Starting phenix.real_space_refine on Sat Aug 8 04:29:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8e79_27938/08_2026/8e79_27938.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e79_27938/08_2026/8e79_27938.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8e79_27938/08_2026/8e79_27938.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e79_27938/08_2026/8e79_27938.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8e79_27938/08_2026/8e79_27938.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e79_27938/08_2026/8e79_27938.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8e79_27938/08_2026/8e79_27938.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8e79_27938/08_2026/8e79_27938.cif" } resolution = 3.71 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= 0.002 sd= 0.092 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 107 5.49 5 Mg 1 5.21 5 S 93 5.16 5 C 15730 2.51 5 N 4538 2.21 5 O 5155 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 114 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25626 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1724 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 211} Chain: "B" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1769 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 15, 'TRANS': 221} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 29 Chain: "C" Number of atoms: 8459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1091, 8459 Classifications: {'peptide': 1091} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 60, 'TRANS': 1029} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 9913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1269, 9913 Classifications: {'peptide': 1269} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 3, 'PTRANS': 57, 'TRANS': 1208} Chain breaks: 2 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "E" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 645 Classifications: {'peptide': 82} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 75} Chain: "N" Number of atoms: 898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 898 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 106} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "O" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 690 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain breaks: 1 Chain: "P" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 764 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} Chain: "R" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 761 Classifications: {'RNAv2': 36} Modifications used: {'rna2p_pyr': 3, 'rna3p_pur': 17, 'rna3p_pyr': 16} Link IDs: {'rna2p': 3, 'rna3p': 32} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12458 SG CYS D 60 107.550 86.659 111.146 1.00124.43 S ATOM 12476 SG CYS D 62 108.212 88.169 113.859 1.00126.44 S ATOM 12585 SG CYS D 75 108.552 84.616 115.158 1.00123.04 S ATOM 12611 SG CYS D 78 106.395 85.410 114.803 1.00121.69 S ATOM 19026 SG CYS D 891 79.841 26.414 87.583 1.00 83.34 S ATOM 19593 SG CYS D 968 78.806 30.593 89.158 1.00 81.92 S ATOM 19635 SG CYS D 975 79.391 29.783 86.621 1.00 77.68 S ATOM 19653 SG CYS D 978 77.274 28.499 86.291 1.00 80.68 S Time building chain proxies: 5.91, per 1000 atoms: 0.23 Number of scatterers: 25626 At special positions: 0 Unit cell: (128.75, 131.84, 196.73, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 93 16.00 P 107 15.00 Mg 1 11.99 O 5155 8.00 N 4538 7.00 C 15730 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.18 Conformation dependent library (CDL) restraints added in 975.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2000 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 78 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 62 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 75 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 60 " pdb=" ZN D2001 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 978 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 975 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 968 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 891 " Number of angles added : 12 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5544 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 42 sheets defined 39.4% alpha, 16.3% beta 43 base pairs and 76 stacking pairs defined. Time for finding SS restraints: 2.70 Creating SS restraints... Processing helix chain 'A' and resid 31 through 43 Processing helix chain 'A' and resid 72 through 80 removed outlier: 3.564A pdb=" N ILE A 76 " --> pdb=" O ASP A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 106 through 110 Processing helix chain 'A' and resid 203 through 224 removed outlier: 3.517A pdb=" N ALA A 207 " --> pdb=" O SER A 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 4.270A pdb=" N THR B 33 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU B 34 " --> pdb=" O PHE B 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 29 through 34' Processing helix chain 'B' and resid 34 through 45 Processing helix chain 'B' and resid 72 through 82 removed outlier: 4.185A pdb=" N SER B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 154 through 158 Processing helix chain 'B' and resid 203 through 224 Processing helix chain 'C' and resid 54 through 66 removed outlier: 4.030A pdb=" N TRP C 63 " --> pdb=" O ASP C 59 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU C 64 " --> pdb=" O SER C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 76 removed outlier: 3.536A pdb=" N GLU C 76 " --> pdb=" O GLU C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 94 Processing helix chain 'C' and resid 118 through 125 Processing helix chain 'C' and resid 234 through 241 Processing helix chain 'C' and resid 244 through 252 removed outlier: 3.890A pdb=" N VAL C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 264 removed outlier: 3.500A pdb=" N ARG C 259 " --> pdb=" O SER C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 282 Processing helix chain 'C' and resid 288 through 301 removed outlier: 3.650A pdb=" N PHE C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 321 Processing helix chain 'C' and resid 334 through 351 Processing helix chain 'C' and resid 380 through 404 removed outlier: 3.591A pdb=" N LEU C 384 " --> pdb=" O THR C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 417 Processing helix chain 'C' and resid 420 through 433 removed outlier: 3.528A pdb=" N VAL C 424 " --> pdb=" O ILE C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 453 removed outlier: 3.532A pdb=" N GLY C 448 " --> pdb=" O ASN C 444 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG C 453 " --> pdb=" O LEU C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 468 removed outlier: 4.308A pdb=" N ALA C 468 " --> pdb=" O ARG C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 480 removed outlier: 4.137A pdb=" N TYR C 480 " --> pdb=" O PRO C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 539 Processing helix chain 'C' and resid 590 through 594 removed outlier: 3.542A pdb=" N ILE C 594 " --> pdb=" O THR C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 600 Processing helix chain 'C' and resid 601 through 610 removed outlier: 3.716A pdb=" N MET C 607 " --> pdb=" O ASN C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 639 removed outlier: 3.726A pdb=" N GLY C 639 " --> pdb=" O ALA C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 744 removed outlier: 3.523A pdb=" N GLU C 744 " --> pdb=" O ARG C 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 854 through 858 Processing helix chain 'C' and resid 921 through 926 removed outlier: 3.817A pdb=" N ARG C 925 " --> pdb=" O GLY C 921 " (cutoff:3.500A) Processing helix chain 'C' and resid 928 through 943 Processing helix chain 'C' and resid 953 through 957 Processing helix chain 'C' and resid 981 through 991 removed outlier: 3.529A pdb=" N CYS C 991 " --> pdb=" O GLY C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1036 through 1040 removed outlier: 3.675A pdb=" N ASP C1039 " --> pdb=" O LEU C1036 " (cutoff:3.500A) Processing helix chain 'C' and resid 1069 through 1072 Processing helix chain 'C' and resid 1073 through 1080 Processing helix chain 'C' and resid 1082 through 1090 Processing helix chain 'C' and resid 1095 through 1109 removed outlier: 4.174A pdb=" N VAL C1100 " --> pdb=" O THR C1096 " (cutoff:3.500A) Processing helix chain 'C' and resid 1118 through 1131 removed outlier: 3.788A pdb=" N LYS C1122 " --> pdb=" O PRO C1118 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU C1131 " --> pdb=" O GLU C1127 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 24 Processing helix chain 'D' and resid 48 through 53 Processing helix chain 'D' and resid 84 through 90 Processing helix chain 'D' and resid 104 through 107 Processing helix chain 'D' and resid 112 through 119 Processing helix chain 'D' and resid 121 through 129 Processing helix chain 'D' and resid 142 through 187 removed outlier: 3.706A pdb=" N ASN D 146 " --> pdb=" O GLU D 142 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU D 187 " --> pdb=" O GLU D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 228 removed outlier: 3.561A pdb=" N ARG D 194 " --> pdb=" O LYS D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 248 removed outlier: 3.672A pdb=" N TYR D 241 " --> pdb=" O