Starting phenix.real_space_refine on Sun Jun 22 13:06:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e79_27938/06_2025/8e79_27938.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e79_27938/06_2025/8e79_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8e79_27938/06_2025/8e79_27938.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e79_27938/06_2025/8e79_27938.map" model { file = "/net/cci-nas-00/data/ceres_data/8e79_27938/06_2025/8e79_27938.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e79_27938/06_2025/8e79_27938.cif" } resolution = 3.71 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.82s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1} 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: {'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 2} 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: {'RNA': 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: 16.06, per 1000 atoms: 0.63 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: 6.75 Conformation dependent library (CDL) restraints added in 3.3 seconds 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: 9.39 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: 14.03 Time building geometry restraints manager: 7.98 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=" N GLY D -1 " pdb=" CA GLY D -1 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.16e+00 bond pdb=" N MET A 1 " pdb=" CA MET A 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.69e+00 bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.61e+00 bond pdb=" CA GLY D1027 " pdb=" C GLY D1027 " ideal model delta sigma weight residual 1.518 1.499 0.019 1.24e-02 6.50e+03 2.29e+00 bond pdb=" N GLY D1027 " pdb=" CA GLY D1027 " ideal model delta sigma weight residual 1.445 1.457 -0.012 8.30e-03 1.45e+04 2.25e+00 ... (remaining 26283 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.24: 34180 1.24 - 2.49: 1570 2.49 - 3.73: 273 3.73 - 4.98: 55 4.98 - 6.22: 4 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=" N SER B 4 " pdb=" CA SER B 4 " pdb=" CB SER B 4 " ideal model delta sigma weight residual 114.17 110.22 3.95 1.14e+00 7.69e-01 1.20e+01 angle pdb=" C GLU D 147 " pdb=" N LEU D 148 " pdb=" CA LEU D 148 " ideal model delta sigma weight residual 120.44 125.15 -4.71 1.36e+00 5.41e-01 1.20e+01 ... (remaining 36077 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.30: 15306 35.30 - 70.60: 586 70.60 - 105.89: 29 105.89 - 141.19: 1 141.19 - 176.49: 5 Dihedral angle restraints: 15927 sinusoidal: 7302 harmonic: 8625 Sorted by residual: dihedral pdb=" CA GLU B 24 " pdb=" C GLU B 24 " pdb=" N PRO B 25 " pdb=" CA PRO B 25 " ideal model delta harmonic sigma weight residual -180.00 -136.07 -43.93 0 5.00e+00 4.00e-02 7.72e+01 dihedral pdb=" O4' C R 19 " pdb=" C1' C R 19 " pdb=" N1 C R 19 " pdb=" C2 C R 19 " ideal model delta sinusoidal sigma weight residual -128.00 -23.91 -104.09 1 1.70e+01 3.46e-03 4.13e+01 dihedral pdb=" CA GLN C1062 " pdb=" C GLN C1062 " pdb=" N PHE C1063 " pdb=" CA PHE C1063 " ideal model delta harmonic sigma weight residual 180.00 148.96 31.04 0 5.00e+00 4.00e-02 3.85e+01 ... (remaining 15924 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2973 0.040 - 0.079: 826 0.079 - 0.118: 284 0.118 - 0.158: 50 0.158 - 0.197: 1 Chirality restraints: 4134 Sorted by residual: chirality pdb=" C1' G R 29 " pdb=" O4' G R 29 " pdb=" C2' G R 29 " pdb=" N9 G R 29 " both_signs ideal model delta sigma weight residual False 2.46 2.26 0.20 2.00e-01 2.50e+01 9.75e-01 chirality pdb=" CA ILE C 594 " pdb=" N ILE C 594 " pdb=" C ILE C 594 " pdb=" CB ILE C 594 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.86e-01 chirality pdb=" CA ILE C 801 " pdb=" N ILE C 801 " pdb=" C ILE C 801 " pdb=" CB ILE C 801 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.47e-01 ... (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: 1.590 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: 0.030 Extract box with map and model: 1.010 Check model and map are aligned: 0.190 Set scattering table: 0.260 Process input model: 75.160 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 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= 0.207 Angle : 0.816 45.142 36094 Z= 0.382 Chirality : 0.042 0.197 4134 Planarity : 0.004 0.083 4364 Dihedral : 16.497 176.492 10383 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 7.02 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.009 0.001 TRP D 778 HIS 0.005 0.001 HIS A 61 PHE 0.013 0.001 PHE N 64 TYR 0.014 0.001 TYR C 344 ARG 0.004 0.000 ARG D 198 Details of bonding type rmsd hydrogen bonds : bond 0.15866 ( 1050) hydrogen bonds : angle 5.92994 ( 2895) metal coordination : bond 0.14019 ( 8) metal coordination : angle 28.89143 ( 12) covalent geometry : bond 0.00403 (26288) covalent geometry : angle 0.62263 (36082) *********************** 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 : 2.465 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: 0.8118 (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: 0.4114 time to fit residues: 227.4164 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 : 2.510 ------------------------------------------------------------------------------- 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 260 optimal weight: 50.0000 chunk 233 optimal weight: 0.4980 chunk 129 optimal weight: 0.0980 chunk 79 optimal weight: 0.0030 chunk 157 optimal weight: 7.9990 chunk 124 optimal weight: 0.6980 chunk 241 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 146 optimal weight: 5.9990 chunk 179 optimal weight: 9.9990 chunk 279 optimal weight: 6.9990 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN B 124 HIS C 935 HIS D 674 ASN N 29 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.174880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.131676 restraints weight = 31409.