.160296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.129707 restraints weight = 15264.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.129342 restraints weight = 15896.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.131025 restraints weight = 14437.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.131462 restraints weight = 10480.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.131525 restraints weight = 10140.222| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12047 Z= 0.136 Angle : 0.599 9.061 16331 Z= 0.306 Chirality : 0.044 0.277 1857 Planarity : 0.004 0.060 2039 Dihedral : 9.059 101.369 1646 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.50 % Allowed : 17.45 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.40 (0.19), residues: 1438 helix: -2.78 (0.18), residues: 546 sheet: -1.80 (0.33), residues: 208 loop : -1.81 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1117 TYR 0.020 0.001 TYR A1192 PHE 0.018 0.001 PHE C 51 TRP 0.013 0.001 TRP A1028 HIS 0.010 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (12037) covalent geometry : angle 0.59225 / 0.30 (16306) SS BOND : bond 0.00498 / 0.36 ( 2) SS BOND : angle 1.02399 / 0.61 ( 4) hydrogen bonds : bond 0.03642 / 2.43 ( 318) hydrogen bonds : angle 5.45680 / 3.83 ( 888) Misc. bond : bond 0.00327 / 0.22 ( 1) link_BETA1-3 : bond 0.00407 / 0.27 ( 1) link_BETA1-3 : angle 2.08782 / 1.25 ( 3) link_BETA1-4 : bond 0.00483 / 0.26 ( 3) link_BETA1-4 : angle 1.21838 / 0.66 ( 9) link_NAG-ASN : bond 0.00350 / 0.24 ( 3) link_NAG-ASN : angle 3.60556 / 2.43 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 173 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 ILE cc_start: 0.8053 (mm) cc_final: 0.7526 (pt) REVERT: A 705 MET cc_start: 0.7597 (ppp) cc_final: 0.7296 (ptt) REVERT: A 721 LYS cc_start: 0.8382 (pttt) cc_final: 0.8084 (ptpt) REVERT: A 744 ARG cc_start: 0.7993 (tpt-90) cc_final: 0.7552 (tpm170) REVERT: A 791 ASP cc_start: 0.6949 (p0) cc_final: 0.6596 (m-30) REVERT: A 792 GLU cc_start: 0.7545 (tp30) cc_final: 0.7318 (tp30) REVERT: A 810 GLU cc_start: 0.8683 (pp20) cc_final: 0.8284 (pp20) REVERT: A 944 LYS cc_start: 0.8095 (tppp) cc_final: 0.7653 (tptt) REVERT: A 1188 ILE cc_start: 0.7623 (tp) cc_final: 0.7414 (tp) REVERT: A 1229 MET cc_start: 0.7185 (mtm) cc_final: 0.6792 (mtp) REVERT: C 77 TYR cc_start: 0.9213 (p90) cc_final: 0.8843 (p90) REVERT: C 289 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7946 (mm-30) outliers start: 32 outliers final: 22 residues processed: 192 average time/residue: 0.1052 time to fit residues: 30.0632 Evaluate side-chains 178 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 156 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 795 ASN Chi-restraints excluded: chain A residue 815 ASP Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1195 VAL Chi-restraints excluded: chain A residue 1218 VAL Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 320 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 45 optimal weight: 0.9990 chunk 30 optimal weight: 0.0470 chunk 94 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 113 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 120 optimal weight: 7.9990 chunk 86 optimal weight: 0.7980 overall best weight: 0.7478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 338 ASN A1100 ASN ** A1236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1245 ASN ** A1279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.160793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.130187 restraints weight = 15137.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.130030 restraints weight = 15265.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.131071 restraints weight = 14273.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.131705 restraints weight = 11671.