ASP D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 267 removed outlier: 3.566A pdb=" N ILE D 261 " --> pdb=" O GLY D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 284 removed outlier: 4.217A pdb=" N GLU D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA D 274 " --> pdb=" O ILE D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 305 removed outlier: 3.934A pdb=" N LYS D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL D 299 " --> pdb=" O ARG D 295 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER D 305 " --> pdb=" O ALA D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 311 removed outlier: 3.548A pdb=" N GLY D 311 " --> pdb=" O SER D 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 308 through 311' Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 338 through 361 removed outlier: 3.630A pdb=" N ASP D 342 " --> pdb=" O SER D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 383 Processing helix chain 'D' and resid 401 through 411 removed outlier: 3.550A pdb=" N LEU D 406 " --> pdb=" O SER D 403 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS D 407 " --> pdb=" O ASP D 404 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N GLY D 408 " --> pdb=" O LEU D 405 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N LYS D 409 " --> pdb=" O LEU D 406 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN D 410 " --> pdb=" O LYS D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 452 removed outlier: 3.799A pdb=" N GLU D 450 " --> pdb=" O LEU D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 463 Processing helix chain 'D' and resid 468 through 479 Processing helix chain 'D' and resid 481 through 492 removed outlier: 4.452A pdb=" N ASP D 485 " --> pdb=" O PRO D 481 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLU D 489 " --> pdb=" O ASP D 485 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA D 492 " --> pdb=" O GLU D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 507 No H-bonds generated for 'chain 'D' and resid 505 through 507' Processing helix chain 'D' and resid 525 through 527 No H-bonds generated for 'chain 'D' and resid 525 through 527' Processing helix chain 'D' and resid 528 through 533 Processing helix chain 'D' and resid 548 through 554 Processing helix chain 'D' and resid 560 through 564 Processing helix chain 'D' and resid 579 through 589 Processing helix chain 'D' and resid 614 through 623 Processing helix chain 'D' and resid 643 through 651 Processing helix chain 'D' and resid 668 through 675 Processing helix chain 'D' and resid 689 through 704 Processing helix chain 'D' and resid 705 through 725 removed outlier: 3.629A pdb=" N VAL D 709 " --> pdb=" O PRO D 705 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR D 725 " --> pdb=" O PHE D 721 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 762 removed outlier: 3.615A pdb=" N ILE D 745 " --> pdb=" O ARG D 741 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG D 752 " --> pdb=" O HIS D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 766 through 793 Processing helix chain 'D' and resid 797 through 805 Processing helix chain 'D' and resid 810 through 819 removed outlier: 3.808A pdb=" N THR D 814 " --> pdb=" O ASN D 810 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 881 removed outlier: 4.078A pdb=" N GLY D 855 " --> pdb=" O ILE D 851 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LYS D 858 " --> pdb=" O HIS D 854 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLY D 859 " --> pdb=" O GLY D 855 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU D 860 " --> pdb=" O ALA D 856 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLY D 871 " --> pdb=" O THR D 867 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N TYR D 872 " --> pdb=" O ALA D 868 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 956 Processing helix chain 'D' and resid 964 through 968 Processing helix chain 'D' and resid 975 through 980 removed outlier: 3.791A pdb=" N TYR D 979 " --> pdb=" O CYS D 975 " (cutoff:3.500A) Processing helix chain 'D' and resid 994 through 1003 removed outlier: 3.538A pdb=" N VAL D 998 " --> pdb=" O ALA D 994 " (cutoff:3.500A) Processing helix chain 'D' and resid 1027 through 1036 Processing helix chain 'D' and resid 1117 through 1126 Processing helix chain 'D' and resid 1126 through 1145 removed outlier: 3.569A pdb=" N VAL D1130 " --> pdb=" O GLY D1126 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLN D1145 " --> pdb=" O VAL D1141 " (cutoff:3.500A) Processing helix chain 'D' and resid 1150 through 1162 removed outlier: 4.389A pdb=" N ILE D1154 " --> pdb=" O HIS D1150 " (cutoff:3.500A) Processing helix chain 'D' and resid 1183 through 1195 removed outlier: 3.995A pdb=" N ALA D1195 " --> pdb=" O ARG D1191 " (cutoff:3.500A) Processing helix chain 'D' and resid 1209 through 1216 Processing helix chain 'D' and resid 1219 through 1227 Processing helix chain 'D' and resid 1228 through 1240 Processing helix chain 'D' and resid 1248 through 1254 Processing helix chain 'D' and resid 1260 through 1263 Processing helix chain 'D' and resid 1264 through 1269 Processing helix chain 'D' and resid 1275 through 1282 Processing helix chain 'E' and resid 33 through 37 removed outlier: 3.963A pdb=" N THR E 36 " --> pdb=" O LEU E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 45 removed outlier: 3.572A pdb=" N LEU E 43 " --> pdb=" O PRO E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 71 removed outlier: 3.512A pdb=" N ILE E 55 " --> pdb=" O TYR E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 102 removed outlier: 3.530A pdb=" N ILE E 94 " --> pdb=" O LYS E 90 " (cutoff:3.500A) Processing helix chain 'N' and resid 19 through 34 Processing helix chain 'N' and resid 76 through 86 removed outlier: 3.727A pdb=" N VAL N 86 " --> pdb=" O LEU N 82 " (cutoff:3.500A) Processing helix chain 'N' and resid 104 through 117 Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 15 removed outlier: 3.648A pdb=" N LEU A 14 " --> pdb=" O ARG A 18 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ARG A 18 " --> pdb=" O LEU A 14 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N ASP A 190 " --> pdb=" O PRO A 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 95 through 100 removed outlier: 7.470A pdb=" N GLU A 135 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ILE A 56 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N GLU A 137 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ILE A 54 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL A 139 " --> pdb=" O THR A 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 95 through 100 removed outlier: 3.833A pdb=" N GLY A 145 " --> pdb=" O TYR A 168 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR A 168 " --> pdb=" O GLY A 145 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 103 through 105 Processing sheet with id=AA5, first strand: chain 'B' and resid 9 through 11 removed outlier: 3.599A pdb=" N PHE B 21 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ASP B 190 " --> pdb=" O PRO B 25 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 9 through 11 removed outlier: 3.599A pdb=" N PHE B 21 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ASP B 190 " --> pdb=" O PRO B 25 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LYS B 191 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N VAL B 178 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE B 193 " --> pdb=" O TYR B 176 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N TYR B 176 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ASP B 195 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N VAL B 174 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N GLU B 197 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 93 through 100 removed outlier: 3.694A pdb=" N SER B 53 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N GLU B 141 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N VAL B 51 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N GLY B 143 " --> pdb=" O ALA B 49 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ALA B 49 " --> pdb=" O GLY B 143 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 85 through 86 Processing sheet with id=AA9, first strand: chain 'B' and resid 103 through 106 removed outlier: 4.011A pdb=" N ALA B 126 " --> pdb=" O VAL B 105 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AB2, first strand: chain 'C' and resid 39 through 40 removed outlier: 6.498A pdb=" N VAL C 39 " --> pdb=" O SER C 973 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 96 through 97 Processing sheet with id=AB4, first strand: chain 'C' and resid 96 through 97 removed outlier: 5.789A pdb=" N ALA C 131 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ASP C 156 " --> pdb=" O ALA C 131 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N LEU C 133 " --> pdb=" O MET C 154 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 166 through 168 Processing sheet with id=AB6, first strand: chain 'C' and resid 376 through 379 removed outlier: 6.440A pdb=" N SER C 177 " --> pdb=" O SER C 456 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 184 through 191 Processing sheet with id=AB8, first strand: chain 'C' and resid 223 through 224 Processing sheet with id=AB9, first strand: chain 'C' and resid 354 through 355 