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.130922 restraints weight = 51058.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.132414 restraints weight = 48354.016| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26296 Z= 0.130 Angle : 0.613 13.060 36094 Z= 0.316 Chirality : 0.043 0.161 4134 Planarity : 0.004 0.071 4364 Dihedral : 17.177 179.126 4679 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.93 % Favored : 94.90 % Rotamer: Outliers : 1.94 % Allowed : 11.03 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.15), residues: 2999 helix: 1.36 (0.16), residues: 1059 sheet: -0.70 (0.26), residues: 390 loop : -1.64 (0.15), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 938 HIS 0.004 0.001 HIS C 323 PHE 0.024 0.001 PHE N 64 TYR 0.016 0.001 TYR D 251 ARG 0.011 0.000 ARG N 114 Details of bonding type rmsd hydrogen bonds : bond 0.04740 ( 1050) hydrogen bonds : angle 4.34219 ( 2895) metal coordination : bond 0.01169 ( 8) metal coordination : angle 8.05860 ( 12) covalent geometry : bond 0.00271 (26288) covalent geometry : angle 0.59512 (36082) *********************** 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 399 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 350 time to evaluate : 2.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.7923 (m-30) cc_final: 0.7549 (p0) REVERT: A 17 ASN cc_start: 0.7970 (p0) cc_final: 0.7576 (p0) REVERT: A 198 THR cc_start: 0.9044 (p) cc_final: 0.8828 (t) REVERT: C 76 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7791 (pp20) REVERT: C 197 LYS cc_start: 0.8610 (mttt) cc_final: 0.8012 (mtmm) REVERT: C 252 PHE cc_start: 0.7514 (m-80) cc_final: 0.7242 (m-10) REVERT: C 551 ASP cc_start: 0.7829 (m-30) cc_final: 0.7134 (t0) REVERT: C 652 GLU cc_start: 0.7784 (pt0) cc_final: 0.7582 (pt0) REVERT: C 672 MET cc_start: 0.8625 (mmm) cc_final: 0.8380 (mmt) REVERT: C 1003 ASP cc_start: 0.8062 (p0) cc_final: 0.7812 (p0) REVERT: D 22 GLN cc_start: 0.8212 (tm-30) cc_final: 0.7945 (tm-30) REVERT: D 65 TYR cc_start: 0.8151 (m-80) cc_final: 0.7912 (m-80) REVERT: D 177 LEU cc_start: -0.2773 (OUTLIER) cc_final: -0.3373 (mt) REVERT: D 242 ARG cc_start: 0.8026 (tpp-160) cc_final: 0.7544 (mmt180) REVERT: D 350 ARG cc_start: 0.8455 (tpp-160) cc_final: 0.8096 (mmt180) REVERT: D 450 GLU cc_start: 0.7765 (tp30) cc_final: 0.7465 (tp30) REVERT: D 488 GLU cc_start: 0.8305 (tp30) cc_final: 0.7821 (tp30) REVERT: D 688 MET cc_start: 0.8460 (mmm) cc_final: 0.8045 (mmt) REVERT: D 854 HIS cc_start: 0.8145 (OUTLIER) cc_final: 0.7341 (t-90) REVERT: E 89 GLU cc_start: 0.8978 (mt-10) cc_final: 0.8735 (mt-10) outliers start: 49 outliers final: 25 residues processed: 381 average time/residue: 0.3984 time to fit residues: 235.1962 Evaluate side-chains 324 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 296 time to evaluate : 2.537 ------------------------------------------------------------------------------- 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 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 C residue 76 GLU Chi-restraints excluded: chain C residue 277 ILE 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 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 919 THR Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain D residue 44 ASP 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 854 HIS Chi-restraints excluded: chain D residue 883 ASP 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 32 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 80 optimal weight: 0.9980 chunk 187 optimal weight: 10.0000 chunk 194 optimal weight: 3.9990 chunk 169 optimal weight: 20.0000 chunk 255 optimal weight: 9.9990 chunk 203 optimal weight: 5.9990 chunk 54 optimal weight: 9.9990 chunk 204 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 189 optimal weight: 6.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 266 ASN D 505 HIS D 882 GLN D 959 GLN N 29 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.172956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.129511 restraints weight = 31337.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.127823 restraints weight = 49801.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.129600 restraints weight = 49018.781| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 26296 Z= 0.174 Angle : 0.599 8.569 36094 Z= 0.314 Chirality : 0.043 0.164 4134 Planarity : 0.004 0.075 4364 Dihedral : 16.951 178.546 4655 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.70 % Favored : 94.20 % Rotamer: Outliers : 3.16 % Allowed : 12.10 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.15), residues: 2999 helix: 1.38 (0.16), residues: 1056 sheet: -0.64 (0.26), residues: 412 loop : -1.59 (0.15), residues: 1531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 938 HIS 0.004 0.001 HIS D 544 PHE 0.028 0.002 PHE N 64 TYR 0.021 0.001 TYR D 65 ARG 0.013 0.000 ARG N 114 Details of bonding type rmsd hydrogen bonds : bond 0.04879 ( 1050) hydrogen bonds : angle 4.26081 ( 2895) metal coordination : bond 0.00990 ( 8) metal coordination : angle 5.27630 ( 12) covalent geometry : bond 0.00417 (26288) covalent geometry : angle 0.59118 (36082) *********************** 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 398 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 318 time to evaluate : 2.