Starting phenix.real_space_refine on Sat Sep 12 01:46:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6nt4_0501/09_2026/6nt4_0501.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nt4_0501/09_2026/6nt4_0501.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6nt4_0501/09_2026/6nt4_0501.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nt4_0501/09_2026/6nt4_0501.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6nt4_0501/09_2026/6nt4_0501.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6nt4_0501/09_2026/6nt4_0501.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6nt4_0501/09_2026/6nt4_0501.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nt4_0501/09_2026/6nt4_0501.map" } resolution = 3.5 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= 0.045 sd= 0.870 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 84 5.16 5 C 7894 2.51 5 N 1856 2.21 5 O 2084 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 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: 11924 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 10432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1278, 10432 Classifications: {'peptide': 1278} Link IDs: {'PTRANS': 41, 'TRANS': 1236} Chain breaks: 5 Chain: "B" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 3, 'TRANS': 60} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 3, 'TRANS': 60} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 421 Unusual residues: {'76F': 5, 'AJP': 1, 'LHG': 1, 'NAG': 5, 'Y01': 1} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'76F:plan-1': 3, '76F:plan-2': 2, '76F:plan-3': 3} Unresolved non-hydrogen planarities: 28 Time building chain proxies: 2.36, per 1000 atoms: 0.20 Number of scatterers: 11924 At special positions: 0 Unit cell: (133, 140, 123, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 84 16.00 P 6 15.00 O 2084 8.00 N 1856 7.00 C 7894 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 337 " distance=2.02 Simple disulfide: pdb=" SG CYS A 328 " - pdb=" SG CYS A 343 " distance=2.03 Simple disulfide: pdb=" SG CYS A 709 " - pdb=" SG CYS A 717 " distance=2.03 Simple disulfide: pdb=" SG CYS A1011 " - pdb=" SG CYS A1030 " distance=2.03 Simple disulfide: pdb=" SG CYS A1368 " - pdb=" SG CYS A1381 " distance=2.03 Simple disulfide: pdb=" SG CYS B 12 " - pdb=" SG CYS B 63 " distance=2.02 Simple disulfide: pdb=" SG CYS B 16 " - pdb=" SG CYS B 36 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 46 " distance=2.02 Simple disulfide: pdb=" SG CYS B 26 " - pdb=" SG CYS B 48 " distance=2.04 Simple disulfide: pdb=" SG CYS C 12 " - pdb=" SG CYS C 63 " distance=2.03 Simple disulfide: pdb=" SG CYS C 16 " - pdb=" SG CYS C 36 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 46 " distance=2.02 Simple disulfide: pdb=" SG CYS C 26 " - pdb=" SG CYS C 48 " distance=2.01 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=2, symmetry=0 Links applied BETA1-3 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " BMA D 3 " - " BMA D 4 " BETA1-6 " BMA D 3 " - " BMA D 5 " NAG-ASN " NAG A1601 " - " ASN A1034 " " NAG A1602 " - " ASN A1015 " " NAG A1603 " - " ASN A 312 " " NAG A1604 " - " ASN A 308 " " NAG A1605 " - " ASN A 300 " " NAG D 1 " - " ASN A 330 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.12 Conformation dependent library (CDL) restraints added in 631.6 milliseconds 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2652 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 3 sheets defined 64.7% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 53 through 58 Processing helix chain 'A' and resid 100 through 110 removed outlier: 4.547A pdb=" N VAL A 105 " --> pdb=" O THR A 101 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR A 106 " --> pdb=" O PHE A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 138 Processing helix chain 'A' and resid 139 through 158 removed outlier: 4.328A pdb=" N SER A 143 " --> pdb=" O GLN A 139 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N TYR A 144 " --> pdb=" O PRO A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 188 removed outlier: 3.847A pdb=" N VAL A 180 " --> pdb=" O TYR A 176 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL A 182 " --> pdb=" O ILE A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 197 Processing helix chain 'A' and resid 199 through 215 removed outlier: 4.180A pdb=" N TRP A 203 " --> pdb=" O ASP A 199 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL A 208 " --> pdb=" O LEU A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 240 removed outlier: 4.059A pdb=" N ARG A 230 " --> pdb=" O ARG A 227 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL A 231 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU A 232 " --> pdb=" O PHE A 229 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL A 238 " --> pdb=" O TRP A 235 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR A 239 " --> pdb=" O ARG A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 276 removed outlier: 3.569A pdb=" N VAL A 248 " --> pdb=" O TRP A 244 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASP A 249 " --> pdb=" O ARG A 245 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ALA A 250 " --> pdb=" O THR A 246 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ASP A 260 " --> pdb=" O THR A 256 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N LEU A 261 " --> pdb=" O SER A 257 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU A 264 " --> pdb=" O ASP A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 311 Processing helix chain 'A' and resid 351 through 355 Processing helix chain 'A' and resid 360 through 373 Processing helix chain 'A' and resid 376 through 389 removed outlier: 4.510A pdb=" N LEU A 380 " --> pdb=" O TYR A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 402 removed outlier: 3.935A pdb=" N PHE A 396 " --> pdb=" O HIS A 392 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 433 removed outlier: 4.987A pdb=" N ASN A 409 " --> pdb=" O PHE A 405 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LYS A 424 " --> pdb=" O THR A 420 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG A 425 " --> pdb=" O HIS A 421 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ALA A 426 " --> pdb=" O MET A 422 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA A 432 " --> pdb=" O GLU A 428 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N GLU A 433 " --> pdb=" O GLU A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 517 Processing helix chain 'A' and resid 521 through 537 Processing helix chain 'A' and resid 544 through 573 removed outlier: 3.917A pdb=" N GLU A 548 " --> pdb=" O ASN A 544 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A 573 " --> pdb=" O LYS A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 582 removed outlier: 3.717A pdb=" N ASP A 581 " --> pdb=" O TYR A 578 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER A 582 " --> pdb=" O PHE A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 604 removed outlier: 3.991A pdb=" N ASP A 587 " --> pdb=" O TRP A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 614 removed outlier: 3.776A pdb=" N PHE A 612 " --> pdb=" O VAL A 608 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG A 613 " --> pdb=" O PHE A 609 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU A 614 " --> pdb=" O ARG A 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 608 through 614' Processing helix chain 'A' and resid 615 through 623 removed outlier: 3.772A pdb=" N PHE A 618 " --> pdb=" O LEU A 615 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS A 622 " --> pdb=" O ARG A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 637 removed outlier: 4.236A pdb=" N MET A 634 " --> pdb=" O PHE A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 663 Processing helix chain 'A' and resid 665 through 670 Processing helix chain 'A' and resid 686 through 700 removed outlier: 3.670A pdb=" N GLY A 700 " --> pdb=" O ARG A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 712 removed outlier: 3.702A pdb=" N MET A 706 " --> pdb=" O TRP A 702 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ASP A 708 " --> pdb=" O GLU A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 730 removed outlier: 3.587A pdb=" N LEU A 730 " --> pdb=" O PHE A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 741 Processing helix chain 'A' and resid 838 through 853 Processing helix chain 'A' and resid 855 through 871 removed outlier: 3.559A pdb=" N GLN A 859 " --> pdb=" O ASN A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 874 No H-bonds generated for 'chain 'A' and resid 872 through 874' Processing helix chain 'A' and resid 885 through 913 removed outlier: 4.277A pdb=" N PHE A 910 " --> pdb=" O ILE A 906 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ALA A 911 " --> pdb=" O ILE A 907 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL A 912 " --> pdb=" O MET A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.920A pdb=" N PHE A 918 " --> pdb=" O