Processing sheet with id=AC1, first strand: chain 'C' and resid 505 through 506 removed outlier: 5.243A pdb=" N GLU C 527 " --> pdb=" O LYS C 518 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N VAL C 520 " --> pdb=" O SER C 525 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N SER C 525 " --> pdb=" O VAL C 520 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 505 through 506 Processing sheet with id=AC3, first strand: chain 'C' and resid 558 through 562 removed outlier: 3.535A pdb=" N VAL C 559 " --> pdb=" O VAL C 571 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL C 571 " --> pdb=" O VAL C 559 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 642 through 643 removed outlier: 6.505A pdb=" N VAL C 642 " --> pdb=" O ILE C 702 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 667 through 671 removed outlier: 6.908A pdb=" N TYR C 657 " --> pdb=" O VAL C 653 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N VAL C 653 " --> pdb=" O TYR C 657 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N THR C 659 " --> pdb=" O GLU C 651 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 708 through 709 Processing sheet with id=AC7, first strand: chain 'C' and resid 895 through 899 removed outlier: 7.045A pdb=" N ILE C 735 " --> pdb=" O GLY C 896 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE C 898 " --> pdb=" O ILE C 735 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU C 737 " --> pdb=" O ILE C 898 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE C 736 " --> pdb=" O ILE C 916 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 748 through 756 removed outlier: 3.945A pdb=" N GLY C 849 " --> pdb=" O TYR C 872 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ALA C 874 " --> pdb=" O VAL C 847 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N VAL C 847 " --> pdb=" O ALA C 874 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 768 through 769 removed outlier: 3.671A pdb=" N GLU C 768 " --> pdb=" O VAL C 806 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL C 806 " --> pdb=" O GLU C 768 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1042 through 1044 Processing sheet with id=AD2, first strand: chain 'C' and resid 1042 through 1044 removed outlier: 7.214A pdb=" N ILE D 522 " --> pdb=" O ARG D 427 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL D 429 " --> pdb=" O ILE D 522 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N LEU D 524 " --> pdb=" O VAL D 429 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL D 431 " --> pdb=" O LEU D 524 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1067 through 1068 removed outlier: 3.806A pdb=" N LYS D 420 " --> pdb=" O PHE C1068 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1136 through 1138 removed outlier: 3.874A pdb=" N GLU D 9 " --> pdb=" O LEU C1138 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU D 10 " --> pdb=" O ASP D1243 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 34 through 35 removed outlier: 3.763A pdb=" N LYS D 40 " --> pdb=" O ASN D 35 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 93 through 102 removed outlier: 10.266A pdb=" N LEU D 97 " --> pdb=" O PRO D 318 " (cutoff:3.500A) removed outlier: 10.284A pdb=" N ALA D 99 " --> pdb=" O ALA D 316 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ALA D 316 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 234 through 235 removed outlier: 3.573A pdb=" N TYR D 134 " --> pdb=" O ILE D 235 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N ILE D 136 " --> pdb=" O ALA D 255 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ALA D 255 " --> pdb=" O ILE D 136 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 328 through 330 Processing sheet with id=AD9, first strand: chain 'D' and resid 611 through 612 Processing sheet with id=AE1, first strand: chain 'D' and resid 897 through 899 removed outlier: 3.763A pdb=" N VAL D 960 " --> pdb=" O VAL D 899 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 1075 through 1081 removed outlier: 3.733A pdb=" N VAL D1075 " --> pdb=" O ILE D1066 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LYS D1079 " --> pdb=" O TYR D1062 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N TYR D1062 " --> pdb=" O LYS D1079 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 1180 through 1182 removed outlier: 6.668A pdb=" N ALA D1202 " --> pdb=" O ILE D1168 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1271 through 1274 removed outlier: 3.615A pdb=" N THR E 107 " --> pdb=" O ALA D1271 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU E 105 " --> pdb=" O GLN D1273 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'N' and resid 9 through 13 removed outlier: 3.519A pdb=" N LEU N 70 " --> pdb=" O MET N 43 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 47 through 52 971 hydrogen bonds defined for protein. 2691 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 102 hydrogen bonds 204 hydrogen bond angles 0 basepair planarities 43 basepair parallelities 76 stacking parallelities Total time for adding SS restraints: 6.53 Time building geometry restraints manager: 3.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 8034 1.33 - 1.45: 3804 1.45 - 1.57: 14075 1.57 - 1.69: 210 1.69 - 1.81: 165 Bond restraints: 26288 Sorted by residual: bond pdb=" C1' DT O 27 " pdb=" N1 DT O 27 " ideal model delta sigma weight residual 1.468 1.520 -0.052 1.40e-02 5.10e+03 1.38e+01 bond pdb=" C3' DT O 19 " pdb=" C2' DT O 19 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" C1' DC P 145 " pdb=" N1 DC P 145 " ideal model delta sigma weight residual 1.468 1.510 -0.042 1.40e-02 5.10e+03 9.07e+00 bond pdb=" C3' DT O 27 " pdb=" C2' DT O 27 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.52e+00 bond pdb=" C3' DA P 118 " pdb=" C2' DA P 118 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 7.99e+00 ... (remaining 26283 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.24: 33852 1.24 - 2.49: 1748 2.49 - 3.73: 412 3.73 - 4.98: 64 4.98 - 6.22: 6 Bond angle restraints: 36082 Sorted by residual: angle pdb=" C LEU D 579 " pdb=" CA LEU D 579 " pdb=" CB LEU D 579 " ideal model delta sigma weight residual 117.23 111.01 6.22 1.36e+00 5.41e-01 2.09e+01 angle pdb=" N VAL C 742 " pdb=" CA VAL C 742 " pdb=" C VAL C 742 " ideal model delta sigma weight residual 112.12 108.34 3.78 8.40e-01 1.42e+00 2.03e+01 angle pdb=" C HIS A 124 " pdb=" N ILE A 125 " pdb=" CA ILE A 125 " ideal model delta sigma weight residual 122.97 118.65 4.32 9.80e-01 1.04e+00 1.94e+01 angle pdb=" N3 DT P 125 " pdb=" C4 DT P 125 " pdb=" O4 DT P 125 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.81e+01 angle pdb=" N3 DT O 34 " pdb=" C4 DT O 34 " pdb=" O4 DT O 34 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.80e+01 ... (remaining 36077 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.30: 15212 35.30 - 70.60: 569 70.60 - 105.89: 23 105.89 - 141.19: 0 141.19 - 176.49: 5 Dihedral angle restraints: 15809 sinusoidal: 7184 harmonic: 8625 Sorted by residual: dihedral pdb=" C4' C R 19 " pdb=" C3' C R 19 " pdb=" C2' C R 19 " pdb=" C1' C R 19 " ideal model delta sinusoidal sigma weight residual 36.34 -37.85 74.20 1 3.10e+00 1.04e-01 7.27e+02 dihedral pdb=" C4' U R 20 " pdb=" C3' U R 20 " pdb=" C2' U R 20 " pdb=" C1' U R 20 " ideal model delta sinusoidal sigma weight residual 36.34 -35.51 71.85 1 3.10e+00 1.04e-01 6.88e+02 dihedral pdb=" C4' U R 31 " pdb=" C3' U R 31 " pdb=" C2' U R 31 " pdb=" C1' U R 31 " ideal model delta sinusoidal sigma weight residual 36.34 -33.45 69.80 1 3.10e+00 1.04e-01 6.54e+02 ... (remaining 15806 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 3445 0.058 - 0.116: 525 0.116 - 0.174: 118 0.174 - 0.231: 13 0.231 - 0.289: 33 Chirality restraints: 4134 Sorted by residual: chirality pdb=" C3' C R 19 " pdb=" C4' C R 19 " pdb=" O3' C R 19 " pdb=" C2' C R 19 " both_signs ideal model delta sigma weight residual False -2.50 -2.79 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" C2' U R 31 " pdb=" C3' U R 31 " pdb=" O2' U R 31 " pdb=" C1' U R 31 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" C2' U R 20 " pdb=" C3' U R 20 " pdb=" O2' U R 20 " pdb=" C1' U R 20 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 4131 not shown) Planarity restraints: 4364 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 24 " 0.055 5.00e-02 4.00e+02 8.30e-02 1.10e+01 pdb=" N PRO B 25 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO B 25 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 25 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 144 " 0.011 2.00e-02 2.50e+03 2.11e-02 4.43e+00 pdb=" C ARG D 144 " -0.036 2.00e-02 2.50e+03 pdb=" O ARG D 144 " 0.013 2.00e-02 2.50e+03 pdb=" N HIS D 145 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C R 19 " 0.023 2.00e-02 2.50e+03 1.35e-02 4.13e+00 pdb=" N1 C R 19 " -0.033 2.00e-02 2.50e+03 pdb=" C2 C R 19 " 0.004 2.00e-02 2.50e+03 pdb=" O2 C R 19 " -0.003 2.00e-02 2.50e+03 pdb=" N3 C R 19 " 0.001 2.00e-02 2.50e+03 pdb=" C4 C R 19 " 0.003 2.00e-02 2.50e+03 pdb=" N4 C R 19 " 0.004 2.00e-02 2.50e+03 pdb=" C5 C R 19 " 0.001 2.00e-02 2.50e+03 pdb=" C6 C R 19 " -0.001 2.00e-02 2.50e+03 ... (remaining 4361 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.38: 84 2.38 - 3.01: 15468 3.01 - 3.64: 36156 3.64 - 4.27: 53668 4.27 - 4.90: 90761 Nonbonded interactions: 196137 Sorted by model distance: nonbonded pdb=" O3' U R 42 " pdb="MG MG D2002 " model vdw 1.756 2.170 nonbonded pdb=" OG1 THR D 970 " pdb=" O GLY D 973 " model vdw 1.915 3.040 nonbonded pdb=" O GLY D 257 " pdb=" OG SER D 260 " model vdw 2.000 3.040 nonbonded pdb=" OD1 ASP D 537 " pdb="MG MG D2002 " model vdw 2.010 2.170 nonbonded pdb=" O THR B 41 " pdb=" OG SER B 45 " model vdw 2.053 3.040 ... (remaining 196132 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 'A' and (resid 1 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 129 or (resid 130 and (name N or \ name CA or name C or name O or name CB )) or resid 131 through 134 or (resid 135 \ and (name N or name CA or name C or name O or name CB )) or resid 136 through 1 \ 52 or (resid 153 through 154 and (name N or name CA or name C or name O or name \ CB )) or resid 155 through 157 or (resid 158 and (name N or name CA or name C or \ name O or name CB )) or resid 159 through 160 or (resid 161 and (name N or name \ CA or name C or name O or name CB )) or resid 162 through 183 or (resid 184 and \ (name N or name CA or name C or name O or name CB )) or resid 185 through 226)) \ selection = (chain 'B' and resid 1 through 226) } 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: 2.