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.7925 (m-30) cc_final: 0.7627 (p0) REVERT: A 15 THR cc_start: 0.8220 (t) cc_final: 0.7972 (m) REVERT: A 17 ASN cc_start: 0.7927 (p0) cc_final: 0.7540 (p0) REVERT: C 76 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7630 (pp20) REVERT: C 197 LYS cc_start: 0.8671 (mttt) cc_final: 0.8106 (mtmm) REVERT: C 551 ASP cc_start: 0.7895 (m-30) cc_final: 0.7229 (t0) REVERT: C 661 MET cc_start: 0.8804 (tmm) cc_final: 0.8366 (tmm) REVERT: C 724 MET cc_start: 0.8118 (ptm) cc_final: 0.7776 (ptm) REVERT: D 177 LEU cc_start: -0.2954 (OUTLIER) cc_final: -0.3595 (mt) REVERT: D 242 ARG cc_start: 0.8035 (tpp-160) cc_final: 0.7563 (mmt180) REVERT: D 294 LYS cc_start: 0.8647 (mttt) cc_final: 0.8429 (mttt) REVERT: D 450 GLU cc_start: 0.7800 (tp30) cc_final: 0.7538 (tp30) REVERT: D 854 HIS cc_start: 0.8391 (OUTLIER) cc_final: 0.7516 (t-90) outliers start: 80 outliers final: 40 residues processed: 373 average time/residue: 0.3738 time to fit residues: 220.1864 Evaluate side-chains 324 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 281 time to evaluate : 2.504 ------------------------------------------------------------------------------- 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 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 165 THR Chi-restraints excluded: chain C residue 257 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 490 GLU 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 34 ILE Chi-restraints excluded: chain D residue 87 VAL 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 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 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 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 32 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 85 optimal weight: 2.9990 chunk 127 optimal weight: 0.8980 chunk 186 optimal weight: 0.3980 chunk 181 optimal weight: 10.0000 chunk 88 optimal weight: 0.9980 chunk 57 optimal weight: 7.9990 chunk 230 optimal weight: 10.0000 chunk 208 optimal weight: 4.9990 chunk 44 optimal weight: 9.9990 chunk 301 optimal weight: 9.9990 chunk 140 optimal weight: 1.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.163285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.124340 restraints weight = 32547.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.123571 restraints weight = 76002.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.125106 restraints weight = 56420.401| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 26296 Z= 0.150 Angle : 0.572 9.413 36094 Z= 0.300 Chirality : 0.042 0.162 4134 Planarity : 0.004 0.072 4364 Dihedral : 16.914 177.450 4655 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.67 % Favored : 94.23 % Rotamer: Outliers : 3.04 % Allowed : 13.52 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.15), residues: 2999 helix: 1.46 (0.16), residues: 1057 sheet: -0.49 (0.26), residues: 411 loop : -1.49 (0.15), residues: 1531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 938 HIS 0.025 0.001 HIS N 29 PHE 0.016 0.001 PHE N 64 TYR 0.020 0.001 TYR D 134 ARG 0.016 0.000 ARG N 114 Details of bonding type rmsd hydrogen bonds : bond 0.04549 ( 1050) hydrogen bonds : angle 4.12086 ( 2895) metal coordination : bond 0.00739 ( 8) metal coordination : angle 4.33760 ( 12) covalent geometry : bond 0.00354 (26288) covalent geometry : angle 0.56697 (36082) *********************** 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 386 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 309 time to evaluate : 3.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.8017 (m-30) cc_final: 0.7655 (p0) REVERT: A 15 THR cc_start: 0.8251 (t) cc_final: 0.8021 (m) REVERT: A 17 ASN cc_start: 0.7889 (p0) cc_final: 0.7508 (p0) REVERT: A 89 GLU cc_start: 0.6963 (mm-30) cc_final: 0.6730 (mp0) REVERT: C 76 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7684 (pp20) REVERT: C 197 LYS cc_start: 0.8748 (mttt) cc_final: 0.8239 (mtmm) REVERT: C 551 ASP cc_start: 0.7744 (m-30) cc_final: 0.7179 (t0) REVERT: C 685 ASN cc_start: 0.8360 (m-40) cc_final: 0.8037 (t0) REVERT: C 800 ASP cc_start: 0.8175 (t0) cc_final: 0.7798 (t0) REVERT: C 1094 ASP cc_start: 0.8615 (p0) cc_final: 0.8364 (p0) REVERT: D 117 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.9046 (tp) REVERT: D 177 LEU cc_start: -0.2864 (OUTLIER) cc_final: -0.3431 (mt) REVERT: D 242 ARG cc_start: 0.7907 (tpp-160) cc_final: 0.7538 (mmt180) REVERT: D 294 LYS cc_start: 0.8570 (mttt) cc_final: 0.8345 (tttt) REVERT: D 450 GLU cc_start: 0.7777 (tp30) cc_final: 0.7561 (tp30) REVERT: D 854 HIS cc_start: 0.8355 (OUTLIER) cc_final: 0.7632 (t-90) outliers start: 77 outliers final: 52 residues processed: 357 average time/residue: 0.4129 time to fit residues: 234.0072 Evaluate side-chains 338 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 282 time to evaluate : 3.608 ------------------------------------------------------------------------------- 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 80 LEU 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 216 VAL Chi-restraints excluded: chain C residue 76 GLU 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 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 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 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 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 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 808 THR 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 68 TYR Chi-restraints excluded: chain N residue 15 PHE Chi-restraints excluded: chain N residue 18 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 302 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 69 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 295 optimal weight: 0.9990 chunk 135 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 chunk 50 optimal weight: 0.3980 chunk 140 optimal weight: 4.9990 chunk 157 optimal weight: 0.