PHE A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 943 removed outlier: 3.874A pdb=" N ASP A 926 " --> pdb=" O TRP A 922 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU A 939 " --> pdb=" O LEU A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 947 through 951 Processing helix chain 'A' and resid 954 through 957 Processing helix chain 'A' and resid 958 through 963 removed outlier: 3.873A pdb=" N LEU A 962 " --> pdb=" O LEU A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 967 removed outlier: 6.138A pdb=" N GLY A 967 " --> pdb=" O LYS A 964 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 964 through 967' Processing helix chain 'A' and resid 968 through 1004 Proline residue: A 980 - end of helix removed outlier: 4.401A pdb=" N MET A 999 " --> pdb=" O VAL A 995 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLN A1002 " --> pdb=" O ILE A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1026 through 1033 removed outlier: 3.520A pdb=" N CYS A1030 " --> pdb=" O ASP A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1047 through 1059 removed outlier: 3.664A pdb=" N THR A1059 " --> pdb=" O LEU A1055 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1073 removed outlier: 4.108A pdb=" N ASP A1069 " --> pdb=" O GLN A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1088 through 1101 removed outlier: 4.522A pdb=" N PHE A1092 " --> pdb=" O MET A1088 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N PHE A1098 " --> pdb=" O PHE A1094 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE A1101 " --> pdb=" O VAL A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1103 through 1107 removed outlier: 3.764A pdb=" N PHE A1107 " --> pdb=" O LEU A1104 " (cutoff:3.500A) Processing helix chain 'A' and resid 1108 through 1124 removed outlier: 4.061A pdb=" N ASP A1113 " --> pdb=" O CYS A1109 " (cutoff:3.500A) Processing helix chain 'A' and resid 1132 through 1141 Processing helix chain 'A' and resid 1142 through 1145 Processing helix chain 'A' and resid 1159 through 1165 removed outlier: 3.559A pdb=" N ILE A1163 " --> pdb=" O ILE A1159 " (cutoff:3.500A) Processing helix chain 'A' and resid 1169 through 1174 removed outlier: 3.943A pdb=" N ILE A1174 " --> pdb=" O GLN A1170 " (cutoff:3.500A) Processing helix chain 'A' and resid 1176 through 1186 Processing helix chain 'A' and resid 1187 through 1190 removed outlier: 3.756A pdb=" N GLU A1190 " --> pdb=" O MET A1187 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1187 through 1190' Processing helix chain 'A' and resid 1197 through 1224 removed outlier: 4.197A pdb=" N VAL A1201 " --> pdb=" O HIS A1197 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A1202 " --> pdb=" O MET A1198 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU A1221 " --> pdb=" O CYS A1217 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ILE A1222 " --> pdb=" O VAL A1218 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER A1223 " --> pdb=" O LEU A1219 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1247 removed outlier: 4.198A pdb=" N ILE A1235 " --> pdb=" O VAL A1231 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N PHE A1236 " --> pdb=" O GLY A1232 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ASP A1237 " --> pdb=" O TRP A1233 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL A1240 " --> pdb=" O PHE A1236 " (cutoff:3.500A) Processing helix chain 'A' and resid 1260 through 1278 removed outlier: 3.967A pdb=" N ARG A1268 " --> pdb=" O ARG A1265 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ILE A1275 " --> pdb=" O ILE A1272 " (cutoff:3.500A) Processing helix chain 'A' and resid 1290 through 1295 Processing helix chain 'A' and resid 1295 through 1321 removed outlier: 4.220A pdb=" N GLU A1319 " --> pdb=" O VAL A1315 " (cutoff:3.500A) Processing helix chain 'A' and resid 1339 through 1350 removed outlier: 3.973A pdb=" N GLN A1348 " --> pdb=" O ILE A1344 " (cutoff:3.500A) Processing helix chain 'A' and resid 1354 through 1363 removed outlier: 4.130A pdb=" N VAL A1358 " --> pdb=" O GLY A1354 " (cutoff:3.500A) Processing helix chain 'A' and resid 1384 through 1390 Processing helix chain 'A' and resid 1393 through 1398 Processing helix chain 'A' and resid 1401 through 1424 removed outlier: 4.343A pdb=" N ALA A1407 " --> pdb=" O ILE A1403 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR A1413 " --> pdb=" O VAL A1409 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU A1416 " --> pdb=" O ASP A1412 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLU A1419 " --> pdb=" O LEU A1415 " (cutoff:3.500A) Processing helix chain 'A' and resid 1426 through 1440 removed outlier: 3.772A pdb=" N TYR A1430 " --> pdb=" O THR A1426 " (cutoff:3.500A) Processing helix chain 'A' and resid 1450 through 1457 removed outlier: 3.618A pdb=" N GLU A1455 " --> pdb=" O GLN A1452 " (cutoff:3.500A) Processing helix chain 'A' and resid 1472 through 1477 removed outlier: 3.655A pdb=" N SER A1476 " --> pdb=" O TYR A1472 " (cutoff:3.500A) Processing helix chain 'A' and resid 1488 through 1504 removed outlier: 3.520A pdb=" N VAL A1492 " --> pdb=" O PHE A1488 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 28 Processing helix chain 'C' and resid 19 through 28 Processing sheet with id=AA1, first strand: chain 'A' and resid 287 through 290 Processing sheet with id=AA2, first strand: chain 'B' and resid 34 through 37 Processing sheet with id=AA3, first strand: chain 'C' and resid 2 through 4 removed outlier: 7.629A pdb=" N GLY C 4 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N TYR C 49 " --> pdb=" O GLY C 4 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N SER C 33 " --> pdb=" O TYR C 49 " (cutoff:3.500A) 576 hydrogen bonds defined for protein. 1608 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: 2.00 Time building geometry restraints manager: 1.49 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: 1776 1.31 - 1.44: 3559 1.44 - 1.57: 6753 1.57 - 1.70: 21 1.70 - 1.82: 131 Bond restraints: 12240 Sorted by residual: bond pdb=" C06 AJP A1611 " pdb=" C07 AJP A1611 " ideal model delta sigma weight residual 1.530 1.319 0.211 2.00e-02 2.50e+03 1.11e+02 bond pdb=" C40 76F A1608 " pdb=" C41 76F A1608 " ideal model delta sigma weight residual 1.330 1.527 -0.197 2.00e-02 2.50e+03 9.73e+01 bond pdb=" C40 76F A1610 " pdb=" C41 76F A1610 " ideal model delta sigma weight residual 1.330 1.527 -0.197 2.00e-02 2.50e+03 9.72e+01 bond pdb=" C21 76F A1608 " pdb=" C22 76F A1608 " ideal model delta sigma weight residual 1.330 1.527 -0.197 2.00e-02 2.50e+03 9.72e+01 bond pdb=" C21 76F A1610 " pdb=" C22 76F A1610 " ideal model delta sigma weight residual 1.330 1.527 -0.197 2.00e-02 2.50e+03 9.69e+01 ... (remaining 12235 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.29: 16558 9.29 - 18.57: 29 18.57 - 27.86: 3 27.86 - 37.14: 1 37.14 - 46.43: 1 Bond angle restraints: 16592 Sorted by residual: angle pdb=" O09 AJP A1611 " pdb=" C05 AJP A1611 " pdb=" O84 AJP A1611 " ideal model delta sigma weight residual 110.48 64.05 46.43 3.00e+00 1.11e-01 2.39e+02 angle pdb=" C04 AJP A1611 " pdb=" C05 AJP A1611 " pdb=" C06 AJP A1611 " ideal model delta sigma weight residual 114.54 144.73 -30.19 3.00e+00 1.11e-01 1.01e+02 angle pdb=" N ASN A1034 " pdb=" CA ASN A1034 " pdb=" C ASN A1034 " ideal model delta sigma weight residual 110.80 128.74 -17.94 2.13e+00 2.20e-01 7.09e+01 angle pdb=" C17 76F A1608 " pdb=" C18 76F A1608 " pdb=" C19 76F A1608 " ideal model delta sigma weight residual 128.07 109.47 18.60 3.00e+00 1.11e-01 3.84e+01 angle pdb=" C17 76F A1609 " pdb=" C18 76F A1609 " pdb=" C19 76F A1609 " ideal model delta sigma weight residual 128.07 109.49 18.58 3.00e+00 1.11e-01 3.84e+01 ... (remaining 16587 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.80: 6560 24.80 - 49.60: 440 49.60 - 74.40: 62 74.40 - 99.19: 20 99.19 - 123.99: 7 Dihedral angle restraints: 7089 sinusoidal: 2969 harmonic: 4120 Sorted by residual: dihedral pdb=" N ASN A1034 " pdb=" C ASN A1034 " pdb=" CA ASN A1034 " pdb=" CB ASN A1034 " ideal model delta harmonic sigma weight residual 122.80 174.25 -51.45 0 2.50e+00 1.60e-01 4.24e+02 dihedral pdb=" C ASN A1034 " pdb=" N ASN A1034 " pdb=" CA ASN A1034 " pdb=" CB ASN A1034 " ideal model delta harmonic sigma weight residual -122.60 -173.84 51.24 0 2.50e+00 1.60e-01 4.20e+02 dihedral pdb=" CB CYS B 26 " pdb=" SG CYS B 26 " pdb=" SG CYS B 48 " pdb=" CB CYS B 48 " ideal model delta sinusoidal sigma weight residual -86.00 -149.01 63.01 1 1.00e+01 1.00e-02 5.24e+01 ... (remaining 7086 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.142: 1867 1.142 - 2.283: 1 2.283 - 3.425: 0 3.425 - 4.567: 2 4.567 - 5.708: 19 Chirality restraints: 1889 Sorted by residual: chirality pdb=" C08 AJP A1611 " pdb=" C07 AJP A1611 " pdb=" C10 AJP A1611 " pdb=" O09 AJP A1611 " both_signs ideal model delta sigma weight residual False 2.56 -3.15 5.71 2.00e-01 2.50e+01 8.15e+02 chirality pdb=" C12 AJP A1611 " pdb=" C07 AJP A1611 " pdb=" C11 AJP A1611 " pdb=" C13 AJP