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.132473 restraints weight = 9830.882| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12047 Z= 0.125 Angle : 0.582 8.600 16331 Z= 0.296 Chirality : 0.044 0.262 1857 Planarity : 0.004 0.055 2039 Dihedral : 8.656 102.735 1644 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.36 % Allowed : 18.00 % Favored : 78.64 % 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: -2.95 (0.20), residues: 1438 helix: -2.31 (0.20), residues: 546 sheet: -1.64 (0.32), residues: 218 loop : -1.61 (0.22), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1117 TYR 0.022 0.001 TYR A1192 PHE 0.018 0.001 PHE C 51 TRP 0.023 0.001 TRP A1028 HIS 0.010 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (12037) covalent geometry : angle 0.57514 / 0.29 (16306) SS BOND : bond 0.00521 / 0.37 ( 2) SS BOND : angle 1.03805 / 0.64 ( 4) hydrogen bonds : bond 0.03093 / 2.07 ( 318) hydrogen bonds : angle 5.06753 / 3.56 ( 888) Misc. bond : bond 0.00993 / 0.66 ( 1) link_BETA1-3 : bond 0.00528 / 0.35 ( 1) link_BETA1-3 : angle 1.86449 / 1.13 ( 3) link_BETA1-4 : bond 0.00417 / 0.23 ( 3) link_BETA1-4 : angle 1.18319 / 0.65 ( 9) link_NAG-ASN : bond 0.00312 / 0.21 ( 3) link_NAG-ASN : angle 3.47065 / 2.33 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 169 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 ILE cc_start: 0.8153 (mm) cc_final: 0.7610 (pt) REVERT: A 441 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7312 (tt0) REVERT: A 513 THR cc_start: 0.8720 (p) cc_final: 0.8477 (t) REVERT: A 654 ASP cc_start: 0.7899 (m-30) cc_final: 0.7667 (m-30) REVERT: A 705 MET cc_start: 0.7605 (ppp) cc_final: 0.7353 (ptt) REVERT: A 721 LYS cc_start: 0.8379 (pttt) cc_final: 0.8077 (ptpt) REVERT: A 744 ARG cc_start: 0.8023 (tpt-90) cc_final: 0.7590 (tpm170) REVERT: A 791 ASP cc_start: 0.6958 (p0) cc_final: 0.6589 (m-30) REVERT: A 810 GLU cc_start: 0.8585 (pp20) cc_final: 0.8316 (pp20) REVERT: A 861 ILE cc_start: 0.8856 (mp) cc_final: 0.8613 (mt) REVERT: A 944 LYS cc_start: 0.8116 (tppp) cc_final: 0.7659 (tptt) REVERT: A 1229 MET cc_start: 0.7295 (mtm) cc_final: 0.6805 (mtp) REVERT: C 77 TYR cc_start: 0.9179 (p90) cc_final: 0.8796 (p90) REVERT: C 289 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7845 (mm-30) outliers start: 43 outliers final: 31 residues processed: 202 average time/residue: 0.0986 time to fit residues: 29.7376 Evaluate side-chains 188 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 156 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 795 ASN Chi-restraints excluded: chain A residue 815 ASP Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1138 VAL Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1191 GLU Chi-restraints excluded: chain A residue 1195 VAL Chi-restraints excluded: chain A residue 1218 VAL Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 190 CYS Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 319 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 136 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 142 optimal weight: 0.0970 chunk 26 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 127 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 96 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 839 GLN ** A1236 HIS ** 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 = 0.3841 r_free = 0.3841 target = 0.163044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.132800 restraints weight = 14969.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.132593 restraints weight = 16997.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.133322 restraints weight = 14702.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.134428 restraints weight = 11679.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.134655 restraints weight = 10511.155| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12047 Z= 0.117 Angle : 0.565 8.796 16331 Z= 0.286 Chirality : 0.043 0.255 1857 Planarity : 0.004 0.052 2039 Dihedral : 8.499 103.042 1644 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.68 % Allowed : 19.09 % Favored : 77.23 % 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: -2.67 (0.21), residues: 1438 helix: -2.03 (0.20), residues: 551 sheet: -1.47 (0.34), residues: 212 loop : -1.49 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 391 TYR 0.020 0.001 TYR A1192 PHE 0.019 0.001 PHE C 51 TRP 