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 935 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 = 0.3929 r_free = 0.3929 target = 0.171018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.127698 restraints weight = 31692.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.124619 restraints weight = 48916.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.127059 restraints weight = 47278.560| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 26296 Z= 0.151 Angle : 0.570 13.766 36094 Z= 0.299 Chirality : 0.042 0.162 4134 Planarity : 0.004 0.070 4364 Dihedral : 16.877 179.079 4655 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.60 % Favored : 94.33 % Rotamer: Outliers : 3.36 % Allowed : 14.47 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.15), residues: 2999 helix: 1.44 (0.17), residues: 1058 sheet: -0.47 (0.26), residues: 405 loop : -1.37 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 938 HIS 0.004 0.001 HIS C1042 PHE 0.017 0.001 PHE C 254 TYR 0.018 0.001 TYR D 134 ARG 0.008 0.000 ARG C 925 Details of bonding type rmsd hydrogen bonds : bond 0.04465 ( 1050) hydrogen bonds : angle 4.06548 ( 2895) metal coordination : bond 0.00692 ( 8) metal coordination : angle 3.62659 ( 12) covalent geometry : bond 0.00357 (26288) covalent geometry : angle 0.56591 (36082) *********************** 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 390 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 305 time to evaluate : 2.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.7999 (m-30) cc_final: 0.7594 (p0) REVERT: A 15 THR cc_start: 0.8356 (t) cc_final: 0.8145 (m) REVERT: A 17 ASN cc_start: 0.7952 (p0) cc_final: 0.7581 (p0) REVERT: C 76 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7720 (pp20) REVERT: C 197 LYS cc_start: 0.8805 (mttt) cc_final: 0.8195 (mtmm) REVERT: C 551 ASP cc_start: 0.7897 (m-30) cc_final: 0.7261 (t0) REVERT: C 800 ASP cc_start: 0.8196 (t0) cc_final: 0.7847 (t0) REVERT: C 1094 ASP cc_start: 0.8654 (p0) cc_final: 0.8347 (p0) REVERT: D 117 LEU cc_start: 0.9457 (OUTLIER) cc_final: 0.9100 (tp) REVERT: D 177 LEU cc_start: -0.2630 (OUTLIER) cc_final: -0.3388 (mt) REVERT: D 242 ARG cc_start: 0.8105 (tpp-160) cc_final: 0.7711 (mmt180) REVERT: D 248 TYR cc_start: 0.8102 (m-80) cc_final: 0.7886 (m-80) REVERT: D 294 LYS cc_start: 0.8569 (mttt) cc_final: 0.8274 (mttt) REVERT: D 450 GLU cc_start: 0.7857 (tp30) cc_final: 0.7650 (tp30) REVERT: D 475 MET cc_start: 0.8726 (mmm) cc_final: 0.8466 (mmm) REVERT: D 854 HIS cc_start: 0.8363 (OUTLIER) cc_final: 0.7599 (t-90) outliers start: 85 outliers final: 58 residues processed: 364 average time/residue: 0.4826 time to fit residues: 282.0870 Evaluate side-chains 350 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 288 time to evaluate : 3.255 ------------------------------------------------------------------------------- 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 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 216 VAL Chi-restraints excluded: chain C residue 76 GLU 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 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 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 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 D residue 34 ILE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 114 LEU 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 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 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 1180 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 109 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 142 optimal weight: 2.9990 chunk 231 optimal weight: 0.7980 chunk 46 optimal weight: 0.0770 chunk 271 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 149 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 306 optimal weight: 40.0000 chunk 110 optimal weight: 4.9990 chunk 160 optimal weight: 10.0000 chunk 258 optimal weight: 20.0000 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 505 HIS D1139 GLN E 70 GLN N 29 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.173465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.130177 restraints weight = 31352.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.128280 restraints weight = 50343.