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 30.130 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.050 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 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 : 0.005 0.345 26296 Z= 0.267 Angle : 0.850 45.142 36094 Z= 0.441 Chirality : 0.052 0.289 4134 Planarity : 0.004 0.083 4364 Dihedral : 16.214 176.492 10265 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.67 % Favored : 93.16 % Rotamer: Outliers : 0.91 % Allowed : 9.57 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.04 % 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: -1.08 (0.15), residues: 2999 helix: 0.91 (0.16), residues: 1044 sheet: -0.88 (0.27), residues: 372 loop : -1.88 (0.15), residues: 1583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 198 TYR 0.014 0.001 TYR C 344 PHE 0.013 0.001 PHE N 64 TRP 0.009 0.001 TRP D 778 HIS 0.005 0.001 HIS A 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.25 (26288) covalent geometry : angle 0.66735 / 0.43 (36082) hydrogen bonds : bond 0.15866 / 10.38 ( 1050) hydrogen bonds : angle 5.92994 / 4.17 ( 2895) metal coordination : bond 0.14019 / 7.40 ( 8) metal coordination : angle 28.89143 / 15.26 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 345 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.7972 (m-30) cc_final: 0.7050 (p0) REVERT: A 17 ASN cc_start: 0.8152 (p0) cc_final: 0.7807 (p0) REVERT: A 221 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7338 (tp) REVERT: B 191 LYS cc_start: 0.8990 (ttmt) cc_final: 0.8710 (ttpp) REVERT: C 219 ARG cc_start: 0.8615 (ttp-110) cc_final: 0.8329 (ptp90) REVERT: C 262 LEU cc_start: 0.8562 (mt) cc_final: 0.8361 (mp) REVERT: C 396 MET cc_start: 0.8412 (ttp) cc_final: 0.8159 (ttp) REVERT: C 645 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7498 (mt-10) REVERT: C 661 MET cc_start: 0.8923 (tmm) cc_final: 0.8713 (tmm) REVERT: C 904 MET cc_start: 0.8942 (mmt) cc_final: 0.8354 (mmt) REVERT: D 177 LEU cc_start: -0.2278 (OUTLIER) cc_final: -0.2939 (mt) REVERT: D 248 TYR cc_start: 0.8712 (m-80) cc_final: 0.8439 (m-80) REVERT: D 278 ARG cc_start: 0.7994 (mtm-85) cc_final: 0.7731 (ptp-170) REVERT: D 443 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7647 (mp) REVERT: D 450 GLU cc_start: 0.8117 (tp30) cc_final: 0.7794 (tp30) REVERT: D 480 ARG cc_start: 0.7663 (mpt180) cc_final: 0.7314 (mpt180) REVERT: D 488 GLU cc_start: 0.7999 (tp30) cc_final: 0.7449 (tp30) REVERT: D 869 ASP cc_start: 0.7923 (OUTLIER) cc_final: 0.7449 (t70) REVERT: D 1097 ARG cc_start: 0.3243 (OUTLIER) cc_final: 0.3029 (ptm-80) REVERT: D 1279 ARG cc_start: 0.7733 (ttm-80) cc_final: 0.7502 (ttm-80) REVERT: N 10 TYR cc_start: 0.8514 (m-80) cc_final: 0.8311 (m-10) REVERT: N 113 ASN cc_start: 0.7948 (m-40) cc_final: 0.7725 (m-40) outliers start: 23 outliers final: 10 residues processed: 360 average time/residue: 0.1739 time to fit residues: 96.9840 Evaluate side-chains 302 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 287 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 768 GLU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 767 HIS Chi-restraints excluded: chain D residue 866 ARG Chi-restraints excluded: chain D residue 869 ASP Chi-restraints excluded: chain D residue 883 ASP Chi-restraints excluded: chain D residue 1097 ARG Chi-restraints excluded: chain N residue 15 PHE Chi-restraints excluded: chain N residue 29 HIS Chi-restraints excluded: chain N residue 41 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 9.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 20 GLN B 124 HIS C 935 HIS D 674 ASN D 882 GLN N 29 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.161898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.123144 restraints weight = 32741.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.123473 restraints weight = 72456.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.124316 restraints weight = 49995.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.123841 restraints weight = 36625.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.125173 restraints weight = 28051.257| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 26296 Z= 0.233 Angle : 0.761 22.098 36094 Z= 0.375 Chirality : 0.056 1.245 4134 Planarity : 0.005 0.078 4364 Dihedral : 16.701 178.148 4561 Min Nonbonded Distance : 1.710 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.37 % Favored : 93.46 % Rotamer: Outliers : 2.81 % Allowed : 11.43 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.15), residues: 2999 helix: 1.08 (0.16), residues: 1043 sheet: -0.96 (0.26), residues: 416 loop : -1.85 (0.15), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 173 TYR 0.020 0.002 TYR D 251 PHE 0.034 0.002 PHE N 64 TRP 0.012 0.001 TRP C 938 HIS 0.005 0.001 HIS D 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00556 / 0.23 (26288) covalent geometry : angle 0.73324 / 0.37 (36082) hydrogen bonds : bond 0.05951 / 4.09 ( 1050) hydrogen bonds : angle 4.66511 / 3.32 ( 2895) metal coordination : bond 0.01702 / 0.71 ( 8) metal coordination : angle 11.09911 / 6.28 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 314 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.7874 (m-30) cc_final: 0.7604 (p0) REVERT: A 17 ASN cc_start: 0.7799 (p0) cc_final: 0.7392 (p0) REVERT: B 123 MET cc_start: 0.8588 (ttm) cc_final: 0.8341 (ttm) REVERT: C 76 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7616 (pp20) REVERT: C 197 LYS cc_start: 0.8597 (mttt) cc_final: 0.8123 (mtmm) REVERT: C 219 ARG cc_start: 0.8165 (ttp-110) cc_final: 0.7948 (ptp90) REVERT: C 551 ASP cc_start: 0.7755 (m-30) cc_final: 0.7157 (t0) REVERT: C 724 MET cc_start: 0.8204 (ptm) cc_final: 0.7865 (ptm) REVERT: C 904 MET cc_start: 0.8757 (mmt) cc_final: 0.8488 (mmt) REVERT: C 1003 ASP cc_start: 0.8148 (p0) cc_final: 0.7947 (p0) REVERT: D 65 TYR cc_start: 0.8068 (m-80) cc_final: 0.7753 (m-80) REVERT: D 177 LEU cc_start: -0.2908 (OUTLIER) cc_final: -0.3575 (mt) REVERT: D 242 ARG cc_start: 0.7857 (tpp-160) cc_final: 0.7358 (mmt180) REVERT: D 350 ARG cc_start: 0.8459 (tpp-160) cc_final: 0.8205 (mmt180) REVERT: D 443 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8409 (mp) REVERT: D 488 GLU cc_start: 0.8312 (tp30) cc_final: 0.7768 (tp30) REVERT: D 854 HIS cc_start: 0.8335 (OUTLIER) cc_final: 0.7245 (t-90) REVERT: D 866 ARG cc_start: 0.6926 (OUTLIER) cc_final: 0.5996 (ttp80) REVERT: D 1112 MET cc_start: 0.8170 (mmm) cc_final: 0.7908 (mmm) outliers start: 71 outliers final: 36 residues processed: 360 average time/residue: 0.1716 time to fit residues: 95.4143 Evaluate side-chains 325 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 284 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 902 GLU Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 666 THR Chi-restraints excluded: chain D residue 854 HIS Chi-restraints excluded: chain D residue 866 ARG Chi-restraints excluded: chain D residue 883 ASP Chi-restraints excluded: chain D residue 910 LEU Chi-restraints excluded: chain D residue 911 ILE Chi-restraints excluded: chain D residue 964 SER Chi-restraints excluded: chain D residue 1097 ARG Chi-restraints excluded: chain D residue 1180 LEU Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain N residue 32 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 32 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 161 optimal weight: 7.9990 chunk 106 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 273 optimal weight: 0.9980 chunk 116 optimal weight: 0.9980 chunk 210 optimal weight: 0.5980 chunk 183 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 266 ASN C 293 GLN C 935 HIS N 29 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.172931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.129168 restraints weight = 31661.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.128345 restraints weight = 54282.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.130119 restraints weight = 48449.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.130217 restraints weight = 29747.