A1611 " both_signs ideal model delta sigma weight residual False 3.01 -2.64 5.65 2.00e-01 2.50e+01 7.97e+02 chirality pdb=" C16 AJP A1611 " pdb=" C11 AJP A1611 " pdb=" C15 AJP A1611 " pdb=" C17 AJP A1611 " both_signs ideal model delta sigma weight residual False -2.70 2.91 -5.61 2.00e-01 2.50e+01 7.87e+02 ... (remaining 1886 not shown) Planarity restraints: 2006 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C20 76F A1608 " -0.164 2.00e-02 2.50e+03 3.21e-01 1.03e+03 pdb=" C21 76F A1608 " 0.423 2.00e-02 2.50e+03 pdb=" C22 76F A1608 " -0.423 2.00e-02 2.50e+03 pdb=" C23 76F A1608 " 0.164 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 76F A1608 " 0.161 2.00e-02 2.50e+03 2.90e-01 8.38e+02 pdb=" C18 76F A1608 " -0.376 2.00e-02 2.50e+03 pdb=" C19 76F A1608 " 0.377 2.00e-02 2.50e+03 pdb=" C20 76F A1608 " -0.161 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C39 76F A1608 " -0.153 2.00e-02 2.50e+03 2.56e-01 6.55e+02 pdb=" C40 76F A1608 " 0.328 2.00e-02 2.50e+03 pdb=" C41 76F A1608 " -0.328 2.00e-02 2.50e+03 pdb=" C42 76F A1608 " 0.153 2.00e-02 2.50e+03 ... (remaining 2003 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 220 2.66 - 3.22: 11949 3.22 - 3.78: 16845 3.78 - 4.34: 21849 4.34 - 4.90: 34618 Nonbonded interactions: 85481 Sorted by model distance: nonbonded pdb=" OD1 ASN A 283 " pdb=" NE2 HIS A 286 " model vdw 2.096 3.120 nonbonded pdb=" O33 AJP A1611 " pdb=" O60 AJP A1611 " model vdw 2.143 3.040 nonbonded pdb=" O40 AJP A1611 " pdb=" O77 AJP A1611 " model vdw 2.144 3.040 nonbonded pdb=" O SER A 86 " pdb=" NZ LYS A 100 " model vdw 2.215 3.120 nonbonded pdb=" O ARG A 840 " pdb=" OG SER A 843 " model vdw 2.223 3.040 ... (remaining 85476 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' } 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: 1.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.130 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.211 12265 Z= 0.498 Angle : 1.338 46.426 16648 Z= 0.597 Chirality : 0.529 5.708 1889 Planarity : 0.013 0.321 2000 Dihedral : 17.141 123.993 4398 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.43 % Allowed : 12.88 % Favored : 86.69 % Rotamer: Outliers : 0.64 % Allowed : 8.28 % Favored : 91.08 % Cbeta Deviations : 0.08 % 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: -4.72 (0.18), residues: 1390 helix: -2.25 (0.15), residues: 815 sheet: -4.45 (0.93), residues: 12 loop : -4.48 (0.20), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 619 TYR 0.016 0.002 TYR A 381 PHE 0.016 0.001 PHE A 850 TRP 0.021 0.001 TRP A1063 HIS 0.006 0.001 HIS A 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00987 / 0.48 (12240) covalent geometry : angle 1.31096 / 0.59 (16592) SS BOND : bond 0.00941 / 0.52 ( 13) SS BOND : angle 1.40628 / 1.03 ( 26) hydrogen bonds : bond 0.15871 / 10.97 ( 576) hydrogen bonds : angle 6.25743 / 4.34 ( 1608) Misc. bond : bond 0.10110 / 5.07 ( 2) link_BETA1-3 : bond 0.01329 / 0.63 ( 3) link_BETA1-3 : angle 10.82146 / 6.58 ( 9) link_BETA1-6 : bond 0.00129 / 0.07 ( 1) link_BETA1-6 : angle 2.43765 / 1.21 ( 3) link_NAG-ASN : bond 0.00298 / 0.15 ( 6) link_NAG-ASN : angle 2.94958 / 2.05 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 253 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.8675 (mm) cc_final: 0.8413 (mm) REVERT: A 131 ARG cc_start: 0.7234 (ttp80) cc_final: 0.7032 (ptt180) REVERT: A 245 ARG cc_start: 0.8333 (mtt180) cc_final: 0.8128 (mtp180) REVERT: A 283 ASN cc_start: 0.8530 (t0) cc_final: 0.7680 (t0) REVERT: A 323 ILE cc_start: 0.9036 (mp) cc_final: 0.8758 (mm) REVERT: A 345 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.8119 (pp30) REVERT: A 552 ARG cc_start: 0.7184 (mtm110) cc_final: 0.6875 (mtp-110) REVERT: A 578 TYR cc_start: 0.8593 (t80) cc_final: 0.8312 (t80) REVERT: A 668 ILE cc_start: 0.9007 (tt) cc_final: 0.8798 (tp) REVERT: A 742 ASN cc_start: 0.9128 (t0) cc_final: 0.8590 (t0) REVERT: A 914 PHE cc_start: 0.7677 (t80) cc_final: 0.7382 (m-80) REVERT: A 1065 GLN cc_start: 0.8679 (tm-30) cc_final: 0.8466 (tm-30) REVERT: A 1087 TYR cc_start: 0.8808 (m-10) cc_final: 0.8584 (m-80) REVERT: A 1188 MET cc_start: 0.5961 (ptm) cc_final: 0.5585 (ptm) REVERT: A 1248 MET cc_start: 0.8277 (ttm) cc_final: 0.7952 (ttp) REVERT: A 1283 LYS cc_start: 0.8482 (tptt) cc_final: 0.8141 (tppt) REVERT: A 1430 TYR cc_start: 0.8418 (m-80) cc_final: 0.7760 (m-80) REVERT: A 1432 MET cc_start: 0.8502 (tmt) cc_final: 0.8162 (tmt) REVERT: A 1443 GLU cc_start: 0.7490 (tm-30) cc_final: 0.7040 (tm-30) REVERT: A 1458 GLU cc_start: 0.7409 (pt0) cc_final: 0.7036 (mt-10) REVERT: A 1471 LYS cc_start: 0.7728 (tppt) cc_final: 0.7323 (tmtt) REVERT: B 44 ASN cc_start: 0.5798 (p0) cc_final: 0.5588 (p0) REVERT: C 11 ASN cc_start: 0.8523 (t0) cc_final: 0.8282 (t0) REVERT: C 21 TYR cc_start: 0.6602 (t80) cc_final: 0.6294 (t80) REVERT: C 23 ASN cc_start: 0.7762 (t0) cc_final: 0.7364 (t0) outliers start: 8 outliers final: 0 residues processed: 258 average time/residue: 0.1055 time to fit residues: 39.0016 Evaluate side-chains 204 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 203 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 153 HIS A 541 HIS A1194 GLN ** A1323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1461 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.158216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.120272 restraints weight = 19237.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.124885 restraints weight = 9236.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.127966 restraints weight = 5749.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.129908 restraints weight = 4174.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.131288 restraints weight = 3385.376| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 12265 Z= 0.178 Angle : 1.003 32.065 16648 Z= 0.444 Chirality : 0.083 2.076 1889 Planarity : 0.005 0.056 2000 Dihedral : 13.438 110.780 1777 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.22 % Allowed : 10.79 % Favored : 88.99 % Rotamer: Outliers : 2.89 % Allowed : 16.72 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.30 (0.20), residues: 1390 helix: -1.09 (0.17), residues: 837 sheet: -5.49 (0.99), residues: 10 loop : -3.95 (0.21), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1027 TYR 0.015 0.001 TYR A 381 PHE 0.027 0.001 PHE A 623 TRP 0.021 0.001 TRP A1437 HIS 0.012 0.001 HIS A1323 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.18 (12240) covalent geometry : angle 0.98471 / 0.44 (16592) SS BOND : bond 0.00440 / 0.26 ( 13) SS BOND : angle 1.36509 / 1.07 ( 26) hydrogen bonds : bond 0.06071 / 4.17 ( 576) hydrogen bonds : angle 4.66361 / 3.26 ( 1608) Misc. bond : bond 0.00061 / 0.03 ( 2) link_BETA1-3 : bond 0.01124 / 0.52 ( 3) link_BETA1-3 : angle 7.05410 / 4.22 ( 9) link_BETA1-6 : bond 0.00566 / 0.30 ( 1) link_BETA1-6 : angle 1.88147 / 0.85 ( 3) link_NAG-ASN : bond 0.00535 / 0.39 ( 6) link_NAG-ASN : angle 3.04441 / 2.20 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 218 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 219 ASP cc_start: 0.7027 (t0) cc_final: 0.6660 (t0) REVERT: A 245 ARG cc_start: 0.8410 (mtt180) cc_final: 0.8194 (mtp180) REVERT: A 283 ASN cc_start: 0.8886 (t0) cc_final: 0.8566 (t0) REVERT: A 320 ASP cc_start: 0.8251 (t0) cc_final: 0.8045 (t0) REVERT: A 323 ILE cc_start: 0.9004 (mp) cc_final: 0.8747 (mm) REVERT: A 345 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.8049 (pp30) REVERT: A 535 PHE cc_start: 0.7694 (OUTLIER) cc_final: 0.7339 (t80) REVERT: A 552 ARG cc_start: 0.7135 (mtm110) cc_final: 0.6781 (mtp-110) REVERT: A 660 MET cc_start: 0.8575 (ttt) cc_final: 0.8312 (ttt) REVERT: A 668 ILE cc_start: 0.9064 (tt) cc_final: 0.8826 (tp) REVERT: A 683 ASN cc_start: 0.8990 (p0) cc_final: 0.8410 (p0) REVERT: A 914 PHE cc_start: 0.7562 (t80) cc_final: 0.7114 (m-80) REVERT: A 960 ARG cc_start: 0.9003 (ttt-90) cc_final: 0.8518 (ttp80) REVERT: A 1025 MET cc_start: 0.8452 (ttt) cc_final: 0.7878 (tpp) REVERT: A 1065 GLN cc_start: 0.8613 (tm-30) cc_final: 0.8409 (tm-30) REVERT: A 1081 ILE cc_start: 0.8599 (mt) cc_final: 0.8271 (mm) REVERT: A 1087 TYR cc_start: 0.8818 (m-10) cc_final: 0.8563 (m-80) REVERT: A 1088 MET cc_start: 0.8960 (ttm) cc_final: 0.8753 (tpp) REVERT: A 1177 MET cc_start: 0.7331 (tpp) cc_final: 0.6841 (tpt) REVERT: A 1283 LYS cc_start: 0.8269 (tptt) cc_final: 0.7993 (tppt) REVERT: A 1430 TYR cc_start: 0.8124 (m-80) cc_final: 0.7462 (m-80) REVERT: A 1443 GLU cc_start: 0.7491 (tm-30) cc_final: 0.7069 (tm-30) REVERT: A 1471 LYS cc_start: 0.7608 (tppt) cc_final: 0.7176 (tmtt) REVERT: A 1488 PHE cc_start: 0.7216 (t80) cc_final: 0.6976 (t80) REVERT: C 21 TYR cc_start: 0.6300 (t80) cc_final: 0.5921 (t80) outliers start: 36 outliers final: 19 residues processed: 241 average time/residue: 0.0997 time to fit residues: 35.5337 Evaluate side-chains 226 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 205 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 535 PHE Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1187 MET Chi-restraints excluded: chain A residue 1208 VAL Chi-restraints excluded: chain A residue 1249 PHE Chi-restraints excluded: chain A residue 1250 LEU Chi-restraints excluded: chain A residue 1276 LEU Chi-restraints excluded: chain A residue 1285 ILE Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1316 PHE Chi-restraints excluded: chain A residue 1318 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 14 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 74 optimal weight: 0.3980 chunk 134 optimal weight: 7.9990 chunk 69 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 101 optimal weight: 8.9990 chunk 65 optimal weight: 0.0470 chunk 86 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 overall best weight: 1.4884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 421 HIS A 584 ASN A 936 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.158279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.119568 restraints weight = 19405.