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.130287 restraints weight = 47212.021| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26296 Z= 0.116 Angle : 0.548 13.994 36094 Z= 0.286 Chirality : 0.041 0.163 4134 Planarity : 0.004 0.066 4364 Dihedral : 16.794 178.402 4655 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.87 % Favored : 95.07 % Rotamer: Outliers : 2.89 % Allowed : 15.54 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.16), residues: 2999 helix: 1.61 (0.17), residues: 1065 sheet: -0.43 (0.26), residues: 411 loop : -1.26 (0.15), residues: 1523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 938 HIS 0.004 0.001 HIS C1042 PHE 0.017 0.001 PHE D 252 TYR 0.021 0.001 TYR D 241 ARG 0.008 0.000 ARG C 925 Details of bonding type rmsd hydrogen bonds : bond 0.03927 ( 1050) hydrogen bonds : angle 3.95017 ( 2895) metal coordination : bond 0.00450 ( 8) metal coordination : angle 3.49036 ( 12) covalent geometry : bond 0.00259 (26288) covalent geometry : angle 0.54408 (36082) *********************** 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 388 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 315 time to evaluate : 2.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.7952 (m-30) cc_final: 0.7543 (p0) REVERT: A 17 ASN cc_start: 0.7978 (p0) cc_final: 0.7586 (p0) REVERT: C 197 LYS cc_start: 0.8766 (mttt) cc_final: 0.8216 (mtmm) REVERT: C 551 ASP cc_start: 0.7788 (m-30) cc_final: 0.7172 (t0) REVERT: C 579 MET cc_start: 0.8609 (ttp) cc_final: 0.8312 (ttt) REVERT: C 659 THR cc_start: 0.8991 (m) cc_final: 0.8482 (p) REVERT: C 713 MET cc_start: 0.8097 (mmt) cc_final: 0.7685 (mmm) REVERT: C 800 ASP cc_start: 0.8175 (t0) cc_final: 0.7683 (t0) REVERT: C 1094 ASP cc_start: 0.8593 (p0) cc_final: 0.8277 (p0) REVERT: D 65 TYR cc_start: 0.8164 (m-80) cc_final: 0.7293 (m-80) REVERT: D 117 LEU cc_start: 0.9445 (OUTLIER) cc_final: 0.9087 (tp) REVERT: D 177 LEU cc_start: -0.2613 (OUTLIER) cc_final: -0.3352 (mt) REVERT: D 242 ARG cc_start: 0.8125 (tpp-160) cc_final: 0.7792 (mmt180) REVERT: D 294 LYS cc_start: 0.8528 (mttt) cc_final: 0.8228 (mttt) REVERT: D 450 GLU cc_start: 0.7852 (tp30) cc_final: 0.7644 (tp30) REVERT: D 475 MET cc_start: 0.8588 (mmm) cc_final: 0.8353 (mmm) REVERT: D 854 HIS cc_start: 0.8287 (OUTLIER) cc_final: 0.7626 (t-90) outliers start: 73 outliers final: 51 residues processed: 363 average time/residue: 0.4112 time to fit residues: 238.8474 Evaluate side-chains 349 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 295 time to evaluate : 3.683 ------------------------------------------------------------------------------- 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 34 LEU Chi-restraints excluded: chain B residue 73 VAL 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 C residue 56 VAL Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 221 THR 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 378 LEU Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 561 VAL 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 789 ILE Chi-restraints excluded: chain C residue 854 SER Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 1031 MET 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 425 SER 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 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 910 LEU Chi-restraints excluded: chain D residue 911 ILE Chi-restraints excluded: chain D residue 957 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 68 TYR Chi-restraints excluded: chain N residue 15 PHE Chi-restraints excluded: chain N residue 18 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 256 optimal weight: 0.5980 chunk 98 optimal weight: 7.9990 chunk 57 optimal weight: 7.9990 chunk 114 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 120 optimal weight: 0.0670 chunk 177 optimal weight: 5.9990 chunk 234 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.2922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3953 r_free = 0.3953 target = 0.173139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.129864 restraints weight = 31573.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.128323 restraints weight = 52223.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.130245 restraints weight = 48998.706| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26296 Z= 0.140 Angle : 0.560 14.455 36094 Z= 0.293 Chirality : 0.042 0.160 4134 Planarity : 0.004 0.065 4364 Dihedral : 16.761 178.390 4652 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.24 % Favored : 94.70 % Rotamer: Outliers : 2.97 % Allowed : 15.90 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.16), residues: 2999 helix: 1.58 (0.17), residues: 1064 sheet: -0.31 (0.27), residues: 400 loop : -1.22 (0.16), residues: 1535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 938 HIS 0.004 0.001 HIS D 505 PHE 0.014 0.001 PHE C 254 TYR 0.015 0.001 TYR D 134 ARG 0.009 0.000 ARG C 925 Details of bonding type rmsd hydrogen bonds : bond 0.04210 ( 1050) hydrogen bonds : angle 3.94494 ( 2895) metal coordination : bond 0.00587 ( 8) metal coordination : angle 3.41495 ( 12) covalent geometry : bond 0.00329 (26288) covalent geometry : angle 0.55689 (36082) *********************** 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 379 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 304 time to evaluate : 2.