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.131251 restraints weight = 26178.189| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26296 Z= 0.147 Angle : 0.653 12.094 36094 Z= 0.330 Chirality : 0.049 0.670 4134 Planarity : 0.004 0.078 4364 Dihedral : 16.491 177.890 4547 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.64 % Favored : 94.26 % Rotamer: Outliers : 3.01 % Allowed : 12.77 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.15), residues: 2999 helix: 1.23 (0.16), residues: 1050 sheet: -0.68 (0.27), residues: 385 loop : -1.70 (0.15), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 925 TYR 0.028 0.001 TYR D 65 PHE 0.013 0.001 PHE C 153 TRP 0.013 0.001 TRP C 938 HIS 0.004 0.001 HIS C1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 (26288) covalent geometry : angle 0.64013 / 0.33 (36082) hydrogen bonds : bond 0.05162 / 3.56 ( 1050) hydrogen bonds : angle 4.36371 / 3.10 ( 2895) metal coordination : bond 0.00983 / 0.43 ( 8) metal coordination : angle 7.17757 / 4.00 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 316 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.7928 (m-30) cc_final: 0.7587 (p0) REVERT: A 15 THR cc_start: 0.8313 (t) cc_final: 0.8063 (m) REVERT: A 17 ASN cc_start: 0.7910 (p0) cc_final: 0.7512 (p0) REVERT: A 89 GLU cc_start: 0.7036 (mm-30) cc_final: 0.6528 (mp0) REVERT: C 76 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7702 (pp20) REVERT: C 197 LYS cc_start: 0.8651 (mttt) cc_final: 0.8058 (mtmm) REVERT: C 262 LEU cc_start: 0.8993 (mt) cc_final: 0.8742 (mp) REVERT: C 551 ASP cc_start: 0.8024 (m-30) cc_final: 0.7242 (t0) REVERT: C 724 MET cc_start: 0.8107 (ptm) cc_final: 0.7803 (ptm) REVERT: C 904 MET cc_start: 0.8758 (mmt) cc_final: 0.8513 (mmt) REVERT: C 1072 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.8037 (mp0) REVERT: D 69 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7977 (ptt90) REVERT: D 177 LEU cc_start: -0.2855 (OUTLIER) cc_final: -0.3499 (mt) REVERT: D 242 ARG cc_start: 0.8070 (tpp-160) cc_final: 0.7588 (mmt180) REVERT: D 248 TYR cc_start: 0.8050 (m-80) cc_final: 0.7813 (m-80) REVERT: D 256 MET cc_start: 0.7971 (OUTLIER) cc_final: 0.7605 (tmm) REVERT: D 294 LYS cc_start: 0.8678 (mttm) cc_final: 0.8427 (tttt) REVERT: D 443 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8345 (mp) REVERT: D 480 ARG cc_start: 0.7665 (mpt180) cc_final: 0.7367 (mmt-90) REVERT: D 488 GLU cc_start: 0.8453 (tp30) cc_final: 0.7963 (tp30) REVERT: D 854 HIS cc_start: 0.8254 (OUTLIER) cc_final: 0.7336 (t-90) outliers start: 76 outliers final: 41 residues processed: 369 average time/residue: 0.1604 time to fit residues: 93.1307 Evaluate side-chains 325 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 277 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 5 GLN Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 579 MET Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 902 GLU Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 44 ASP Chi-restraints excluded: chain D residue 69 ARG Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 666 THR Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 767 HIS Chi-restraints excluded: chain D residue 854 HIS Chi-restraints excluded: chain D residue 883 ASP Chi-restraints excluded: chain D residue 910 LEU Chi-restraints excluded: chain D residue 911 ILE Chi-restraints excluded: chain D residue 964 SER Chi-restraints excluded: chain D residue 1180 LEU Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain N residue 29 HIS Chi-restraints excluded: chain N residue 32 LEU Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 111 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 11 optimal weight: 8.9990 chunk 197 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 292 optimal weight: 9.9990 chunk 271 optimal weight: 2.9990 chunk 280 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 185 optimal weight: 0.0570 overall best weight: 0.9102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 505 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.163986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.126173 restraints weight = 32367.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.127278 restraints weight = 71534.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.127290 restraints weight = 42829.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.127274 restraints weight = 29307.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.127667 restraints weight = 26167.816| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26296 Z= 0.131 Angle : 0.618 11.415 36094 Z= 0.315 Chirality : 0.046 0.530 4134 Planarity : 0.004 0.073 4364 Dihedral : 16.384 176.654 4539 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.64 % Favored : 94.26 % Rotamer: Outliers : 3.08 % Allowed : 13.40 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.15), residues: 2999 helix: 1.38 (0.16), residues: 1056 sheet: -0.60 (0.26), residues: 411 loop : -1.56 (0.15), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 925 TYR 0.021 0.001 TYR D 134 PHE 0.016 0.001 PHE D 252 TRP 0.012 0.001 TRP C 938 HIS 0.016 0.001 HIS N 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (26288) covalent geometry : angle 0.61127 / 0.31 (36082) hydrogen bonds : bond 0.04651 / 3.22 ( 1050) hydrogen bonds : angle 4.18895 / 2.97 ( 2895) metal coordination : bond 0.00666 / 0.27 ( 8) metal coordination : angle 4.90733 / 2.71 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 320 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.7864 (m-30) cc_final: 0.7602 (p0) REVERT: A 15 THR cc_start: 0.8246 (t) cc_final: 0.8000 (m) REVERT: A 17 ASN cc_start: 0.7847 (p0) cc_final: 0.7467 (p0) REVERT: A 89 GLU cc_start: 0.6876 (mm-30) cc_final: 0.6471 (mp0) REVERT: C 76 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7764 (pp20) REVERT: C 197 LYS cc_start: 0.8655 (mttt) cc_final: 0.8152 (mtmm) REVERT: C 262 LEU cc_start: 0.9086 (mt) cc_final: 0.8833 (mp) REVERT: C 528 ILE cc_start: 0.8785 (mm) cc_final: 0.8578 (mm) REVERT: C 551 ASP cc_start: 0.7756 (m-30) cc_final: 0.7159 (t0) REVERT: C 904 MET cc_start: 0.8733 (mmt) cc_final: 0.8528 (mmt) REVERT: C 1072 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8042 (mp0) REVERT: C 1094 ASP cc_start: 0.8652 (p0) cc_final: 0.8428 (p0) REVERT: D 117 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.9009 (tp) REVERT: D 177 LEU cc_start: -0.2936 (OUTLIER) cc_final: -0.3562 (mt) REVERT: D 242 ARG cc_start: 0.7884 (tpp-160) cc_final: 0.7456 (mmt180) REVERT: D 294 LYS cc_start: 0.8672 (mttm) cc_final: 0.8395 (tttt) REVERT: D 854 HIS cc_start: 0.8259 (OUTLIER) cc_final: 0.7484 (t-90) REVERT: E 89 GLU cc_start: 0.8844 (mt-10) cc_final: 0.8580 (mt-10) outliers start: 78 outliers final: 51 residues processed: 372 average time/residue: 0.1623 time to fit residues: 95.3399 Evaluate side-chains 337 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 281 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 5 GLN Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 902 GLU Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 44 ASP Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 666 THR Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 767 HIS Chi-restraints excluded: chain D residue 854 HIS Chi-restraints excluded: chain D residue 883 ASP Chi-restraints excluded: chain D residue 910 LEU Chi-restraints excluded: chain D residue 911 ILE Chi-restraints excluded: chain D residue 964 SER Chi-restraints excluded: chain D residue 1180 LEU Chi-restraints excluded: chain D residue 1238 ILE Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain N residue 15 PHE Chi-restraints excluded: chain N residue 32 LEU Chi-restraints excluded: chain N residue 44 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 23 optimal weight: 3.9990 chunk 305 optimal weight: 30.0000 chunk 256 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 134 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 299 optimal weight: 50.0000 chunk 107 optimal weight: 0.9990 chunk 295 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 29 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.173424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.129861 restraints weight = 31341.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.129047 restraints weight = 52734.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.130632 restraints weight = 48230.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.130876 restraints weight = 29065.