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.124320 restraints weight = 9299.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.127461 restraints weight = 5781.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.129536 restraints weight = 4195.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.130869 restraints weight = 3385.854| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12265 Z= 0.153 Angle : 0.914 32.074 16648 Z= 0.409 Chirality : 0.080 2.086 1889 Planarity : 0.005 0.056 2000 Dihedral : 12.066 110.942 1777 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.93 % Favored : 89.86 % Rotamer: Outliers : 4.02 % Allowed : 19.53 % Favored : 76.45 % 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: -2.65 (0.22), residues: 1390 helix: -0.60 (0.18), residues: 829 sheet: -4.81 (1.17), residues: 10 loop : -3.60 (0.23), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1225 TYR 0.016 0.001 TYR C 49 PHE 0.020 0.001 PHE A1434 TRP 0.026 0.001 TRP A1437 HIS 0.013 0.001 HIS A1323 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (12240) covalent geometry : angle 0.89734 / 0.41 (16592) SS BOND : bond 0.00414 / 0.24 ( 13) SS BOND : angle 1.08369 / 0.81 ( 26) hydrogen bonds : bond 0.05373 / 3.67 ( 576) hydrogen bonds : angle 4.35671 / 3.06 ( 1608) Misc. bond : bond 0.00026 / 0.01 ( 2) link_BETA1-3 : bond 0.01133 / 0.53 ( 3) link_BETA1-3 : angle 6.64071 / 3.98 ( 9) link_BETA1-6 : bond 0.00137 / 0.07 ( 1) link_BETA1-6 : angle 1.90016 / 0.99 ( 3) link_NAG-ASN : bond 0.00265 / 0.19 ( 6) link_NAG-ASN : angle 2.31574 / 1.69 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 218 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.5537 (ttt) cc_final: 0.4643 (tpp) REVERT: A 219 ASP cc_start: 0.6915 (t0) cc_final: 0.6701 (t0) REVERT: A 245 ARG cc_start: 0.8426 (mtt180) cc_final: 0.8208 (mtp180) REVERT: A 283 ASN cc_start: 0.8891 (t0) cc_final: 0.8626 (t0) REVERT: A 320 ASP cc_start: 0.8386 (t0) cc_final: 0.8051 (t0) REVERT: A 336 MET cc_start: 0.8278 (mtm) cc_final: 0.8071 (mmm) REVERT: A 345 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.8051 (pp30) REVERT: A 535 PHE cc_start: 0.7483 (OUTLIER) cc_final: 0.7158 (t80) REVERT: A 552 ARG cc_start: 0.7165 (mtm110) cc_final: 0.6774 (mtp-110) REVERT: A 583 TRP cc_start: 0.8243 (t-100) cc_final: 0.7697 (t60) REVERT: A 668 ILE cc_start: 0.9020 (tt) cc_final: 0.8785 (tp) REVERT: A 683 ASN cc_start: 0.8985 (p0) cc_final: 0.8438 (p0) REVERT: A 876 GLU cc_start: 0.7992 (pt0) cc_final: 0.7778 (tt0) REVERT: A 914 PHE cc_start: 0.7465 (t80) cc_final: 0.7013 (m-80) REVERT: A 977 GLU cc_start: 0.8250 (tp30) cc_final: 0.7984 (tt0) REVERT: A 1025 MET cc_start: 0.8510 (ttt) cc_final: 0.7956 (tpp) REVERT: A 1065 GLN cc_start: 0.8565 (tm-30) cc_final: 0.8257 (tp40) REVERT: A 1081 ILE cc_start: 0.8438 (mt) cc_final: 0.8136 (mm) REVERT: A 1083 GLU cc_start: 0.8574 (pt0) cc_final: 0.7985 (tt0) REVERT: A 1087 TYR cc_start: 0.8805 (m-10) cc_final: 0.8603 (m-80) REVERT: A 1088 MET cc_start: 0.9057 (ttm) cc_final: 0.8793 (tpp) REVERT: A 1177 MET cc_start: 0.7132 (tpp) cc_final: 0.6683 (tpt) REVERT: A 1283 LYS cc_start: 0.8221 (tptt) cc_final: 0.7929 (tppt) REVERT: A 1430 TYR cc_start: 0.8104 (m-80) cc_final: 0.7459 (m-80) REVERT: A 1443 GLU cc_start: 0.7501 (tm-30) cc_final: 0.7101 (tm-30) REVERT: A 1471 LYS cc_start: 0.7581 (tppt) cc_final: 0.7165 (tmtt) REVERT: C 21 TYR cc_start: 0.6003 (t80) cc_final: 0.5614 (t80) REVERT: C 44 ASN cc_start: 0.8919 (p0) cc_final: 0.8641 (p0) outliers start: 50 outliers final: 35 residues processed: 250 average time/residue: 0.0919 time to fit residues: 34.6488 Evaluate side-chains 239 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 202 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 535 PHE Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 926 ASP Chi-restraints excluded: chain A residue 936 ASN Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 1066 ILE Chi-restraints excluded: chain A residue 1152 ILE Chi-restraints excluded: chain A residue 1187 MET Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain A residue 1249 PHE Chi-restraints excluded: chain A residue 1250 LEU Chi-restraints excluded: chain A residue 1276 LEU Chi-restraints excluded: chain A residue 1285 ILE Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1316 PHE Chi-restraints excluded: chain A residue 1343 ILE Chi-restraints excluded: chain A residue 1418 TYR Chi-restraints excluded: chain A residue 1440 PHE Chi-restraints excluded: chain A residue 1501 PHE Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 48 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 57 optimal weight: 6.9990 chunk 133 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 125 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 105 optimal weight: 0.5980 chunk 87 optimal weight: 4.9990 chunk 90 optimal weight: 8.9990 chunk 11 optimal weight: 0.9990 chunk 137 optimal weight: 6.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1439 GLN C 54 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.157757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.119028 restraints weight = 19360.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.123742 restraints weight = 9328.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.126858 restraints weight = 5824.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.128944 restraints weight = 4239.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.130264 restraints weight = 3420.854| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 12265 Z= 0.163 Angle : 0.899 32.445 16648 Z= 0.404 Chirality : 0.079 2.073 1889 Planarity : 0.005 0.056 2000 Dihedral : 11.559 103.233 1777 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.22 % Allowed : 10.07 % Favored : 89.71 % Rotamer: Outliers : 4.82 % Allowed : 20.18 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.41 (0.22), residues: 1390 helix: -0.43 (0.18), residues: 830 sheet: -4.38 (1.25), residues: 10 loop : -3.47 (0.23), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 77 TYR 0.019 0.001 TYR A 578 PHE 0.017 0.001 PHE A 630 TRP 0.027 0.001 TRP A1437 HIS 0.014 0.001 HIS C 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (12240) covalent geometry : angle 0.88338 / 0.40 (16592) SS BOND : bond 0.00499 / 0.32 ( 13) SS BOND : angle 1.12120 / 0.85 ( 26) hydrogen bonds : bond 0.05300 / 3.63 ( 576) hydrogen bonds : angle 4.28128 / 3.01 ( 1608) Misc. bond : bond 0.00022 / 0.01 ( 2) link_BETA1-3 : bond 0.01265 / 0.59 ( 3) link_BETA1-3 : angle 6.49713 / 3.91 ( 9) link_BETA1-6 : bond 0.00035 / 0.02 ( 1) link_BETA1-6 : angle 2.12934 / 1.12 ( 3) link_NAG-ASN : bond 0.00313 / 0.23 ( 6) link_NAG-ASN : angle 2.25267 / 1.64 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 219 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.5688 (ttt) cc_final: 0.4853 (tpp) REVERT: A 219 ASP cc_start: 0.6927 (t0) cc_final: 0.6640 (t0) REVERT: A 245 ARG cc_start: 0.8403 (mtt180) cc_final: 0.8193 (mtp180) REVERT: A 283 ASN cc_start: 0.8877 (t0) cc_final: 0.8618 (t0) REVERT: A 320 ASP cc_start: 0.8416 (t0) cc_final: 0.8030 (t0) REVERT: A 336 MET cc_start: 0.8282 (mtm) cc_final: 0.8053 (mmm) REVERT: A 345 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.8043 (pp30) REVERT: A 535 PHE cc_start: 0.7503 (OUTLIER) cc_final: 0.7169 (t80) REVERT: A 552 ARG cc_start: 0.7144 (mtm110) cc_final: 0.6783 (mtp-110) REVERT: A 578 TYR cc_start: 0.8020 (t80) cc_final: 0.7774 (t80) REVERT: A 583 TRP cc_start: 0.8336 (t-100) cc_final: 0.7911 (t-100) REVERT: A 668 ILE cc_start: 0.9102 (tt) cc_final: 0.8866 (tp) REVERT: A 683 ASN cc_start: 0.8985 (p0) cc_final: 0.8453 (p0) REVERT: A 914 PHE cc_start: 0.7461 (t80) cc_final: 0.7021 (m-80) REVERT: A 977 GLU cc_start: 0.8402 (tp30) cc_final: 0.8024 (tt0) REVERT: A 1025 MET cc_start: 0.8517 (ttt) cc_final: 0.7957 (tpp) REVERT: A 1065 GLN cc_start: 0.8600 (tm-30) cc_final: 0.8318 (tp40) REVERT: A 1081 ILE cc_start: 0.8505 (mt) cc_final: 0.8249 (mm) REVERT: A 1083 GLU cc_start: 0.8526 (pt0) cc_final: 