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.7940 (m-30) cc_final: 0.7563 (p0) REVERT: A 17 ASN cc_start: 0.7940 (p0) cc_final: 0.7550 (p0) REVERT: C 197 LYS cc_start: 0.8708 (mttt) cc_final: 0.8125 (mtmm) REVERT: C 551 ASP cc_start: 0.7727 (m-30) cc_final: 0.7143 (t0) REVERT: C 659 THR cc_start: 0.8997 (m) cc_final: 0.8511 (p) REVERT: C 713 MET cc_start: 0.8093 (mmt) cc_final: 0.7684 (mmm) REVERT: C 800 ASP cc_start: 0.8168 (t0) cc_final: 0.7707 (t0) REVERT: C 1072 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8104 (mp0) REVERT: C 1094 ASP cc_start: 0.8608 (p0) cc_final: 0.8246 (p0) REVERT: D 117 LEU cc_start: 0.9454 (OUTLIER) cc_final: 0.9098 (tp) REVERT: D 177 LEU cc_start: -0.2172 (OUTLIER) cc_final: -0.3239 (mt) REVERT: D 242 ARG cc_start: 0.8087 (tpp-160) cc_final: 0.7758 (mmt180) REVERT: D 475 MET cc_start: 0.8545 (mmm) cc_final: 0.7943 (ttm) REVERT: D 554 GLU cc_start: 0.8431 (mm-30) cc_final: 0.8061 (mm-30) REVERT: D 854 HIS cc_start: 0.8348 (OUTLIER) cc_final: 0.7614 (t-90) outliers start: 75 outliers final: 56 residues processed: 349 average time/residue: 0.3765 time to fit residues: 206.4967 Evaluate side-chains 348 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 288 time to evaluate : 2.510 ------------------------------------------------------------------------------- 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 34 LEU 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 216 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 221 THR 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 378 LEU Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 381 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 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 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 87 VAL Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 114 LEU 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 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 957 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 68 TYR Chi-restraints excluded: chain N residue 18 PHE Chi-restraints excluded: chain N residue 44 VAL 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 106 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 chunk 113 optimal weight: 2.9990 chunk 286 optimal weight: 0.9990 chunk 274 optimal weight: 4.9990 chunk 190 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 150 optimal weight: 3.9990 chunk 196 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 540 GLN D1139 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 = 0.3929 r_free = 0.3929 target = 0.170806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.127996 restraints weight = 31588.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.127270 restraints weight = 54126.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.128838 restraints weight = 48186.587| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 26296 Z= 0.152 Angle : 0.575 14.303 36094 Z= 0.300 Chirality : 0.042 0.160 4134 Planarity : 0.004 0.065 4364 Dihedral : 16.755 178.076 4652 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.50 % Favored : 94.43 % Rotamer: Outliers : 2.85 % Allowed : 16.61 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.16), residues: 2999 helix: 1.56 (0.17), residues: 1064 sheet: -0.31 (0.27), residues: 400 loop : -1.21 (0.16), residues: 1535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 938 HIS 0.005 0.001 HIS D 505 PHE 0.022 0.001 PHE D 252 TYR 0.016 0.001 TYR N 68 ARG 0.009 0.000 ARG C 925 Details of bonding type rmsd hydrogen bonds : bond 0.04359 ( 1050) hydrogen bonds : angle 3.95319 ( 2895) metal coordination : bond 0.00709 ( 8) metal coordination : angle 3.07669 ( 12) covalent geometry : bond 0.00362 (26288) covalent geometry : angle 0.57234 (36082) *********************** 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 377 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 305 time to evaluate : 2.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.7980 (m-30) cc_final: 0.7560 (p0) REVERT: A 17 ASN cc_start: 0.7897 (p0) cc_final: 0.7478 (p0) REVERT: A 78 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8653 (mp) REVERT: C 345 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8782 (tp) REVERT: C 551 ASP cc_start: 0.7681 (m-30) cc_final: 0.7071 (t0) REVERT: C 659 THR cc_start: 0.9038 (m) cc_final: 0.8551 (p) REVERT: C 797 ARG cc_start: 0.7809 (ptp-110) cc_final: 0.6886 (mtm-85) REVERT: C 800 ASP cc_start: 0.8228 (t0) cc_final: 0.7757 (t0) REVERT: C 1072 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8072 (mp0) REVERT: C 1094 ASP cc_start: 0.8644 (p0) cc_final: 0.8287 (p0) REVERT: C 1103 TYR cc_start: 0.7942 (t80) cc_final: 0.7602 (t80) REVERT: D 1 MET cc_start: 0.6442 (mtm) cc_final: 0.6138 (mpp) REVERT: D 117 LEU cc_start: 0.9478 (OUTLIER) cc_final: 0.9134 (tp) REVERT: D 177 LEU cc_start: -0.2170 (OUTLIER) cc_final: -0.3305 (mt) REVERT: D 242 ARG cc_start: 0.8119 (tpp-160) cc_final: 0.7762 (mmt180) REVERT: D 248 TYR cc_start: 0.7702 (m-80) cc_final: 0.7212 (m-10) REVERT: D 475 MET cc_start: 0.8481 (mmm) cc_final: 0.7881 (ttm) REVERT: D 854 HIS cc_start: 0.8347 (OUTLIER) cc_final: 0.7575 (t-90) REVERT: N 99 ARG cc_start: 0.7295 (pmm-80) cc_final: 0.7030 (pmm-80) outliers start: 72 outliers final: 58 residues processed: 352 average time/residue: 0.3848 time to fit residues: 216.5898 Evaluate side-chains 353 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 289 time to evaluate : 2.740 ------------------------------------------------------------------------------- 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 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 C residue 56 VAL Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 221 THR 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 378 LEU Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 381 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 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 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 87 VAL Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 413 PHE 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 883 ASP Chi-restraints excluded: chain D residue 911 ILE Chi-restraints excluded: chain D residue 957 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 68 TYR Chi-restraints excluded: chain N residue 18 PHE Chi-restraints excluded: chain N residue 29 HIS 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 36 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 199 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 138 optimal weight: 0.7980 chunk 276 optimal weight: 4.9990 chunk 289 optimal weight: 9.9990 chunk 207 optimal weight: 0.7980 chunk 244 optimal weight: 6.