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.133004 restraints weight = 25470.537| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26296 Z= 0.136 Angle : 0.608 11.034 36094 Z= 0.311 Chirality : 0.046 0.404 4134 Planarity : 0.004 0.071 4364 Dihedral : 16.321 175.625 4537 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.60 % Favored : 94.30 % Rotamer: Outliers : 3.48 % Allowed : 14.27 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.15), residues: 2999 helix: 1.41 (0.16), residues: 1058 sheet: -0.49 (0.26), residues: 405 loop : -1.43 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 925 TYR 0.023 0.001 TYR D 134 PHE 0.012 0.001 PHE C 153 TRP 0.012 0.001 TRP C 938 HIS 0.005 0.001 HIS D 854 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (26288) covalent geometry : angle 0.60264 / 0.31 (36082) hydrogen bonds : bond 0.04500 / 3.12 ( 1050) hydrogen bonds : angle 4.09045 / 2.90 ( 2895) metal coordination : bond 0.00689 / 0.29 ( 8) metal coordination : angle 4.33269 / 2.27 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 304 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.7863 (m-30) cc_final: 0.7609 (p0) REVERT: A 15 THR cc_start: 0.8258 (t) cc_final: 0.8031 (m) REVERT: A 17 ASN cc_start: 0.7919 (p0) cc_final: 0.7503 (p0) REVERT: A 89 GLU cc_start: 0.6936 (mm-30) cc_final: 0.6512 (mp0) REVERT: C 76 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7724 (pp20) REVERT: C 197 LYS cc_start: 0.8693 (mttt) cc_final: 0.8134 (mtmm) REVERT: C 551 ASP cc_start: 0.7837 (m-30) cc_final: 0.7220 (t0) REVERT: C 685 ASN cc_start: 0.8293 (OUTLIER) cc_final: 0.8021 (t0) REVERT: C 797 ARG cc_start: 0.7577 (OUTLIER) cc_final: 0.7168 (mtm-85) REVERT: C 800 ASP cc_start: 0.8162 (t0) cc_final: 0.7768 (t0) REVERT: C 918 ASN cc_start: 0.8000 (OUTLIER) cc_final: 0.7757 (m-40) REVERT: C 1072 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8058 (mp0) REVERT: C 1094 ASP cc_start: 0.8662 (p0) cc_final: 0.8407 (p0) REVERT: D 117 LEU cc_start: 0.9423 (OUTLIER) cc_final: 0.9076 (tp) REVERT: D 177 LEU cc_start: -0.2750 (OUTLIER) cc_final: -0.3320 (mt) REVERT: D 242 ARG cc_start: 0.8063 (tpp-160) cc_final: 0.7751 (mmt180) REVERT: D 251 TYR cc_start: 0.7758 (m-80) cc_final: 0.7326 (m-80) REVERT: D 294 LYS cc_start: 0.8711 (mttm) cc_final: 0.8425 (mttt) REVERT: D 480 ARG cc_start: 0.7540 (mpt180) cc_final: 0.7148 (mpt180) REVERT: D 854 HIS cc_start: 0.8264 (OUTLIER) cc_final: 0.7428 (t-90) REVERT: N 114 ARG cc_start: 0.8465 (tmm-80) cc_final: 0.8237 (ttp80) outliers start: 88 outliers final: 59 residues processed: 360 average time/residue: 0.1492 time to fit residues: 85.3406 Evaluate side-chains 355 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 288 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 5 GLN Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 579 MET Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 645 GLU Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 685 ASN Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 797 ARG Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 902 GLU Chi-restraints excluded: chain C residue 918 ASN Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 666 THR Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 767 HIS Chi-restraints excluded: chain D residue 854 HIS Chi-restraints excluded: chain D residue 866 ARG Chi-restraints excluded: chain D residue 883 ASP Chi-restraints excluded: chain D residue 910 LEU Chi-restraints excluded: chain D residue 911 ILE Chi-restraints excluded: chain D residue 964 SER Chi-restraints excluded: chain D residue 1180 LEU Chi-restraints excluded: chain D residue 1238 ILE Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain N residue 15 PHE Chi-restraints excluded: chain N residue 18 PHE Chi-restraints excluded: chain N residue 109 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 49 optimal weight: 9.9990 chunk 142 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 297 optimal weight: 7.9990 chunk 235 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 96 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 chunk 79 optimal weight: 0.4980 chunk 272 optimal weight: 5.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 124 HIS N 29 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.162092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.124473 restraints weight = 32580.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.125207 restraints weight = 75257.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.125540 restraints weight = 42733.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.125318 restraints weight = 29961.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.125743 restraints weight = 26406.271| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 26296 Z= 0.188 Angle : 0.647 9.469 36094 Z= 0.332 Chirality : 0.047 0.305 4134 Planarity : 0.005 0.073 4364 Dihedral : 16.294 173.698 4537 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.50 % Favored : 93.43 % Rotamer: Outliers : 3.76 % Allowed : 14.83 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.15), residues: 2999 helix: 1.26 (0.16), residues: 1065 sheet: -0.68 (0.26), residues: 410 loop : -1.43 (0.15), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 925 TYR 0.024 0.002 TYR D 134 PHE 0.032 0.002 PHE N 18 TRP 0.009 0.001 TRP C 938 HIS 0.005 0.001 HIS D 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.19 (26288) covalent geometry : angle 0.64333 / 0.33 (36082) hydrogen bonds : bond 0.05001 / 3.48 ( 1050) hydrogen bonds : angle 4.17646 / 2.97 ( 2895) metal coordination : bond 0.00927 / 0.39 ( 8) metal coordination : angle 4.03738 / 2.25 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 297 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.7910 (m-30) cc_final: 0.7603 (p0) REVERT: A 15 THR cc_start: 0.8373 (t) cc_final: 0.8138 (m) REVERT: A 17 ASN cc_start: 0.7821 (p0) cc_final: 0.7441 (p0) REVERT: A 78 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8730 (mp) REVERT: C 76 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7700 (pp20) REVERT: C 197 LYS cc_start: 0.8668 (mttt) cc_final: 0.8185 (mtmm) REVERT: C 551 ASP cc_start: 0.7647 (m-30) cc_final: 0.7095 (t0) REVERT: C 685 ASN cc_start: 0.8351 (OUTLIER) cc_final: 0.8088 (t0) REVERT: C 800 ASP cc_start: 0.8091 (t0) cc_final: 0.7746 (t0) REVERT: C 1072 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8128 (mp0) REVERT: C 1094 ASP cc_start: 0.8738 (p0) cc_final: 0.8475 (p0) REVERT: D 117 LEU cc_start: 0.9464 (OUTLIER) cc_final: 0.9101 (tp) REVERT: D 177 LEU cc_start: -0.2500 (OUTLIER) cc_final: -0.3307 (mt) REVERT: D 242 ARG cc_start: 0.7926 (tpp-160) cc_final: 0.7543 (mmt180) REVERT: D 294 LYS cc_start: 0.8623 (mttm) cc_final: 0.8326 (mttt) REVERT: D 480 ARG cc_start: 0.7653 (mpt180) cc_final: 0.7392 (mpt180) REVERT: D 854 HIS cc_start: 0.8424 (OUTLIER) cc_final: 0.7598 (t-90) REVERT: D 866 ARG cc_start: 0.6790 (OUTLIER) cc_final: 0.6023 (ttp80) outliers start: 95 outliers final: 65 residues processed: 363 average time/residue: 0.1508 time to fit residues: 86.8191 Evaluate side-chains 352 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 279 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 5 GLN Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 577 ASP Chi-restraints excluded: chain C residue 579 MET Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 685 ASN Chi-restraints excluded: chain C residue 786 GLU Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 902 GLU Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 44 ASP Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 413 PHE Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 666 THR Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 767 HIS Chi-restraints excluded: chain D residue 801 THR Chi-restraints excluded: chain D residue 808 THR Chi-restraints excluded: chain D residue 854 HIS Chi-restraints excluded: chain D residue 866 ARG Chi-restraints excluded: chain D residue 883 ASP Chi-restraints excluded: chain D residue 910 LEU Chi-restraints excluded: chain D residue 911 ILE Chi-restraints excluded: chain D residue 964 SER Chi-restraints excluded: chain D residue 1238 ILE Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain N residue 15 PHE Chi-restraints excluded: chain N residue 29 HIS Chi-restraints excluded: chain N residue 31 LYS Chi-restraints excluded: chain N residue 32 LEU Chi-restraints excluded: chain N residue 109 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 86 optimal weight: 2.9990 chunk 244 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 287 optimal weight: 8.9990 chunk 84 optimal weight: 1.9990 chunk 69 optimal weight: 9.9990 chunk 240 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 114 optimal weight: 0.8980 chunk 256 optimal weight: 2.9990 chunk 18 optimal weight: 8.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 959 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.170010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.127585 restraints weight = 31432.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.128478 restraints weight = 58561.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.129417 restraints weight = 41291.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.129466 restraints weight = 26616.