0.7985 (tt0) REVERT: A 1087 TYR cc_start: 0.8863 (m-10) cc_final: 0.8657 (m-80) REVERT: A 1177 MET cc_start: 0.7074 (tpp) cc_final: 0.6696 (tpt) REVERT: A 1265 ARG cc_start: 0.8185 (mtm-85) cc_final: 0.7859 (mtm180) REVERT: A 1283 LYS cc_start: 0.8232 (tptt) cc_final: 0.7993 (tppt) REVERT: A 1430 TYR cc_start: 0.8120 (m-80) cc_final: 0.7436 (m-80) REVERT: A 1443 GLU cc_start: 0.7463 (tm-30) cc_final: 0.7242 (tm-30) REVERT: A 1471 LYS cc_start: 0.7567 (tppt) cc_final: 0.7061 (tptp) REVERT: C 21 TYR cc_start: 0.6279 (t80) cc_final: 0.5744 (t80) REVERT: C 44 ASN cc_start: 0.8856 (p0) cc_final: 0.8578 (p0) outliers start: 60 outliers final: 47 residues processed: 256 average time/residue: 0.0961 time to fit residues: 36.7902 Evaluate side-chains 256 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 207 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 417 MET Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 535 PHE Chi-restraints excluded: chain A residue 690 SER Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 926 ASP Chi-restraints excluded: chain A residue 936 ASN Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1066 ILE Chi-restraints excluded: chain A residue 1152 ILE Chi-restraints excluded: chain A residue 1181 CYS Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain A residue 1237 ASP Chi-restraints excluded: chain A residue 1241 VAL Chi-restraints excluded: chain A residue 1246 VAL Chi-restraints excluded: chain A residue 1249 PHE Chi-restraints excluded: chain A residue 1250 LEU Chi-restraints excluded: chain A residue 1276 LEU Chi-restraints excluded: chain A residue 1285 ILE Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1316 PHE Chi-restraints excluded: chain A residue 1320 PHE Chi-restraints excluded: chain A residue 1322 MET Chi-restraints excluded: chain A residue 1343 ILE Chi-restraints excluded: chain A residue 1418 TYR Chi-restraints excluded: chain A residue 1440 PHE Chi-restraints excluded: chain A residue 1501 PHE Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 62 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 87 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 48 optimal weight: 0.7980 chunk 64 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 59 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 61 optimal weight: 0.0070 chunk 12 optimal weight: 0.8980 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 GLN A 936 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.162463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.123681 restraints weight = 19334.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.128550 restraints weight = 9186.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.131741 restraints weight = 5663.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.133858 restraints weight = 4088.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.135283 restraints weight = 3286.797| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12265 Z= 0.130 Angle : 0.863 31.987 16648 Z= 0.383 Chirality : 0.079 2.061 1889 Planarity : 0.004 0.057 2000 Dihedral : 10.867 88.590 1777 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.78 % Favored : 91.01 % Rotamer: Outliers : 3.54 % Allowed : 22.35 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.01 (0.22), residues: 1390 helix: -0.11 (0.18), residues: 824 sheet: -3.73 (1.59), residues: 10 loop : -3.27 (0.24), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1027 TYR 0.016 0.001 TYR A 196 PHE 0.015 0.001 PHE C 15 TRP 0.020 0.001 TRP A1437 HIS 0.009 0.001 HIS A1323 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 (12240) covalent geometry : angle 0.85155 / 0.38 (16592) SS BOND : bond 0.00311 / 0.18 ( 13) SS BOND : angle 0.88325 / 0.64 ( 26) hydrogen bonds : bond 0.04462 / 3.07 ( 576) hydrogen bonds : angle 3.98552 / 2.81 ( 1608) Misc. bond : bond 0.00015 / 0.01 ( 2) link_BETA1-3 : bond 0.01917 / 0.91 ( 3) link_BETA1-3 : angle 5.56240 / 3.32 ( 9) link_BETA1-6 : bond 0.00187 / 0.10 ( 1) link_BETA1-6 : angle 1.48766 / 0.70 ( 3) link_NAG-ASN : bond 0.00366 / 0.26 ( 6) link_NAG-ASN : angle 1.79312 / 1.33 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 223 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 LEU cc_start: 0.4074 (OUTLIER) cc_final: 0.3768 (pp) REVERT: A 157 MET cc_start: 0.4875 (OUTLIER) cc_final: 0.4568 (ptp) REVERT: A 219 ASP cc_start: 0.7008 (t0) cc_final: 0.6804 (t0) REVERT: A 320 ASP cc_start: 0.8445 (t0) cc_final: 0.8026 (t0) REVERT: A 345 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.8133 (pp30) REVERT: A 535 PHE cc_start: 0.7410 (OUTLIER) cc_final: 0.7121 (t80) REVERT: A 536 MET cc_start: 0.8892 (tmm) cc_final: 0.8276 (tmm) REVERT: A 552 ARG cc_start: 0.7217 (mtm110) cc_final: 0.6874 (mtp-110) REVERT: A 583 TRP cc_start: 0.8275 (t-100) cc_final: 0.7740 (t60) REVERT: A 668 ILE cc_start: 0.9068 (tt) cc_final: 0.8824 (tp) REVERT: A 683 ASN cc_start: 0.8985 (p0) cc_final: 0.8465 (p0) REVERT: A 846 ARG cc_start: 0.7268 (ttm170) cc_final: 0.6838 (mmm-85) REVERT: A 894 ASP cc_start: 0.7602 (t0) cc_final: 0.7375 (t0) REVERT: A 914 PHE cc_start: 0.7420 (t80) cc_final: 0.6922 (m-80) REVERT: A 926 ASP cc_start: 0.8225 (OUTLIER) cc_final: 0.7900 (t70) REVERT: A 977 GLU cc_start: 0.8345 (tp30) cc_final: 0.7970 (tt0) REVERT: A 1025 MET cc_start: 0.8553 (ttt) cc_final: 0.8014 (tpp) REVERT: A 1065 GLN cc_start: 0.8503 (tm-30) cc_final: 0.8216 (tp40) REVERT: A 1083 GLU cc_start: 0.8377 (pt0) cc_final: 0.7880 (tt0) REVERT: A 1141 MET cc_start: 0.8284 (tpt) cc_final: 0.7903 (tpp) REVERT: A 1177 MET cc_start: 0.6845 (tpp) cc_final: 0.6506 (tpt) REVERT: A 1265 ARG cc_start: 0.8205 (mtm-85) cc_final: 0.7829 (mtm180) REVERT: A 1283 LYS cc_start: 0.8202 (tptt) cc_final: 0.7963 (tppt) REVERT: A 1335 ASN cc_start: 0.8973 (p0) cc_final: 0.8742 (p0) REVERT: A 1419 GLU cc_start: 0.8707 (pp20) cc_final: 0.8395 (pp20) REVERT: A 1430 TYR cc_start: 0.8030 (m-80) cc_final: 0.7349 (m-80) REVERT: A 1443 GLU cc_start: 0.7638 (tm-30) cc_final: 0.7315 (tm-30) REVERT: A 1471 LYS cc_start: 0.7280 (tppt) cc_final: 0.6850 (tptp) REVERT: C 21 TYR cc_start: 0.6099 (t80) cc_final: 0.5551 (t80) REVERT: C 44 ASN cc_start: 0.8724 (p0) cc_final: 0.8405 (p0) outliers start: 44 outliers final: 31 residues processed: 255 average time/residue: 0.0872 time to fit residues: 33.8485 Evaluate side-chains 247 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 211 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 157 MET Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 535 PHE Chi-restraints excluded: chain A residue 690 SER Chi-restraints excluded: chain A residue 926 ASP Chi-restraints excluded: chain A residue 936 ASN Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 1152 ILE Chi-restraints excluded: chain A residue 1181 CYS Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain A residue 1237 ASP Chi-restraints excluded: chain A residue 1246 VAL Chi-restraints excluded: chain A residue 1250 LEU Chi-restraints excluded: chain A residue 1276 LEU Chi-restraints excluded: chain A residue 1285 ILE Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1316 PHE Chi-restraints excluded: chain A residue 1320 PHE Chi-restraints excluded: chain A residue 1343 ILE Chi-restraints excluded: chain A residue 1418 TYR Chi-restraints excluded: chain A residue 1440 PHE Chi-restraints excluded: chain A residue 1501 PHE Chi-restraints excluded: chain C residue 16 CYS Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 48 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 38 optimal weight: 8.9990 chunk 99 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 chunk 48 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 111 optimal weight: 0.9980 chunk 78 optimal weight: 8.9990 chunk 90 optimal weight: 10.0000 chunk 51 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 392 HIS A1056 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.161923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.123384 restraints weight = 19033.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.128183 restraints weight = 9142.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.131347 restraints weight = 5673.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.133392 restraints weight = 4101.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.134831 restraints weight = 3312.029| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 12265 Z= 0.136 Angle : 0.865 32.182 16648 Z= 0.382 Chirality : 0.078 2.062 1889 Planarity : 0.004 0.056 2000 Dihedral : 10.644 88.882 1777 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.85 % Favored : 90.94 % Rotamer: Outliers : 4.10 % Allowed : 23.15 % Favored : 72.