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1139 GLN N 29 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.166657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.127963 restraints weight = 32003.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.127375 restraints weight = 70476.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.128700 restraints weight = 56135.364| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26296 Z= 0.142 Angle : 0.575 14.652 36094 Z= 0.299 Chirality : 0.042 0.160 4134 Planarity : 0.004 0.074 4364 Dihedral : 16.738 177.998 4652 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.37 % Favored : 94.60 % Rotamer: Outliers : 2.93 % Allowed : 16.61 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.16), residues: 2999 helix: 1.55 (0.16), residues: 1064 sheet: -0.30 (0.27), residues: 392 loop : -1.19 (0.16), residues: 1543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 938 HIS 0.015 0.001 HIS N 29 PHE 0.013 0.001 PHE C 254 TYR 0.013 0.001 TYR D 915 ARG 0.009 0.000 ARG C 925 Details of bonding type rmsd hydrogen bonds : bond 0.04257 ( 1050) hydrogen bonds : angle 3.93766 ( 2895) metal coordination : bond 0.00637 ( 8) metal coordination : angle 2.95658 ( 12) covalent geometry : bond 0.00337 (26288) covalent geometry : angle 0.57237 (36082) *********************** 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 372 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 298 time to evaluate : 2.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.7901 (m-30) cc_final: 0.7601 (p0) REVERT: A 17 ASN cc_start: 0.7765 (p0) cc_final: 0.7344 (p0) REVERT: A 78 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8693 (mp) REVERT: C 197 LYS cc_start: 0.8563 (mttt) cc_final: 0.8129 (mtmm) REVERT: C 345 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8802 (tp) REVERT: C 433 THR cc_start: 0.8930 (m) cc_final: 0.8297 (p) REVERT: C 551 ASP cc_start: 0.7537 (m-30) cc_final: 0.6993 (t0) REVERT: C 659 THR cc_start: 0.8967 (m) cc_final: 0.8562 (p) REVERT: C 672 MET cc_start: 0.8414 (mmm) cc_final: 0.8146 (mmt) REVERT: C 713 MET cc_start: 0.8067 (mmt) cc_final: 0.7676 (mmm) REVERT: C 797 ARG cc_start: 0.7754 (ptp-110) cc_final: 0.6893 (mtm-85) REVERT: C 800 ASP cc_start: 0.8039 (t0) cc_final: 0.7652 (t0) REVERT: C 854 SER cc_start: 0.8476 (OUTLIER) cc_final: 0.8209 (p) REVERT: C 1072 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8083 (mp0) REVERT: C 1094 ASP cc_start: 0.8551 (p0) cc_final: 0.7758 (p0) REVERT: C 1103 TYR cc_start: 0.7904 (t80) cc_final: 0.7565 (t80) REVERT: D 117 LEU cc_start: 0.9446 (OUTLIER) cc_final: 0.9103 (tp) REVERT: D 155 MET cc_start: 0.7160 (ppp) cc_final: 0.6082 (ttp) REVERT: D 177 LEU cc_start: -0.2078 (OUTLIER) cc_final: -0.3263 (mt) REVERT: D 242 ARG cc_start: 0.7959 (tpp-160) cc_final: 0.7613 (mmt180) REVERT: D 475 MET cc_start: 0.8357 (mmm) cc_final: 0.7809 (ttm) REVERT: D 854 HIS cc_start: 0.8349 (OUTLIER) cc_final: 0.7604 (t-90) REVERT: N 99 ARG cc_start: 0.7207 (pmm-80) cc_final: 0.7007 (pmm-80) outliers start: 74 outliers final: 58 residues processed: 346 average time/residue: 0.3716 time to fit residues: 205.2966 Evaluate side-chains 355 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 290 time to evaluate : 2.560 ------------------------------------------------------------------------------- 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 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 216 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 221 THR 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 378 LEU Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 381 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 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 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 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 413 PHE 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 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 957 ILE Chi-restraints excluded: chain D residue 1176 LEU 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 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 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 74 optimal weight: 0.0020 chunk 123 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 281 optimal weight: 0.2980 chunk 242 optimal weight: 0.0980 chunk 55 optimal weight: 2.9990 chunk 159 optimal weight: 7.9990 chunk 256 optimal weight: 0.9990 chunk 113 optimal weight: 0.7980 chunk 265 optimal weight: 0.7980 chunk 222 optimal weight: 0.8980 overall best weight: 0.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.170144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.126878 restraints weight = 31879.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.124888 restraints weight = 52341.