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.129942 restraints weight = 24955.538| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 26296 Z= 0.205 Angle : 0.650 8.864 36094 Z= 0.334 Chirality : 0.047 0.306 4134 Planarity : 0.005 0.074 4364 Dihedral : 16.255 172.966 4537 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.10 % Favored : 93.83 % Rotamer: Outliers : 3.72 % Allowed : 15.62 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.15), residues: 2999 helix: 1.26 (0.16), residues: 1062 sheet: -0.68 (0.26), residues: 410 loop : -1.44 (0.15), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 925 TYR 0.018 0.002 TYR D 915 PHE 0.017 0.001 PHE C 906 TRP 0.009 0.001 TRP C 938 HIS 0.037 0.001 HIS N 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.20 (26288) covalent geometry : angle 0.64655 / 0.33 (36082) hydrogen bonds : bond 0.05074 / 3.52 ( 1050) hydrogen bonds : angle 4.20650 / 2.99 ( 2895) metal coordination : bond 0.01027 / 0.45 ( 8) metal coordination : angle 3.65709 / 1.99 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 291 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.7892 (m-30) cc_final: 0.7528 (p0) REVERT: A 17 ASN cc_start: 0.7874 (p0) cc_final: 0.7498 (p0) REVERT: A 78 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8685 (mp) REVERT: B 5 GLN cc_start: 0.7285 (OUTLIER) cc_final: 0.6839 (mp10) REVERT: C 76 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7773 (pp20) REVERT: C 197 LYS cc_start: 0.8783 (mttt) cc_final: 0.8195 (mtmm) REVERT: C 551 ASP cc_start: 0.7768 (m-30) cc_final: 0.7081 (t0) REVERT: C 800 ASP cc_start: 0.8202 (t0) cc_final: 0.7888 (t0) REVERT: C 1072 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8155 (mp0) REVERT: C 1094 ASP cc_start: 0.8773 (p0) cc_final: 0.8502 (p0) REVERT: D 117 LEU cc_start: 0.9502 (OUTLIER) cc_final: 0.9165 (tp) REVERT: D 155 MET cc_start: 0.7226 (ppp) cc_final: 0.6326 (ttp) REVERT: D 177 LEU cc_start: -0.2356 (OUTLIER) cc_final: -0.3294 (mt) REVERT: D 242 ARG cc_start: 0.8084 (tpp-160) cc_final: 0.7722 (mmt180) REVERT: D 294 LYS cc_start: 0.8632 (mttm) cc_final: 0.8315 (mttt) REVERT: D 854 HIS cc_start: 0.8382 (OUTLIER) cc_final: 0.7561 (t-90) REVERT: D 866 ARG cc_start: 0.6818 (OUTLIER) cc_final: 0.5967 (ttp80) REVERT: D 869 ASP cc_start: 0.8465 (OUTLIER) cc_final: 0.8097 (t70) REVERT: N 16 SER cc_start: 0.9175 (p) cc_final: 0.8861 (t) outliers start: 94 outliers final: 67 residues processed: 357 average time/residue: 0.1563 time to fit residues: 88.5662 Evaluate side-chains 354 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 278 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 5 GLN Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 548 ILE Chi-restraints excluded: chain C residue 579 MET Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 645 GLU Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 854 SER Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 902 GLU Chi-restraints excluded: chain C residue 971 ILE Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 44 ASP Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 413 PHE Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 666 THR Chi-restraints excluded: chain D residue 767 HIS Chi-restraints excluded: chain D residue 801 THR Chi-restraints excluded: chain D residue 808 THR Chi-restraints excluded: chain D residue 854 HIS Chi-restraints excluded: chain D residue 866 ARG Chi-restraints excluded: chain D residue 869 ASP Chi-restraints excluded: chain D residue 883 ASP Chi-restraints excluded: chain D residue 910 LEU Chi-restraints excluded: chain D residue 911 ILE Chi-restraints excluded: chain D residue 964 SER Chi-restraints excluded: chain D residue 1238 ILE Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain N residue 15 PHE Chi-restraints excluded: chain N residue 18 PHE Chi-restraints excluded: chain N residue 30 ILE Chi-restraints excluded: chain N residue 31 LYS Chi-restraints excluded: chain N residue 109 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 137 optimal weight: 0.6980 chunk 292 optimal weight: 10.0000 chunk 255 optimal weight: 10.0000 chunk 91 optimal weight: 0.0670 chunk 285 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 163 optimal weight: 2.9990 chunk 247 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 126 optimal weight: 0.9990 chunk 263 optimal weight: 10.0000 overall best weight: 1.5524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 540 GLN D1104 HIS N 29 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.169752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.126317 restraints weight = 31584.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.125910 restraints weight = 54689.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.127438 restraints weight = 47489.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.127466 restraints weight = 29478.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.128544 restraints weight = 26011.126| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 26296 Z= 0.155 Angle : 0.617 8.966 36094 Z= 0.317 Chirality : 0.046 0.317 4134 Planarity : 0.004 0.071 4364 Dihedral : 16.165 172.696 4537 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.60 % Favored : 94.33 % Rotamer: Outliers : 3.56 % Allowed : 15.78 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.15), residues: 2999 helix: 1.38 (0.16), residues: 1063 sheet: -0.62 (0.26), residues: 402 loop : -1.38 (0.15), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 925 TYR 0.016 0.001 TYR D 65 PHE 0.023 0.001 PHE D 252 TRP 0.012 0.001 TRP C 938 HIS 0.006 0.001 HIS N 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (26288) covalent geometry : angle 0.61338 / 0.32 (36082) hydrogen bonds : bond 0.04640 / 3.23 ( 1050) hydrogen bonds : angle 4.10411 / 2.91 ( 2895) metal coordination : bond 0.00680 / 0.29 ( 8) metal coordination : angle 3.60596 / 2.01 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 300 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.7866 (m-30) cc_final: 0.7565 (p0) REVERT: A 17 ASN cc_start: 0.7833 (p0) cc_final: 0.7398 (p0) REVERT: A 78 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8656 (mp) REVERT: A 89 GLU cc_start: 0.7064 (mm-30) cc_final: 0.6628 (mp0) REVERT: C 76 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7700 (pp20) REVERT: C 197 LYS cc_start: 0.8771 (mttt) cc_final: 0.8129 (mtmm) REVERT: C 551 ASP cc_start: 0.7734 (m-30) cc_final: 0.7123 (t0) REVERT: C 800 ASP cc_start: 0.8136 (t0) cc_final: 0.7846 (t0) REVERT: C 1072 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8098 (mp0) REVERT: C 1094 ASP cc_start: 0.8700 (p0) cc_final: 0.8387 (p0) REVERT: D 117 LEU cc_start: 0.9479 (OUTLIER) cc_final: 0.9141 (tp) REVERT: D 155 MET cc_start: 0.7223 (ppp) cc_final: 0.6461 (ttp) REVERT: D 177 LEU cc_start: -0.1912 (OUTLIER) cc_final: -0.3178 (mt) REVERT: D 242 ARG cc_start: 0.8076 (tpp-160) cc_final: 0.7720 (mmt180) REVERT: D 294 LYS cc_start: 0.8596 (mttm) cc_final: 0.8300 (mttt) REVERT: D 480 ARG cc_start: 0.7674 (mpt180) cc_final: 0.7240 (mpt180) REVERT: D 854 HIS cc_start: 0.8359 (OUTLIER) cc_final: 0.7517 (t-90) REVERT: D 869 ASP cc_start: 0.8412 (OUTLIER) cc_final: 0.8084 (t70) REVERT: N 16 SER cc_start: 0.9114 (p) cc_final: 0.8777 (t) outliers start: 90 outliers final: 68 residues processed: 358 average time/residue: 0.1554 time to fit residues: 88.0837 Evaluate side-chains 358 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 283 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 5 GLN Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 577 ASP Chi-restraints excluded: chain C residue 579 MET Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 645 GLU Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 786 GLU Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 902 GLU Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 666 THR Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 767 HIS Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 808 THR Chi-restraints excluded: chain D residue 854 HIS Chi-restraints excluded: chain D residue 866 ARG Chi-restraints excluded: chain D residue 869 ASP Chi-restraints excluded: chain D residue 880 VAL Chi-restraints excluded: chain D residue 883 ASP Chi-restraints excluded: chain D residue 910 LEU Chi-restraints excluded: chain D residue 911 ILE Chi-restraints excluded: chain D residue 964 SER Chi-restraints excluded: chain D residue 1176 LEU Chi-restraints excluded: chain D residue 1238 ILE Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain N residue 15 PHE Chi-restraints excluded: chain N residue 18 PHE Chi-restraints excluded: chain N residue 29 HIS Chi-restraints excluded: chain N residue 31 LYS Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 109 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 234 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 196 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 173 optimal weight: 10.0000 chunk 178 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 35 optimal weight: 9.9990 chunk 75 optimal weight: 0.7980 chunk 183 optimal weight: 6.9990 chunk 93 optimal weight: 0.6980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 29 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.170805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.128326 restraints weight = 31511.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.128164 restraints weight = 58617.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.129763 restraints weight = 47101.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.129360 restraints weight = 32023.