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.22), residues: 1390 helix: 0.00 (0.18), residues: 824 sheet: -3.54 (1.72), residues: 10 loop : -3.22 (0.24), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1138 TYR 0.021 0.001 TYR A 578 PHE 0.015 0.001 PHE C 15 TRP 0.016 0.001 TRP A1437 HIS 0.010 0.001 HIS A 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (12240) covalent geometry : angle 0.85342 / 0.38 (16592) SS BOND : bond 0.00399 / 0.26 ( 13) SS BOND : angle 1.07920 / 0.84 ( 26) hydrogen bonds : bond 0.04430 / 3.06 ( 576) hydrogen bonds : angle 3.95184 / 2.80 ( 1608) Misc. bond : bond 0.00015 / 0.01 ( 2) link_BETA1-3 : bond 0.01704 / 0.81 ( 3) link_BETA1-3 : angle 5.47183 / 3.28 ( 9) link_BETA1-6 : bond 0.00059 / 0.03 ( 1) link_BETA1-6 : angle 1.48379 / 0.76 ( 3) link_NAG-ASN : bond 0.00313 / 0.23 ( 6) link_NAG-ASN : angle 1.86637 / 1.41 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 216 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.7319 (mp0) cc_final: 0.6706 (mp0) REVERT: A 219 ASP cc_start: 0.7015 (t0) cc_final: 0.6712 (t0) REVERT: A 283 ASN cc_start: 0.8807 (t0) cc_final: 0.8416 (t0) REVERT: A 320 ASP cc_start: 0.8405 (t0) cc_final: 0.7945 (t0) REVERT: A 345 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.8169 (pp30) REVERT: A 535 PHE cc_start: 0.7518 (OUTLIER) cc_final: 0.7223 (t80) REVERT: A 536 MET cc_start: 0.8928 (tmm) cc_final: 0.8242 (tmm) REVERT: A 552 ARG cc_start: 0.7235 (mtm110) cc_final: 0.6914 (mtp-110) REVERT: A 583 TRP cc_start: 0.8306 (t-100) cc_final: 0.7951 (t-100) REVERT: A 668 ILE cc_start: 0.9094 (tt) cc_final: 0.8856 (tp) REVERT: A 683 ASN cc_start: 0.8977 (p0) cc_final: 0.8462 (p0) REVERT: A 846 ARG cc_start: 0.7313 (ttm170) cc_final: 0.6897 (mmm-85) REVERT: A 894 ASP cc_start: 0.7706 (t0) cc_final: 0.7457 (t0) REVERT: A 914 PHE cc_start: 0.7486 (t80) cc_final: 0.7041 (m-80) REVERT: A 926 ASP cc_start: 0.8220 (OUTLIER) cc_final: 0.7932 (t70) REVERT: A 977 GLU cc_start: 0.8354 (tp30) cc_final: 0.8007 (tt0) REVERT: A 1025 MET cc_start: 0.8541 (ttt) cc_final: 0.8007 (tpp) REVERT: A 1065 GLN cc_start: 0.8539 (tm-30) cc_final: 0.8252 (tp40) REVERT: A 1083 GLU cc_start: 0.8335 (pt0) cc_final: 0.7964 (tt0) REVERT: A 1141 MET cc_start: 0.8288 (tpt) cc_final: 0.7919 (tpp) REVERT: A 1177 MET cc_start: 0.6846 (tpp) cc_final: 0.6519 (tpt) REVERT: A 1265 ARG cc_start: 0.8189 (mtm-85) cc_final: 0.7914 (mtm180) REVERT: A 1283 LYS cc_start: 0.8244 (tptt) cc_final: 0.8001 (tppt) REVERT: A 1369 ARG cc_start: 0.7437 (mmm160) cc_final: 0.6951 (ttt90) REVERT: A 1419 GLU cc_start: 0.8737 (pp20) cc_final: 0.8388 (pp20) REVERT: A 1430 TYR cc_start: 0.8096 (m-80) cc_final: 0.7418 (m-80) REVERT: A 1443 GLU cc_start: 0.7510 (tm-30) cc_final: 0.6996 (tm-30) REVERT: A 1471 LYS cc_start: 0.7308 (tppt) cc_final: 0.6873 (tptp) REVERT: C 21 TYR cc_start: 0.6255 (t80) cc_final: 0.5715 (t80) REVERT: C 44 ASN cc_start: 0.8712 (p0) cc_final: 0.8387 (p0) REVERT: C 62 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.7488 (ptm-80) outliers start: 51 outliers final: 39 residues processed: 252 average time/residue: 0.0850 time to fit residues: 32.4651 Evaluate side-chains 256 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 213 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 535 PHE Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 690 SER Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain A residue 926 ASP Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 1066 ILE Chi-restraints excluded: chain A residue 1152 ILE Chi-restraints excluded: chain A residue 1181 CYS Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain A residue 1237 ASP Chi-restraints excluded: chain A residue 1246 VAL Chi-restraints excluded: chain A residue 1250 LEU Chi-restraints excluded: chain A residue 1276 LEU Chi-restraints excluded: chain A residue 1285 ILE Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1316 PHE Chi-restraints excluded: chain A residue 1320 PHE Chi-restraints excluded: chain A residue 1322 MET Chi-restraints excluded: chain A residue 1343 ILE Chi-restraints excluded: chain A residue 1418 TYR Chi-restraints excluded: chain A residue 1440 PHE Chi-restraints excluded: chain A residue 1467 GLN Chi-restraints excluded: chain A residue 1501 PHE Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 16 CYS Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 62 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 14 optimal weight: 6.9990 chunk 115 optimal weight: 7.9990 chunk 89 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 124 optimal weight: 0.0170 chunk 67 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 118 optimal weight: 0.6980 chunk 11 optimal weight: 9.9990 chunk 24 optimal weight: 0.9990 overall best weight: 1.3422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 392 HIS A 936 ASN ** A1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.161574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.122888 restraints weight = 18949.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.127648 restraints weight = 9162.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.130786 restraints weight = 5706.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.132895 restraints weight = 4138.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.134204 restraints weight = 3330.236| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12265 Z= 0.141 Angle : 0.876 32.247 16648 Z= 0.386 Chirality : 0.078 2.062 1889 Planarity : 0.004 0.055 2000 Dihedral : 10.502 88.144 1777 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.85 % Favored : 90.94 % Rotamer: Outliers : 4.10 % Allowed : 23.87 % Favored : 72.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.23), residues: 1390 helix: 0.05 (0.18), residues: 825 sheet: -3.52 (1.71), residues: 10 loop : -3.13 (0.24), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 77 TYR 0.023 0.001 TYR A 578 PHE 0.019 0.001 PHE C 15 TRP 0.015 0.001 TRP A1437 HIS 0.011 0.001 HIS A 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (12240) covalent geometry : angle 0.86458 / 0.38 (16592) SS BOND : bond 0.00504 / 0.25 ( 13) SS BOND : angle 1.09540 / 0.83 ( 26) hydrogen bonds : bond 0.04476 / 3.08 ( 576) hydrogen bonds : angle 3.96343 / 2.80 ( 1608) Misc. bond : bond 0.00015 / 0.01 ( 2) link_BETA1-3 : bond 0.01631 / 0.77 ( 3) link_BETA1-3 : angle 5.39012 / 3.24 ( 9) link_BETA1-6 : bond 0.00073 / 0.04 ( 1) link_BETA1-6 : angle 1.52227 / 0.78 ( 3) link_NAG-ASN : bond 0.00300 / 0.22 ( 6) link_NAG-ASN : angle 1.85639 / 1.39 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 215 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 219 ASP cc_start: 0.6999 (t0) cc_final: 0.6698 (t0) REVERT: A 283 ASN cc_start: 0.8807 (t0) cc_final: 0.8415 (t0) REVERT: A 320 ASP cc_start: 0.8376 (t0) cc_final: 0.7875 (t0) REVERT: A 345 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.8149 (pp30) REVERT: A 535 PHE cc_start: 0.7522 (OUTLIER) cc_final: 0.7194 (t80) REVERT: A 536 MET cc_start: 0.8929 (tmm) cc_final: 0.8223 (tmm) REVERT: A 552 ARG cc_start: 0.7231 (mtm110) cc_final: 0.6910 (mtp-110) REVERT: A 583 TRP cc_start: 0.8281 (t-100) cc_final: 0.7862 (t-100) REVERT: A 668 ILE cc_start: 0.9101 (tt) cc_final: 0.8865 (tp) REVERT: A 683 ASN cc_start: 0.8977 (p0) cc_final: 0.8465 (p0) REVERT: A 846 ARG cc_start: 0.7344 (ttm170) cc_final: 0.6934 (mmm-85) REVERT: A 894 ASP cc_start: 0.7718 (t0) cc_final: 0.7458 (t0) REVERT: A 914 PHE cc_start: 0.7464 (t80) cc_final: 0.6985 (m-80) REVERT: A 926 ASP cc_start: 0.8242 (OUTLIER) cc_final: 0.7966 (t70) REVERT: A 977 GLU cc_start: 0.8344 (tp30) cc_final: 0.7967 (tt0) REVERT: A 1025 MET cc_start: 0.8521 (ttt) cc_final: 0.7963 (tpp) REVERT: A 1065 GLN cc_start: 0.8539 (tm-30) cc_final: 0.8277 (tp40) REVERT: A 1083 GLU cc_start: 0.8365 (pt0) cc_final: 0.8118 (tt0) REVERT: A 1177 MET cc_start: 0.6846 (tpp) cc_final: 0.6543 (tpt) REVERT: A 1283 LYS cc_start: 0.8216 (tptt) cc_final: 0.7964 (tppt) REVERT: A 1369 ARG cc_start: 0.7431 (mmm160) cc_final: 0.6956 (ttt90) REVERT: A 1419 GLU cc_start: 0.8778 (pp20) cc_final: 0.8434 (pp20) REVERT: A 1443 GLU cc_start: 0.7220 (tm-30) cc_final: 0.6893 (tm-30) REVERT: A 1458 GLU cc_start: 0.7710 (pt0) cc_final: 0.7330 (mt-10) REVERT: A 1471 LYS cc_start: 0.7371 (tppt) cc_final: 0.6930 (tptp) REVERT: C 21 TYR cc_start: 0.6258 (t80) cc_final: 0.5765 (t80) REVERT: C 44 ASN cc_start: 0.8650 (p0) cc_final: 0.8358 (p0) REVERT: C 62 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.7524 (ptm-80) outliers start: 51 outliers final: 39 residues processed: 248 average time/residue: 0.0874 time to fit residues: 32.7995 Evaluate side-chains 253 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 210 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 535 PHE Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 690 SER Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 926 ASP Chi-restraints excluded: chain A residue 936 ASN Chi-restraints excluded: chain A residue 949 THR Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 1066 ILE Chi-restraints excluded: chain A residue 1152 ILE Chi-restraints excluded: chain A residue 1181 CYS Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain A residue 1237 ASP Chi-restraints excluded: chain A residue 1246 VAL Chi-restraints excluded: chain A residue 1250 LEU Chi-restraints excluded: chain A residue 1276 LEU Chi-restraints excluded: chain A residue 1285 ILE Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1316 PHE Chi-restraints excluded: chain A residue 1320 PHE Chi-restraints excluded: chain A residue 1322 MET Chi-restraints excluded: chain A residue 1343 ILE Chi-restraints excluded: chain A residue 1418 TYR Chi-restraints excluded: chain A residue 1501 PHE Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 62 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 125 optimal weight: 0.0040 chunk 62 optimal weight: 7.9990 chunk 22 optimal weight: 7.9990 chunk 5 optimal weight: 0.2980 chunk 7 optimal weight: 0.0050 chunk 4 optimal weight: 9.9990 chunk 97 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 116 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 overall best weight: 0.3406 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 HIS A 936 ASN ** A1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.165562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.126741 restraints weight = 18834.