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.126721 restraints weight = 50616.295| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 26296 Z= 0.111 Angle : 0.565 15.185 36094 Z= 0.292 Chirality : 0.041 0.189 4134 Planarity : 0.004 0.070 4364 Dihedral : 16.625 178.255 4652 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.73 % Favored : 95.23 % Rotamer: Outliers : 2.33 % Allowed : 17.48 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.16), residues: 2999 helix: 1.72 (0.17), residues: 1065 sheet: -0.11 (0.28), residues: 376 loop : -1.08 (0.16), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 938 HIS 0.016 0.001 HIS N 29 PHE 0.023 0.001 PHE D 252 TYR 0.013 0.001 TYR C 344 ARG 0.009 0.000 ARG C 925 Details of bonding type rmsd hydrogen bonds : bond 0.03648 ( 1050) hydrogen bonds : angle 3.80531 ( 2895) metal coordination : bond 0.00335 ( 8) metal coordination : angle 2.48703 ( 12) covalent geometry : bond 0.00242 (26288) covalent geometry : angle 0.56287 (36082) ********************** 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 366 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 307 time to evaluate : 2.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.7969 (m-30) cc_final: 0.7581 (p0) REVERT: A 17 ASN cc_start: 0.7904 (p0) cc_final: 0.7482 (p0) REVERT: A 123 MET cc_start: 0.8158 (ptp) cc_final: 0.7935 (ptp) REVERT: C 62 GLU cc_start: 0.7019 (mt-10) cc_final: 0.6650 (mt-10) REVERT: C 197 LYS cc_start: 0.8710 (mttt) cc_final: 0.8175 (mtmm) REVERT: C 415 GLN cc_start: 0.8600 (tt0) cc_final: 0.8377 (tt0) REVERT: C 433 THR cc_start: 0.8885 (m) cc_final: 0.8273 (p) REVERT: C 551 ASP cc_start: 0.7703 (m-30) cc_final: 0.7101 (t0) REVERT: C 579 MET cc_start: 0.8603 (ttp) cc_final: 0.8375 (ttt) REVERT: C 659 THR cc_start: 0.8980 (m) cc_final: 0.8496 (p) REVERT: C 713 MET cc_start: 0.8256 (mmt) cc_final: 0.7920 (mmm) REVERT: C 800 ASP cc_start: 0.8107 (t0) cc_final: 0.7644 (t0) REVERT: C 1072 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8059 (mp0) REVERT: C 1103 TYR cc_start: 0.7860 (t80) cc_final: 0.7517 (t80) REVERT: D 117 LEU cc_start: 0.9459 (OUTLIER) cc_final: 0.9109 (tp) REVERT: D 155 MET cc_start: 0.7379 (ppp) cc_final: 0.6361 (ttp) REVERT: D 177 LEU cc_start: -0.2141 (OUTLIER) cc_final: -0.3248 (mt) REVERT: D 242 ARG cc_start: 0.8159 (tpp-160) cc_final: 0.7772 (mmt180) REVERT: D 248 TYR cc_start: 0.7841 (m-80) cc_final: 0.7274 (m-10) REVERT: D 475 MET cc_start: 0.8371 (mmm) cc_final: 0.7837 (ttm) REVERT: D 854 HIS cc_start: 0.8190 (OUTLIER) cc_final: 0.7679 (t-90) outliers start: 59 outliers final: 45 residues processed: 346 average time/residue: 0.3780 time to fit residues: 207.9789 Evaluate side-chains 350 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 301 time to evaluate : 2.519 ------------------------------------------------------------------------------- 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 B residue 5 GLN Chi-restraints excluded: chain B residue 34 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 216 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 93 LEU 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 666 THR Chi-restraints excluded: chain C residue 786 GLU Chi-restraints excluded: chain C residue 854 SER Chi-restraints excluded: chain C residue 861 LEU 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 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 413 PHE Chi-restraints excluded: chain D residue 425 SER 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 883 ASP Chi-restraints excluded: chain D residue 911 ILE Chi-restraints excluded: chain D residue 957 ILE 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 N residue 18 PHE Chi-restraints excluded: chain N residue 29 HIS 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 82 optimal weight: 0.9980 chunk 209 optimal weight: 2.9990 chunk 191 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 chunk 186 optimal weight: 0.0770 chunk 282 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 253 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.7738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 29 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.169595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.126136 restraints weight = 31781.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.124643 restraints weight = 54661.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.126304 restraints weight = 51208.523| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2887 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= 0.117 Angle : 0.567 15.075 36094 Z= 0.292 Chirality : 0.041 0.208 4134 Planarity : 0.004 0.068 4364 Dihedral : 16.577 178.197 4650 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.97 % Favored : 95.00 % Rotamer: Outliers : 2.17 % Allowed : 17.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.16), residues: 2999 helix: 1.71 (0.17), residues: 1072 sheet: -0.19 (0.27), residues: 390 loop : -1.02 (0.16), residues: 1537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 938 HIS 0.005 0.001 HIS C1042 PHE 0.013 0.001 PHE C 153 TYR 0.022 0.001 TYR C 344 ARG 0.010 0.000 ARG C 925 Details of bonding type rmsd hydrogen bonds : bond 0.03769 ( 1050) hydrogen bonds : angle 3.79772 ( 2895) metal coordination : bond 0.00447 ( 8) metal coordination : angle 2.55365 ( 12) covalent geometry : bond 0.00267 (26288) covalent geometry : angle 0.56476 (36082) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8213.27 seconds wall clock time: 145 minutes 12.99 seconds (8712.99 seconds total)