0.011 0.001 TRP A 412 HIS 0.009 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (12037) covalent geometry : angle 0.55831 / 0.28 (16306) SS BOND : bond 0.00394 / 0.28 ( 2) SS BOND : angle 0.77795 / 0.49 ( 4) hydrogen bonds : bond 0.02873 / 1.91 ( 318) hydrogen bonds : angle 4.83910 / 3.41 ( 888) Misc. bond : bond 0.00222 / 0.15 ( 1) link_BETA1-3 : bond 0.00501 / 0.33 ( 1) link_BETA1-3 : angle 1.76057 / 1.07 ( 3) link_BETA1-4 : bond 0.00422 / 0.23 ( 3) link_BETA1-4 : angle 1.19176 / 0.65 ( 9) link_NAG-ASN : bond 0.00297 / 0.20 ( 3) link_NAG-ASN : angle 3.42670 / 2.29 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 159 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 ILE cc_start: 0.8079 (mm) cc_final: 0.7540 (pt) REVERT: A 441 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.6893 (tm-30) REVERT: A 689 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7550 (tp30) REVERT: A 705 MET cc_start: 0.7630 (ppp) cc_final: 0.7349 (ptt) REVERT: A 721 LYS cc_start: 0.8372 (pttt) cc_final: 0.8115 (ptpt) REVERT: A 744 ARG cc_start: 0.7983 (tpt-90) cc_final: 0.7615 (tpm170) REVERT: A 791 ASP cc_start: 0.6903 (p0) cc_final: 0.6524 (m-30) REVERT: A 944 LYS cc_start: 0.8108 (tppp) cc_final: 0.7685 (tptt) REVERT: A 1229 MET cc_start: 0.7166 (mtm) cc_final: 0.6698 (mtp) REVERT: C 77 TYR cc_start: 0.9139 (p90) cc_final: 0.8809 (p90) outliers start: 47 outliers final: 39 residues processed: 198 average time/residue: 0.1008 time to fit residues: 29.8479 Evaluate side-chains 190 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 150 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 709 PHE Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain A residue 795 ASN Chi-restraints excluded: chain A residue 815 ASP Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1138 VAL Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1191 GLU Chi-restraints excluded: chain A residue 1195 VAL Chi-restraints excluded: chain A residue 1196 VAL Chi-restraints excluded: chain A residue 1218 VAL Chi-restraints excluded: chain A residue 1236 HIS Chi-restraints excluded: chain A residue 1292 TYR Chi-restraints excluded: chain A residue 1294 THR Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 190 CYS Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 319 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 47 optimal weight: 1.9990 chunk 126 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 10 optimal weight: 0.0270 chunk 43 optimal weight: 10.0000 chunk 38 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 overall best weight: 0.8842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 429 ASN ** A1236 HIS ** 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 = 0.3829 r_free = 0.3829 target = 0.162143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.131985 restraints weight = 15079.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.131620 restraints weight = 16601.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.133053 restraints weight = 15826.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.133537 restraints weight = 10919.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.133847 restraints weight = 10324.527| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12047 Z= 0.136 Angle : 0.576 8.755 16331 Z= 0.292 Chirality : 0.044 0.265 1857 Planarity : 0.004 0.051 2039 Dihedral : 8.457 102.532 1644 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 4.15 % Allowed : 19.56 % Favored : 76.29 % 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: -2.56 (0.21), residues: 1438 helix: -1.89 (0.21), residues: 554 sheet: -1.48 (0.34), residues: 214 loop : -1.44 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 391 TYR 0.022 0.001 TYR A1192 PHE 0.020 0.001 PHE C 51 TRP 0.010 0.001 TRP A 412 HIS 0.010 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (12037) covalent geometry : angle 0.56943 / 0.29 (16306) SS BOND : bond 0.00439 / 0.31 ( 2) SS BOND : angle 0.84732 / 0.52 ( 4) hydrogen bonds : bond 0.02854 / 1.91 ( 318) hydrogen bonds : angle 4.76312 / 3.35 ( 888) Misc. bond : bond 0.00205 / 0.14 ( 1) link_BETA1-3 : bond 0.00549 / 0.37 ( 1) link_BETA1-3 : angle 1.80280 / 1.09 ( 3) link_BETA1-4 : bond 0.00408 / 0.23 ( 3) link_BETA1-4 : angle 1.13737 / 0.63 ( 9) link_NAG-ASN : bond 0.00299 / 0.19 ( 3) link_NAG-ASN : angle 3.45611 / 2.31 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 168 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 GLN cc_start: 0.7705 (OUTLIER) cc_final: 0.7164 (mt0) REVERT: A 321 ILE cc_start: 0.8061 (mm) cc_final: 0.7517 (pt) REVERT: A 366 MET cc_start: 0.6164 (mmt) cc_final: 0.5833 (mmt) REVERT: A 441 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7062 (tm-30) REVERT: A 458 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8706 (mt) REVERT: A 689 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7527 (tp30) REVERT: A 721 LYS cc_start: 0.8352 (pttt) cc_final: 0.8109 (ptpt) REVERT: A 744 ARG cc_start: 0.7969 (tpt-90) cc_final: 0.7569 (tpm170) REVERT: A 944 LYS cc_start: 0.8151 (tppp) cc_final: 0.7700 (tptt) REVERT: A 1229 MET cc_start: 0.7212 (mtm) cc_final: 0.6724 (mtt) REVERT: C 32 ARG cc_start: 0.8447 (ptp90) cc_final: 0.8246 (mtm-85) REVERT: C 77 TYR cc_start: 0.9154 (p90) cc_final: 0.8846 (p90) outliers start: 53 outliers final: 45 residues processed: 205 average time/residue: 0.1056 time to fit residues: 31.9011 Evaluate side-chains 208 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 160 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 709 PHE Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain A residue 795 ASN Chi-restraints excluded: chain A residue 815 ASP Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 856 MET Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1138 VAL Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1191 GLU Chi-restraints excluded: chain A residue 1195 VAL Chi-restraints excluded: chain A residue 1196 VAL Chi-restraints excluded: chain A residue 1218 VAL Chi-restraints excluded: chain A residue 1236 HIS Chi-restraints excluded: chain A residue 1292 TYR Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 190 CYS Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 319 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 75 optimal weight: 0.6980 chunk 122 optimal weight: 0.7980 chunk 16 optimal weight: 0.0970 chunk 101 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 chunk 84 optimal weight: 0.0770 chunk 128 optimal weight: 1.9990 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 280 ASN ** A1236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1285 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.162744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.132291 restraints weight = 14790.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.131938 restraints weight = 14553.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.134299 restraints weight = 12491.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.134354 restraints weight = 9621.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.135419 restraints weight = 9792.929| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 12047 Z= 0.103 Angle : 0.555 8.949 16331 Z= 0.282 Chirality : 0.043 0.242 1857 Planarity : 0.004 0.047 2039 Dihedral : 8.256 101.979 1644 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.83 % Allowed : 20.50 % Favored : 75.67 % 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: -2.35 (0.21), residues: 1438 helix: -1.64 (0.21), residues: 553 sheet: -1.45 (0.34), residues: 214 loop : -1.37 (0.23), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 274 TYR 0.019 0.001 TYR A1192 PHE 0.022 0.001 PHE A 219 TRP 0.018 0.001 TRP C 224 HIS 0.009 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.10 (12037) covalent geometry : angle 0.54913 / 0.28 (16306) SS BOND : bond 0.00354 / 0.25 ( 2) SS BOND : angle 0.65123 / 0.39 ( 4) hydrogen bonds : bond 0.02744 / 1.86 ( 318) hydrogen bonds : angle 4.58193 / 3.24 ( 888) Misc. bond : bond 0.00147 / 0.10 ( 1) link_BETA1-3 : bond 0.00525 / 0.35 ( 1) link_BETA1-3 : angle 1.63779 / 1.02 ( 3) link_BETA1-4 : bond 0.00425 / 0.24 ( 3) link_BETA1-4 : angle 1.19363 / 0.65 ( 