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.131671 restraints weight = 8993.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.134936 restraints weight = 5537.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.137128 restraints weight = 3983.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.138528 restraints weight = 3182.819| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12265 Z= 0.128 Angle : 0.867 31.941 16648 Z= 0.381 Chirality : 0.078 2.052 1889 Planarity : 0.004 0.056 2000 Dihedral : 10.088 83.116 1777 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.42 % Favored : 91.37 % Rotamer: Outliers : 3.22 % Allowed : 24.84 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.23), residues: 1390 helix: 0.15 (0.18), residues: 831 sheet: -3.53 (1.74), residues: 10 loop : -3.06 (0.24), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1027 TYR 0.016 0.001 TYR A 196 PHE 0.012 0.001 PHE C 15 TRP 0.014 0.001 TRP A 121 HIS 0.011 0.001 HIS A 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 (12240) covalent geometry : angle 0.85816 / 0.38 (16592) SS BOND : bond 0.00278 / 0.16 ( 13) SS BOND : angle 0.92070 / 0.67 ( 26) hydrogen bonds : bond 0.03976 / 2.76 ( 576) hydrogen bonds : angle 3.82578 / 2.71 ( 1608) Misc. bond : bond 0.00005 / 0.00 ( 2) link_BETA1-3 : bond 0.02047 / 0.98 ( 3) link_BETA1-3 : angle 5.01038 / 2.97 ( 9) link_BETA1-6 : bond 0.00400 / 0.21 ( 1) link_BETA1-6 : angle 1.30587 / 0.69 ( 3) link_NAG-ASN : bond 0.00362 / 0.25 ( 6) link_NAG-ASN : angle 1.62543 / 1.22 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 226 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 ASP cc_start: 0.6866 (t0) cc_final: 0.6566 (t0) REVERT: A 320 ASP cc_start: 0.8308 (t0) cc_final: 0.7803 (t0) REVERT: A 345 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.8127 (pp30) REVERT: A 535 PHE cc_start: 0.7385 (OUTLIER) cc_final: 0.7148 (t80) REVERT: A 536 MET cc_start: 0.8862 (tmm) cc_final: 0.8184 (tmm) REVERT: A 552 ARG cc_start: 0.7221 (mtm110) cc_final: 0.6876 (mtp-110) REVERT: A 583 TRP cc_start: 0.8207 (t-100) cc_final: 0.7656 (t-100) REVERT: A 668 ILE cc_start: 0.9065 (tt) cc_final: 0.8829 (tp) REVERT: A 676 ASP cc_start: 0.7716 (p0) cc_final: 0.7446 (p0) REVERT: A 683 ASN cc_start: 0.8989 (p0) cc_final: 0.8500 (p0) REVERT: A 846 ARG cc_start: 0.7331 (ttm170) cc_final: 0.6939 (mmm-85) REVERT: A 914 PHE cc_start: 0.7278 (t80) cc_final: 0.6758 (m-80) REVERT: A 926 ASP cc_start: 0.8241 (OUTLIER) cc_final: 0.7945 (t70) REVERT: A 977 GLU cc_start: 0.8277 (tp30) cc_final: 0.7898 (tt0) REVERT: A 1025 MET cc_start: 0.8561 (ttt) cc_final: 0.8061 (tpp) REVERT: A 1065 GLN cc_start: 0.8490 (tm-30) cc_final: 0.8221 (tp40) REVERT: A 1083 GLU cc_start: 0.8284 (pt0) cc_final: 0.8031 (tt0) REVERT: A 1141 MET cc_start: 0.8264 (tpt) cc_final: 0.7875 (tpp) REVERT: A 1177 MET cc_start: 0.6649 (tpp) cc_final: 0.6252 (tpt) REVERT: A 1283 LYS cc_start: 0.8245 (tptt) cc_final: 0.7968 (tppt) REVERT: A 1443 GLU cc_start: 0.7311 (tm-30) cc_final: 0.6812 (tm-30) REVERT: A 1471 LYS cc_start: 0.7401 (tppt) cc_final: 0.6972 (tptp) REVERT: C 44 ASN cc_start: 0.8518 (p0) cc_final: 0.8211 (p0) outliers start: 40 outliers final: 29 residues processed: 252 average time/residue: 0.0872 time to fit residues: 33.2949 Evaluate side-chains 247 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 215 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 535 PHE Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 624 TRP Chi-restraints excluded: chain A residue 690 SER Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 926 ASP Chi-restraints excluded: chain A residue 936 ASN Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 1250 LEU Chi-restraints excluded: chain A residue 1276 LEU Chi-restraints excluded: chain A residue 1285 ILE Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1316 PHE Chi-restraints excluded: chain A residue 1320 PHE Chi-restraints excluded: chain A residue 1343 ILE Chi-restraints excluded: chain A residue 1418 TYR Chi-restraints excluded: chain A residue 1440 PHE Chi-restraints excluded: chain A residue 1501 PHE Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 48 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 30 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 131 optimal weight: 9.9990 chunk 29 optimal weight: 0.7980 chunk 134 optimal weight: 8.9990 chunk 55 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 54 optimal weight: 0.0020 chunk 67 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 936 ASN ** A1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1133 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 = 0.3939 r_free = 0.3939 target = 0.165523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.126545 restraints weight = 18941.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.131406 restraints weight = 9177.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.134623 restraints weight = 5706.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.136762 restraints weight = 4128.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.138181 restraints weight = 3325.216| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 12265 Z= 0.127 Angle : 0.867 31.969 16648 Z= 0.379 Chirality : 0.078 2.053 1889 Planarity : 0.004 0.055 2000 Dihedral : 9.856 80.560 1777 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.35 % Favored : 91.44 % Rotamer: Outliers : 3.30 % Allowed : 25.64 % Favored : 71.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.22), residues: 1390 helix: 0.13 (0.18), residues: 833 sheet: None (None), residues: 0 loop : -3.01 (0.24), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 77 TYR 0.017 0.001 TYR C 21 PHE 0.022 0.001 PHE A1434 TRP 0.011 0.001 TRP A1437 HIS 0.009 0.001 HIS A 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (12240) covalent geometry : angle 0.85772 / 0.38 (16592) SS BOND : bond 0.00279 / 0.16 ( 13) SS BOND : angle 0.92255 / 0.67 ( 26) hydrogen bonds : bond 0.03929 / 2.72 ( 576) hydrogen bonds : angle 3.82285 / 2.72 ( 1608) Misc. bond : bond 0.00008 / 0.00 ( 2) link_BETA1-3 : bond 0.01847 / 0.87 ( 3) link_BETA1-3 : angle 4.94863 / 2.94 ( 9) link_BETA1-6 : bond 0.00153 / 0.08 ( 1) link_BETA1-6 : angle 1.33429 / 0.72 ( 3) link_NAG-ASN : bond 0.00332 / 0.24 ( 6) link_NAG-ASN : angle 1.65991 / 1.26 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 218 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 ASP cc_start: 0.6905 (t0) cc_final: 0.6603 (t0) REVERT: A 227 ARG cc_start: 0.8285 (ttm170) cc_final: 0.8022 (ttm170) REVERT: A 283 ASN cc_start: 0.8743 (t0) cc_final: 0.8341 (t0) REVERT: A 320 ASP cc_start: 0.8254 (t0) cc_final: 0.7741 (t0) REVERT: A 345 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.8203 (pp30) REVERT: A 535 PHE cc_start: 0.7482 (OUTLIER) cc_final: 0.7229 (t80) REVERT: A 536 MET cc_start: 0.8908 (tmm) cc_final: 0.8210 (tmm) REVERT: A 552 ARG cc_start: 0.7222 (mtm110) cc_final: 0.6886 (mtp-110) REVERT: A 583 TRP cc_start: 0.8215 (t-100) cc_final: 0.7859 (t-100) REVERT: A 668 ILE cc_start: 0.9112 (tt) cc_final: 0.8882 (tp) REVERT: A 676 ASP cc_start: 0.7707 (p0) cc_final: 0.7467 (p0) REVERT: A 683 ASN cc_start: 0.8914 (p0) cc_final: 0.8452 (p0) REVERT: A 846 ARG cc_start: 0.7246 (ttm170) cc_final: 0.6886 (mmm-85) REVERT: A 914 PHE cc_start: 0.7283 (t80) cc_final: 0.6760 (m-80) REVERT: A 926 ASP cc_start: 0.8228 (OUTLIER) cc_final: 0.7966 (t70) REVERT: A 977 GLU cc_start: 0.8272 (tp30) cc_final: 0.7936 (tt0) REVERT: A 1025 MET cc_start: 0.8537 (ttt) cc_final: 0.8065 (tpp) REVERT: A 1065 GLN cc_start: 0.8536 (tm-30) cc_final: 0.8279 (tp40) REVERT: A 1079 GLN cc_start: 0.8980 (OUTLIER) cc_final: 0.8589 (tm-30) REVERT: A 1141 MET cc_start: 0.8294 (tpt) cc_final: 0.7897 (tpp) REVERT: A 1177 MET cc_start: 0.6448 (tpp) cc_final: 0.6196 (tpt) REVERT: A 1283 LYS cc_start: 0.8300 (tptt) cc_final: 0.7999 (tppt) REVERT: A 1443 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.6860 (tm-30) REVERT: A 1471 LYS cc_start: 0.7360 (tppt) cc_final: 0.6956 (tptp) REVERT: C 44 ASN cc_start: 0.8493 (p0) cc_final: 0.8237 (p0) outliers start: 41 outliers final: 32 residues processed: 246 average time/residue: 0.0941 time to fit residues: 35.0444 Evaluate side-chains 250 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 213 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 157 MET Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 535 PHE Chi-restraints excluded: chain A residue 624 TRP Chi-restraints excluded: chain A residue 690 SER Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 926 ASP Chi-restraints excluded: chain A residue 936 ASN Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 1079 GLN Chi-restraints excluded: chain A residue 1237 ASP Chi-restraints excluded: chain A residue 1246 VAL Chi-restraints excluded: chain A residue 1250 LEU Chi-restraints excluded: chain A residue 1276 LEU Chi-restraints excluded: chain A residue 1285 ILE Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1316 PHE Chi-restraints excluded: chain A residue 1320 PHE Chi-restraints excluded: chain A residue 1343 ILE Chi-restraints excluded: chain A residue 1418 TYR Chi-restraints excluded: chain A residue 1440 PHE Chi-restraints excluded: chain A residue 1443 GLU Chi-restraints excluded: chain A residue 1501 PHE Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 16 CYS Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 48 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 2 optimal weight: 5.9990 chunk 76 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 chunk 22 optimal weight: 8.9990 chunk 122 optimal weight: 7.9990 chunk 99 optimal weight: 9.9990 chunk 94 optimal weight: 4.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 936 ASN ** A1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1133 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 = 0.3906 r_free = 0.3906 target = 0.162304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.123190 restraints weight = 19100.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.127925 restraints weight = 9277.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.131095 restraints weight = 5802.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.133208 restraints weight = 4221.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.134634 restraints weight = 3405.056| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 12265 Z= 0.154 Angle : 0.886 32.106 16648 Z= 0.392 Chirality : 0.078 2.058 1889 Planarity : 0.005 0.055 2000 Dihedral : 9.824 82.573 1777 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.71 % Favored : 91.08 % Rotamer: Outliers : 3.22 % Allowed : 25.80 % Favored : 70.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.22), residues: 1390 helix: 0.14 (0.18), residues: 829 sheet: None (None), residues: 0 loop : -3.01 (0.24), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 77 TYR 0.027 0.001 TYR A 578 PHE 0.016 0.001 PHE A 156 TRP 0.014 0.001 TRP A1437 HIS 0.009 0.001 HIS A 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (12240) covalent geometry : angle 0.87606 / 0.39 (16592) SS BOND : bond 0.00334 / 0.20 ( 13) SS BOND : angle 0.98380 / 0.73 ( 26) hydrogen bonds : bond 0.04279 / 2.95 ( 576) hydrogen bonds : angle 3.90012 / 2.76 ( 1608) Misc. bond : bond 0.00018 / 0.01 ( 2) link_BETA1-3 : bond 0.01740 / 0.84 ( 3) link_BETA1-3 : angle 5.13894 / 3.07 ( 9) link_BETA1-6 : bond 0.00108 / 0.06 ( 1) link_BETA1-6 : angle 1.60031 / 0.83 ( 3) link_NAG-ASN : bond 0.00289 / 0.21 ( 6) link_NAG-ASN : angle 1.79428 / 1.35 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 209 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 ASP cc_start: 0.6863 (t0) cc_final: 0.6610 (t0) REVERT: A 227 ARG cc_start: 0.8317 (ttm170) cc_final: 0.8049 (ttm170) REVERT: A 283 ASN cc_start: 0.8759 (t0) cc_final: 0.8369 (t0) REVERT: A 320 ASP cc_start: 0.8347 (t0) cc_final: 0.7797 (t0) REVERT: A 345 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.8202 (pp30) REVERT: A 535 PHE cc_start: 0.7493 (OUTLIER) cc_final: 0.7218 (t80) REVERT: A 536 MET cc_start: 0.8927 (tmm) cc_final: 0.8184 (tmm) REVERT: A 552 ARG cc_start: 0.7259 (mtm110) cc_final: 0.6908 (mtp-110) REVERT: A 583 TRP cc_start: 0.8324 (t-100) cc_final: 0.7865 (t-100) REVERT: A 668 ILE cc_start: 0.9113 (tt) cc_final: 0.8891 (tp) REVERT: A 676 ASP cc_start: 0.7738 (p0) cc_final: 0.7497 (p0) REVERT: A 683 ASN cc_start: 0.8927 (p0) cc_final: 0.8484 (p0) REVERT: A 846 ARG cc_start: 0.7289 (ttm170) cc_final: 0.6909 (mmm-85) REVERT: A 914 PHE cc_start: 0.7351 (t80) cc_final: 0.6811 (m-80) REVERT: A 926 ASP cc_start: 0.8238 (OUTLIER) cc_final: 0.7985 (t70) REVERT: A 977 GLU cc_start: 0.8281 (tp30) cc_final: 0.7917 (tt0) REVERT: A 1025 MET cc_start: 0.8560 (ttt) cc_final: 0.8018 (tpp) REVERT: A 1065 GLN cc_start: 0.8578 (tm-30) cc_final: 0.8318 (tp40) REVERT: A 1079 GLN cc_start: 0.9062 (OUTLIER) cc_final: 0.8622 (tm-30) REVERT: A 1141 MET cc_start: 0.8299 (tpt) cc_final: 0.7920 (tpp) REVERT: A 1177 MET cc_start: 0.6469 (tpp) cc_final: 0.6215 (tpt) REVERT: A 1283 LYS cc_start: 0.8302 (tptt) cc_final: 0.7987 (tppt) REVERT: A 1443 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.6938 (tm-30) REVERT: A 1471 LYS cc_start: 0.7428 (tppt) cc_final: 0.6999 (tptp) REVERT: C 44 ASN cc_start: 0.8552 (p0) cc_final: 0.8272 (p0) outliers start: 40 outliers final: 33 residues processed: 238 average time/residue: 0.0894 time to fit residues: 32.0312 Evaluate side-chains 244 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 206 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 535 PHE Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 624 TRP Chi-restraints excluded: chain A residue 690 SER Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 926 ASP Chi-restraints excluded: chain A residue 936 ASN Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 1079 GLN Chi-restraints excluded: chain A residue 1237 ASP Chi-restraints excluded: chain A residue 1246 VAL Chi-restraints excluded: chain A residue 1250 LEU Chi-restraints excluded: chain A residue 1276 LEU Chi-restraints excluded: chain A residue 1285 ILE Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1316 PHE Chi-restraints excluded: chain A residue 1320 PHE Chi-restraints excluded: chain A residue 1322 MET Chi-restraints excluded: chain A residue 1343 ILE Chi-restraints excluded: chain A residue 1418 TYR Chi-restraints excluded: chain A residue 1440 PHE Chi-restraints excluded: chain A residue 1443 GLU Chi-restraints excluded: chain A residue 1501 PHE Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 16 CYS Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 48 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 8 optimal weight: 7.9990 chunk 107 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 92 optimal weight: 10.0000 chunk 102 optimal weight: 0.0980 chunk 108 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 120 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 936 ASN ** A1079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1348 GLN B 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.165400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.126156 restraints weight = 19020.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.130975 restraints weight = 9214.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.134224 restraints weight = 5748.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.136396 restraints weight = 4160.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.137764 restraints weight = 3341.286| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 12265 Z= 0.128 Angle : 0.875 31.891 16648 Z= 0.381 Chirality : 0.078 2.053 1889 Planarity : 0.004 0.055 2000 Dihedral : 9.634 85.153 1777 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.20 % Favored : 91.58 % Rotamer: Outliers : 3.38 % Allowed : 26.13 % Favored : 70.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.22), residues: 1390 helix: 0.20 (0.18), residues: 827 sheet: None (None), residues: 0 loop : -2.96 (0.24), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1268 TYR 0.036 0.001 TYR A 578 PHE 0.021 0.001 PHE A1434 TRP 0.015 0.001 TRP A1437 HIS 0.009 0.001 HIS A 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (12240) covalent geometry : angle 0.86642 / 0.38 (16592) SS BOND : bond 0.00273 / 0.16 ( 13) SS BOND : angle 0.86912 / 0.61 ( 26) hydrogen bonds : bond 0.03986 / 2.75 ( 576) hydrogen bonds : angle 3.81114 / 2.71 ( 1608) Misc. bond : bond 0.00008 / 0.00 ( 2) link_BETA1-3 : bond 0.01956 / 0.93 ( 3) link_BETA1-3 : angle 4.89629 / 2.91 ( 9) link_BETA1-6 : bond 0.00302 / 0.16 ( 1) link_BETA1-6 : angle 1.32911 / 0.69 ( 3) link_NAG-ASN : bond 0.00335 / 0.24 ( 6) link_NAG-ASN : angle 1.60799 / 1.21 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2187.99 seconds wall clock time: 38 minutes 18.38 seconds (2298.38 seconds total)