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.130522 restraints weight = 27219.705| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 26296 Z= 0.176 Angle : 0.632 9.046 36094 Z= 0.325 Chirality : 0.046 0.329 4134 Planarity : 0.004 0.073 4364 Dihedral : 16.138 171.933 4537 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.10 % Favored : 93.83 % Rotamer: Outliers : 3.52 % Allowed : 16.17 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.15), residues: 2999 helix: 1.33 (0.16), residues: 1063 sheet: -0.69 (0.26), residues: 408 loop : -1.37 (0.15), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 925 TYR 0.015 0.001 TYR D 915 PHE 0.016 0.001 PHE C 214 TRP 0.010 0.001 TRP C 938 HIS 0.024 0.001 HIS N 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 (26288) covalent geometry : angle 0.62882 / 0.32 (36082) hydrogen bonds : bond 0.04769 / 3.31 ( 1050) hydrogen bonds : angle 4.13022 / 2.93 ( 2895) metal coordination : bond 0.00828 / 0.36 ( 8) metal coordination : angle 3.34807 / 1.90 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 290 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.7887 (m-30) cc_final: 0.7542 (p0) REVERT: A 17 ASN cc_start: 0.7877 (p0) cc_final: 0.7441 (p0) REVERT: A 78 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8682 (mp) REVERT: A 89 GLU cc_start: 0.7099 (mm-30) cc_final: 0.6661 (mp0) REVERT: C 345 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8781 (tp) REVERT: C 551 ASP cc_start: 0.7743 (m-30) cc_final: 0.7126 (t0) REVERT: C 800 ASP cc_start: 0.8170 (t0) cc_final: 0.7872 (t0) REVERT: C 854 SER cc_start: 0.8504 (OUTLIER) cc_final: 0.8237 (p) REVERT: C 1072 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8129 (mp0) REVERT: C 1094 ASP cc_start: 0.8691 (p0) cc_final: 0.8399 (p0) REVERT: D 117 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.9157 (tp) REVERT: D 155 MET cc_start: 0.7172 (ppp) cc_final: 0.6432 (ttp) REVERT: D 177 LEU cc_start: -0.2010 (OUTLIER) cc_final: -0.3304 (mt) REVERT: D 242 ARG cc_start: 0.8094 (tpp-160) cc_final: 0.7740 (mmt180) REVERT: D 294 LYS cc_start: 0.8596 (mttm) cc_final: 0.8283 (mttt) REVERT: D 854 HIS cc_start: 0.8370 (OUTLIER) cc_final: 0.7563 (t-90) REVERT: D 869 ASP cc_start: 0.8494 (OUTLIER) cc_final: 0.8126 (t70) REVERT: N 16 SER cc_start: 0.9090 (p) cc_final: 0.8691 (t) outliers start: 89 outliers final: 71 residues processed: 352 average time/residue: 0.1593 time to fit residues: 88.5137 Evaluate side-chains 360 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 281 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 5 GLN Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 577 ASP Chi-restraints excluded: chain C residue 579 MET Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 645 GLU Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 786 GLU Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 854 SER Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 902 GLU Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 413 PHE Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 666 THR Chi-restraints excluded: chain D residue 767 HIS Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 808 THR Chi-restraints excluded: chain D residue 854 HIS Chi-restraints excluded: chain D residue 866 ARG Chi-restraints excluded: chain D residue 869 ASP Chi-restraints excluded: chain D residue 880 VAL Chi-restraints excluded: chain D residue 883 ASP Chi-restraints excluded: chain D residue 910 LEU Chi-restraints excluded: chain D residue 911 ILE Chi-restraints excluded: chain D residue 964 SER Chi-restraints excluded: chain D residue 1176 LEU Chi-restraints excluded: chain D residue 1238 ILE Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain N residue 15 PHE Chi-restraints excluded: chain N residue 18 PHE Chi-restraints excluded: chain N residue 31 LYS Chi-restraints excluded: chain N residue 32 LEU Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 109 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 222 optimal weight: 0.0980 chunk 16 optimal weight: 0.7980 chunk 130 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 133 optimal weight: 0.6980 chunk 140 optimal weight: 0.0370 chunk 143 optimal weight: 1.9990 chunk 174 optimal weight: 20.0000 chunk 234 optimal weight: 0.8980 chunk 280 optimal weight: 0.0060 chunk 101 optimal weight: 0.4980 overall best weight: 0.2674 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D1139 GLN E 70 GLN N 29 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.174890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.131932 restraints weight = 31400.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.131557 restraints weight = 50091.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.132772 restraints weight = 47534.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.132983 restraints weight = 29341.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.137261 restraints weight = 25398.046| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 26296 Z= 0.113 Angle : 0.603 9.104 36094 Z= 0.311 Chirality : 0.044 0.316 4134 Planarity : 0.004 0.066 4364 Dihedral : 15.984 172.656 4534 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.04 % Favored : 94.93 % Rotamer: Outliers : 2.37 % Allowed : 17.28 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.16), residues: 2999 helix: 1.61 (0.17), residues: 1063 sheet: -0.33 (0.27), residues: 385 loop : -1.28 (0.15), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 925 TYR 0.017 0.001 TYR D 248 PHE 0.022 0.001 PHE D 252 TRP 0.018 0.001 TRP C 938 HIS 0.005 0.001 HIS C1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (26288) covalent geometry : angle 0.60067 / 0.31 (36082) hydrogen bonds : bond 0.03956 / 2.75 ( 1050) hydrogen bonds : angle 3.95267 / 2.78 ( 2895) metal coordination : bond 0.00342 / 0.15 ( 8) metal coordination : angle 2.84460 / 1.62 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5998 Ramachandran restraints generated. 2999 Oldfield, 0 Emsley, 2999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 304 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.7806 (m-30) cc_final: 0.7529 (p0) REVERT: A 17 ASN cc_start: 0.7880 (p0) cc_final: 0.7450 (p0) REVERT: A 89 GLU cc_start: 0.6948 (mm-30) cc_final: 0.6623 (mp0) REVERT: C 551 ASP cc_start: 0.7757 (m-30) cc_final: 0.7187 (t0) REVERT: C 672 MET cc_start: 0.8459 (mmm) cc_final: 0.8182 (mmt) REVERT: C 713 MET cc_start: 0.8181 (mmt) cc_final: 0.7807 (mmm) REVERT: C 1072 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8076 (mp0) REVERT: C 1094 ASP cc_start: 0.8641 (p0) cc_final: 0.8295 (p0) REVERT: D 117 LEU cc_start: 0.9463 (OUTLIER) cc_final: 0.9135 (tp) REVERT: D 155 MET cc_start: 0.7290 (ppp) cc_final: 0.6535 (ttp) REVERT: D 177 LEU cc_start: -0.2165 (OUTLIER) cc_final: -0.3211 (mt) REVERT: D 242 ARG cc_start: 0.8164 (tpp-160) cc_final: 0.7817 (mmt180) REVERT: D 248 TYR cc_start: 0.7650 (m-80) cc_final: 0.7191 (m-10) REVERT: D 854 HIS cc_start: 0.8224 (OUTLIER) cc_final: 0.7530 (t-90) REVERT: N 16 SER cc_start: 0.9091 (p) cc_final: 0.8701 (t) outliers start: 60 outliers final: 47 residues processed: 345 average time/residue: 0.1563 time to fit residues: 85.2368 Evaluate side-chains 343 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 292 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 5 GLN Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 786 GLU Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 666 THR Chi-restraints excluded: chain D residue 767 HIS Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 808 THR Chi-restraints excluded: chain D residue 854 HIS Chi-restraints excluded: chain D residue 883 ASP Chi-restraints excluded: chain D residue 911 ILE Chi-restraints excluded: chain D residue 1176 LEU Chi-restraints excluded: chain D residue 1238 ILE Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain N residue 15 PHE Chi-restraints excluded: chain N residue 18 PHE Chi-restraints excluded: chain N residue 31 LYS Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 109 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 187 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 289 optimal weight: 10.0000 chunk 215 optimal weight: 2.9990 chunk 267 optimal weight: 0.0470 chunk 136 optimal weight: 0.1980 chunk 189 optimal weight: 5.9990 chunk 305 optimal weight: 30.0000 overall best weight: 1.2484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 17 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.173003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.129813 restraints weight = 31297.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.128633 restraints weight = 48298.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.129949 restraints weight = 48626.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.130195 restraints weight = 31219.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.133107 restraints weight = 26142.347| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26296 Z= 0.142 Angle : 0.617 11.977 36094 Z= 0.316 Chirality : 0.045 0.307 4134 Planarity : 0.004 0.067 4364 Dihedral : 15.967 171.499 4534 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.60 % Favored : 94.36 % Rotamer: Outliers : 2.45 % Allowed : 17.48 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.16), residues: 2999 helix: 1.57 (0.16), residues: 1069 sheet: -0.51 (0.26), residues: 406 loop : -1.21 (0.16), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 925 TYR 0.015 0.001 TYR N 68 PHE 0.012 0.001 PHE C 254 TRP 0.011 0.001 TRP C 938 HIS 0.005 0.001 HIS C1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (26288) covalent geometry : angle 0.61516 / 0.32 (36082) hydrogen bonds : bond 0.04299 / 2.97 ( 1050) hydrogen bonds : angle 3.96374 / 2.81 ( 2895) metal coordination : bond 0.00630 / 0.27 ( 8) metal coordination : angle 2.89113 / 1.62 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3505.93 seconds wall clock time: 61 minutes 25.30 seconds (3685.30 seconds total)