9) link_NAG-ASN : bond 0.00349 / 0.22 ( 3) link_NAG-ASN : angle 3.27633 / 2.17 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 179 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 GLN cc_start: 0.7615 (OUTLIER) cc_final: 0.7100 (mt0) REVERT: A 321 ILE cc_start: 0.8040 (mm) cc_final: 0.7500 (pt) REVERT: A 441 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7216 (tm-30) REVERT: A 654 ASP cc_start: 0.7729 (m-30) cc_final: 0.7504 (m-30) REVERT: A 689 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7357 (tp30) REVERT: A 744 ARG cc_start: 0.7955 (tpt-90) cc_final: 0.7545 (tpm170) REVERT: A 789 LYS cc_start: 0.8168 (mmmt) cc_final: 0.7878 (mmtt) REVERT: A 861 ILE cc_start: 0.8875 (mp) cc_final: 0.8640 (mt) REVERT: A 944 LYS cc_start: 0.8074 (tppp) cc_final: 0.7700 (tptt) REVERT: A 1229 MET cc_start: 0.7155 (mtm) cc_final: 0.6662 (mtt) REVERT: A 1286 GLU cc_start: 0.8363 (tp30) cc_final: 0.7591 (mm-30) REVERT: C 77 TYR cc_start: 0.9119 (p90) cc_final: 0.8840 (p90) REVERT: C 273 MET cc_start: 0.8678 (tpp) cc_final: 0.8470 (tpp) outliers start: 49 outliers final: 38 residues processed: 211 average time/residue: 0.1064 time to fit residues: 33.2118 Evaluate side-chains 203 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 163 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain A residue 795 ASN Chi-restraints excluded: chain A residue 815 ASP Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1191 GLU Chi-restraints excluded: chain A residue 1196 VAL Chi-restraints excluded: chain A residue 1218 VAL Chi-restraints excluded: chain A residue 1236 HIS Chi-restraints excluded: chain A residue 1292 TYR Chi-restraints excluded: chain A residue 1294 THR Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 190 CYS Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 319 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 116 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 38 optimal weight: 0.0980 chunk 129 optimal weight: 6.9990 chunk 138 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 291 HIS ** A1236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1279 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 = 0.3748 r_free = 0.3748 target = 0.153834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.123271 restraints weight = 15419.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.122480 restraints weight = 18203.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.123731 restraints weight = 16943.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.124456 restraints weight = 12152.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.124743 restraints weight = 11086.878| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12047 Z= 0.189 Angle : 0.619 9.632 16331 Z= 0.312 Chirality : 0.046 0.301 1857 Planarity : 0.004 0.053 2039 Dihedral : 8.472 99.763 1644 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 4.54 % Allowed : 21.13 % Favored : 74.33 % 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: -2.39 (0.21), residues: 1438 helix: -1.71 (0.21), residues: 551 sheet: -1.52 (0.33), residues: 214 loop : -1.34 (0.23), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 272 TYR 0.022 0.002 TYR A1192 PHE 0.022 0.002 PHE C 51 TRP 0.015 0.001 TRP A 412 HIS 0.010 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.19 (12037) covalent geometry : angle 0.61208 / 0.31 (16306) SS BOND : bond 0.00473 / 0.34 ( 2) SS BOND : angle 0.91762 / 0.52 ( 4) hydrogen bonds : bond 0.03061 / 2.06 ( 318) hydrogen bonds : angle 4.74249 / 3.33 ( 888) Misc. bond : bond 0.00289 / 0.19 ( 1) link_BETA1-3 : bond 0.00406 / 0.27 ( 1) link_BETA1-3 : angle 1.96455 / 1.18 ( 3) link_BETA1-4 : bond 0.00349 / 0.18 ( 3) link_BETA1-4 : angle 1.16370 / 0.65 ( 9) link_NAG-ASN : bond 0.00261 / 0.18 ( 3) link_NAG-ASN : angle 3.67471 / 2.47 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 164 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 GLN cc_start: 0.7851 (OUTLIER) cc_final: 0.7401 (mt0) REVERT: A 266 CYS cc_start: 0.7763 (t) cc_final: 0.7509 (t) REVERT: A 321 ILE cc_start: 0.8086 (mm) cc_final: 0.7557 (pt) REVERT: A 441 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7107 (tm-30) REVERT: A 654 ASP cc_start: 0.7741 (m-30) cc_final: 0.7444 (m-30) REVERT: A 744 ARG cc_start: 0.8061 (tpt-90) cc_final: 0.7532 (tpm170) REVERT: A 789 LYS cc_start: 0.8265 (mmmt) cc_final: 0.7913 (mmtt) REVERT: A 944 LYS cc_start: 0.8168 (tppp) cc_final: 0.7569 (tptt) REVERT: A 960 SER cc_start: 0.8942 (p) cc_final: 0.8475 (m) REVERT: A 1193 TYR cc_start: 0.8820 (OUTLIER) cc_final: 0.8306 (t80) REVERT: A 1229 MET cc_start: 0.7489 (mtm) cc_final: 0.6975 (mtt) REVERT: A 1286 GLU cc_start: 0.8461 (tp30) cc_final: 0.7781 (mm-30) REVERT: C 77 TYR cc_start: 0.9210 (p90) cc_final: 0.8947 (p90) outliers start: 58 outliers final: 48 residues processed: 207 average time/residue: 0.0976 time to fit residues: 30.6454 Evaluate side-chains 212 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 161 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain A residue 795 ASN Chi-restraints excluded: chain A residue 810 GLU Chi-restraints excluded: chain A residue 815 ASP Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1138 VAL Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1154 THR Chi-restraints excluded: chain A residue 1191 GLU Chi-restraints excluded: chain A residue 1192 TYR Chi-restraints excluded: chain A residue 1193 TYR Chi-restraints excluded: chain A residue 1196 VAL Chi-restraints excluded: chain A residue 1218 VAL Chi-restraints excluded: chain A residue 1236 HIS Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1292 TYR Chi-restraints excluded: chain A residue 1294 THR Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 190 CYS Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 320 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 127 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 129 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 56 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 130 optimal weight: 0.9980 chunk 120 optimal weight: 0.9990 chunk 73 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 291 HIS ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1285 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 = 0.3850 r_free = 0.3850 target = 0.163689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.134433 restraints weight = 14725.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.133471 restraints weight = 17601.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.135031 restraints weight = 14979.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.135510 restraints weight = 10689.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.135948 restraints weight = 10890.717| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12047 Z= 0.133 Angle : 0.592 11.100 16331 Z= 0.299 Chirality : 0.044 0.267 1857 Planarity : 0.004 0.048 2039 Dihedral : 8.346 99.102 1644 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.91 % Allowed : 21.75 % Favored : 74.33 % 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: -2.23 (0.21), residues: 1438 helix: -1.56 (0.21), residues: 547 sheet: -1.45 (0.34), residues: 208 loop : -1.28 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1117 TYR 0.019 0.001 TYR A1192 PHE 0.022 0.001 PHE C 51 TRP 0.037 0.002 TRP A1028 HIS 0.010 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.13 (12037) covalent geometry : angle 0.58575 / 0.30 (16306) SS BOND : bond 0.00405 / 0.29 ( 2) SS BOND : angle 0.76914 / 0.48 ( 4) hydrogen bonds : bond 0.02789 / 1.85 ( 318) hydrogen bonds : angle 4.62620 / 3.27 ( 888) Misc. bond : bond 0.00453 / 0.30 ( 1) link_BETA1-3 : bond 0.00458 / 0.31 ( 1) link_BETA1-3 : angle 1.79912 / 1.10 ( 3) link_BETA1-4 : bond 0.00375 / 0.20 ( 3) link_BETA1-4 : angle 1.15726 / 0.63 ( 9) link_NAG-ASN : bond 0.00286 / 0.19 ( 3) link_NAG-ASN : angle 3.36806 / 2.24 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 166 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 GLN cc_start: 0.7768 (OUTLIER) cc_final: 0.7317 (mt0) REVERT: A 266 CYS cc_start: 0.7577 (t) cc_final: 0.6953 (t) REVERT: A 321 ILE cc_start: 0.8067 (mm) cc_final: 0.7577 (pt) REVERT: A 441 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7141 (tm-30) REVERT: A 458 LEU cc_start: 0.8934 (mt) cc_final: 0.8436 (mt) REVERT: A 654 ASP cc_start: 0.7646 (m-30) cc_final: 0.7353 (m-30) REVERT: A 689 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7581 (tp30) REVERT: A 744 ARG cc_start: 0.7985 (tpt-90) cc_final: 0.7574 (tpm170) REVERT: A 881 ASN cc_start: 0.7896 (p0) cc_final: 0.7682 (p0) REVERT: A 932 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7501 (mm) REVERT: A 944 LYS cc_start: 0.8128 (tppp) cc_final: 0.7557 (tptt) REVERT: A 960 SER cc_start: 0.8868 (p) cc_final: 0.8427 (m) REVERT: A 1193 TYR cc_start: 0.8807 (OUTLIER) cc_final: 0.8381 (t80) REVERT: A 1229 MET cc_start: 0.7359 (mtm) cc_final: 0.6862 (mtt) REVERT: A 1286 GLU cc_start: 0.8318 (tp30) cc_final: 0.7688 (mm-30) REVERT: A 1294 THR cc_start: 0.8617 (OUTLIER) cc_final: 0.8331 (m) REVERT: C 77 TYR cc_start: 0.9145 (p90) cc_final: 0.8878 (p90) outliers start: 50 outliers final: 41 residues processed: 204 average time/residue: 0.0968 time to fit residues: 29.9393 Evaluate side-chains 204 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 158 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 795 ASN Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 810 GLU Chi-restraints excluded: chain A residue 815 ASP Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1154 THR Chi-restraints excluded: chain A residue 1191 GLU Chi-restraints excluded: chain A residue 1193 TYR Chi-restraints excluded: chain A residue 1196 VAL Chi-restraints excluded: chain A residue 1218 VAL Chi-restraints excluded: chain A residue 1236 HIS Chi-restraints excluded: chain A residue 1292 TYR Chi-restraints excluded: chain A residue 1294 THR Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 190 CYS Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 319 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 48 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 125 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 71 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 11 optimal weight: 0.0970 chunk 27 optimal weight: 0.5980 chunk 98 optimal weight: 0.8980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 291 HIS ** A1236 HIS ** 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 = 0.3833 r_free = 0.3833 target = 0.162091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.131539 restraints weight = 14976.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.131223 restraints weight = 15562.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.132356 restraints weight = 15690.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.133234 restraints weight = 11176.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.133616 restraints weight = 10581.477| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12047 Z= 0.120 Angle : 0.589 11.295 16331 Z= 0.298 Chirality : 0.044 0.253 1857 Planarity : 0.004 0.047 2039 Dihedral : 8.289 97.660 1644 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.68 % Allowed : 22.14 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.14 (0.21), residues: 1438 helix: -1.46 (0.21), residues: 557 sheet: -1.38 (0.34), residues: 208 loop : -1.24 (0.24), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 32 TYR 0.018 0.001 TYR A1192 PHE 0.027 0.001 PHE A 219 TRP 0.027 0.001 TRP A1028 HIS 0.009 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 (12037) covalent geometry : angle 0.58291 / 0.30 (16306) SS BOND : bond 0.00410 / 0.29 ( 2) SS BOND : angle 0.74025 / 0.43 ( 4) hydrogen bonds : bond 0.02674 / 1.79 ( 318) hydrogen bonds : angle 4.54095 / 3.21 ( 888) Misc. bond : bond 0.00322 / 0.21 ( 1) link_BETA1-3 : bond 0.00499 / 0.33 ( 1) link_BETA1-3 : angle 1.71605 / 1.05 ( 3) link_BETA1-4 : bond 0.00414 / 0.22 ( 3) link_BETA1-4 : angle 1.16288 / 0.63 ( 9) link_NAG-ASN : bond 0.00274 / 0.19 ( 3) link_NAG-ASN : angle 3.28809 / 2.19 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 162 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 GLN cc_start: 0.7768 (OUTLIER) cc_final: 0.7254 (mt0) REVERT: A 266 CYS cc_start: 0.7570 (t) cc_final: 0.6919 (t) REVERT: A 321 ILE cc_start: 0.8128 (mm) cc_final: 0.7589 (pt) REVERT: A 441 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7283 (tm-30) REVERT: A 458 LEU cc_start: 0.8866 (mt) cc_final: 0.8429 (mt) REVERT: A 606 ASP cc_start: 0.6743 (OUTLIER) cc_final: 0.5889 (p0) REVERT: A 654 ASP cc_start: 0.7649 (m-30) cc_final: 0.7374 (m-30) REVERT: A 689 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7626 (tp30) REVERT: A 744 ARG cc_start: 0.7988 (tpt-90) cc_final: 0.7551 (tpm170) REVERT: A 881 ASN cc_start: 0.7852 (p0) cc_final: 0.7615 (p0) REVERT: A 932 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7450 (mm) REVERT: A 944 LYS cc_start: 0.8125 (tppp) cc_final: 0.7567 (tptt) REVERT: A 1193 TYR cc_start: 0.8801 (OUTLIER) cc_final: 0.8374 (t80) REVERT: A 1229 MET cc_start: 0.7329 (mtm) cc_final: 0.6830 (mtt) REVERT: A 1286 GLU cc_start: 0.8233 (tp30) cc_final: 0.7681 (mm-30) REVERT: A 1291 MET cc_start: 0.7798 (pmm) cc_final: 0.7572 (pmm) REVERT: A 1294 THR cc_start: 0.8589 (OUTLIER) cc_final: 0.8296 (m) REVERT: C 77 TYR cc_start: 0.9131 (p90) cc_final: 0.8883 (p90) REVERT: C 337 LEU cc_start: 0.8409 (mt) cc_final: 0.8146 (mt) outliers start: 47 outliers final: 38 residues processed: 197 average time/residue: 0.0986 time to fit residues: 29.0826 Evaluate side-chains 204 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 160 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 795 ASN Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 810 GLU Chi-restraints excluded: chain A residue 815 ASP Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1191 GLU Chi-restraints excluded: chain A residue 1193 TYR Chi-restraints excluded: chain A residue 1196 VAL Chi-restraints excluded: chain A residue 1218 VAL Chi-restraints excluded: chain A residue 1236 HIS Chi-restraints excluded: chain A residue 1292 TYR Chi-restraints excluded: chain A residue 1294 THR Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 190 CYS Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 319 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 66 optimal weight: 2.9990 chunk 82 optimal weight: 0.4980 chunk 8 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 142 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 291 HIS ** A1236 HIS ** 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 = 0.3811 r_free = 0.3811 target = 0.160205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.129811 restraints weight = 14836.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.129941 restraints weight = 15771.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.132194 restraints weight = 14174.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.132046 restraints weight = 9467.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.132830 restraints weight = 9288.057| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12047 Z= 0.139 Angle : 0.597 10.876 16331 Z= 0.302 Chirality : 0.045 0.265 1857 Planarity : 0.004 0.049 2039 Dihedral : 8.295 94.667 1644 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.07 % Allowed : 21.75 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.13 (0.21), residues: 1438 helix: -1.38 (0.21), residues: 555 sheet: -1.45 (0.33), residues: 216 loop : -1.26 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 32 TYR 0.019 0.001 TYR A1192 PHE 0.022 0.001 PHE C 51 TRP 0.025 0.002 TRP A1028 HIS 0.009 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 (12037) covalent geometry : angle 0.59096 / 0.30 (16306) SS BOND : bond 0.00438 / 0.31 ( 2) SS BOND : angle 0.84409 / 0.50 ( 4) hydrogen bonds : bond 0.02728 / 1.82 ( 318) hydrogen bonds : angle 4.54502 / 3.21 ( 888) Misc. bond : bond 0.00336 / 0.22 ( 1) link_BETA1-3 : bond 0.00432 / 0.29 ( 1) link_BETA1-3 : angle 1.78361 / 1.09 ( 3) link_BETA1-4 : bond 0.00398 / 0.22 ( 3) link_BETA1-4 : angle 1.15252 / 0.64 ( 9) link_NAG-ASN : bond 0.00262 / 0.18 ( 3) link_NAG-ASN : angle 3.35097 / 2.24 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1800.47 seconds wall clock time: 32 minutes 18.48 seconds (1938.48 seconds total)